$ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes All Packages
All Classes All Packages
All Classes All Packages
$
- $3D_atom_query - Static variable in class com.actelion.research.util.Sketch
- $3D_basis_objs - Static variable in class com.actelion.research.util.Sketch
- $3D_dihed_chiral - Static variable in class com.actelion.research.util.Sketch
- $3D_exclus_dradius - Static variable in class com.actelion.research.util.Sketch
- $3D_exclus_ignore - Static variable in class com.actelion.research.util.Sketch
- $3D_exclus_radius - Static variable in class com.actelion.research.util.Sketch
- $3D_marker_rf - Static variable in class com.actelion.research.util.Sketch
- $3D_maxval - Static variable in class com.actelion.research.util.Sketch
- $3D_minval - Static variable in class com.actelion.research.util.Sketch
- $3D_name - Static variable in class com.actelion.research.util.Sketch
- $3D_num_basis_objs - Static variable in class com.actelion.research.util.Sketch
- $3D_point_ddist - Static variable in class com.actelion.research.util.Sketch
- $3D_point_dir - Static variable in class com.actelion.research.util.Sketch
- $3D_point_dist - Static variable in class com.actelion.research.util.Sketch
- $3D_tolerance - Static variable in class com.actelion.research.util.Sketch
- $Abbrev_atch - Static variable in class com.actelion.research.util.Sketch
- $Arc_endpts - Static variable in class com.actelion.research.util.Sketch
- $ArrowDir - Static variable in class com.actelion.research.util.Sketch
- $ArrowShaftSp - Static variable in class com.actelion.research.util.Sketch
- $ArrowSize - Static variable in class com.actelion.research.util.Sketch
- $ArrowStyle - Static variable in class com.actelion.research.util.Sketch
- $ArrowType - Static variable in class com.actelion.research.util.Sketch
- $Atom_aamap_num - Static variable in class com.actelion.research.util.Sketch
- $Atom_aamapped - Static variable in class com.actelion.research.util.Sketch
- $Atom_alias - Static variable in class com.actelion.research.util.Sketch
- $Atom_AttachLen - Static variable in class com.actelion.research.util.Sketch
- $Atom_can_reverse - Static variable in class com.actelion.research.util.Sketch
- $Atom_chg - Static variable in class com.actelion.research.util.Sketch
- $Atom_coords - Static variable in class com.actelion.research.util.Sketch
- $Atom_dispflags - Static variable in class com.actelion.research.util.Sketch
- $Atom_DotWidth - Static variable in class com.actelion.research.util.Sketch
- $Atom_exact_change - Static variable in class com.actelion.research.util.Sketch
- $Atom_fixed - Static variable in class com.actelion.research.util.Sketch
- $Atom_h0bit - Static variable in class com.actelion.research.util.Sketch
- $Atom_hpos - Static variable in class com.actelion.research.util.Sketch
- $Atom_hshow - Static variable in class com.actelion.research.util.Sketch
- $Atom_list - Static variable in class com.actelion.research.util.Sketch
- $Atom_margin_width - Static variable in class com.actelion.research.util.Sketch
- $Atom_msdif - Static variable in class com.actelion.research.util.Sketch
- $Atom_npos - Static variable in class com.actelion.research.util.Sketch
- $Atom_number - Static variable in class com.actelion.research.util.Sketch
- $Atom_NumSize - Static variable in class com.actelion.research.util.Sketch
- $Atom_Orig_coords - Static variable in class com.actelion.research.util.Sketch
- $Atom_rad - Static variable in class com.actelion.research.util.Sketch
- $Atom_rbcount - Static variable in class com.actelion.research.util.Sketch
- $Atom_rgroupAtch - Static variable in class com.actelion.research.util.Sketch
- $Atom_rxn_stereo - Static variable in class com.actelion.research.util.Sketch
- $Atom_stereo_care - Static variable in class com.actelion.research.util.Sketch
- $Atom_substcount - Static variable in class com.actelion.research.util.Sketch
- $Atom_symbol - Static variable in class com.actelion.research.util.Sketch
- $Atom_tplatchpt - Static variable in class com.actelion.research.util.Sketch
- $Atom_type - Static variable in class com.actelion.research.util.Sketch
- $Atom_unsat - Static variable in class com.actelion.research.util.Sketch
- $Atom_valence - Static variable in class com.actelion.research.util.Sketch
- $Atom_value - Static variable in class com.actelion.research.util.Sketch
- $Atom_zcoord - Static variable in class com.actelion.research.util.Sketch
- $Begsketch - Static variable in class com.actelion.research.util.Sketch
- $BigMetaData - Static variable in class com.actelion.research.util.Sketch
- $Bond_alt_stereo - Static variable in class com.actelion.research.util.Sketch
- $Bond_atoms - Static variable in class com.actelion.research.util.Sketch
- $Bond_bond_spacing - Static variable in class com.actelion.research.util.Sketch
- $Bond_crossed - Static variable in class com.actelion.research.util.Sketch
- $Bond_dbl_side - Static variable in class com.actelion.research.util.Sketch
- $Bond_dbl_width - Static variable in class com.actelion.research.util.Sketch
- $Bond_hash_spacing - Static variable in class com.actelion.research.util.Sketch
- $Bond_qtopo - Static variable in class com.actelion.research.util.Sketch
- $Bond_rxn_center - Static variable in class com.actelion.research.util.Sketch
- $Bond_stereo_care - Static variable in class com.actelion.research.util.Sketch
- $Bond_stereo_type - Static variable in class com.actelion.research.util.Sketch
- $Bond_topo - Static variable in class com.actelion.research.util.Sketch
- $Bond_type - Static variable in class com.actelion.research.util.Sketch
- $Circ_Arc_Points - Static variable in class com.actelion.research.util.Sketch
- $Comment - Static variable in class com.actelion.research.util.Sketch
- $Crop_coords - Static variable in class com.actelion.research.util.Sketch
- $Endsketch - Static variable in class com.actelion.research.util.Sketch
- $Fill_color - Static variable in class com.actelion.research.util.Sketch
- $Fill_RGB2Color - Static variable in class com.actelion.research.util.Sketch
- $Fill_style - Static variable in class com.actelion.research.util.Sketch
- $Font - Static variable in class com.actelion.research.util.Sketch
- $Is_A_Model - Static variable in class com.actelion.research.util.Sketch
- $Locked - Static variable in class com.actelion.research.util.Sketch
- $MDLEditText - Static variable in class com.actelion.research.util.Sketch
- $MetaData - Static variable in class com.actelion.research.util.Sketch
- $Model_Rotated - Static variable in class com.actelion.research.util.Sketch
- $Mol_type - Static variable in class com.actelion.research.util.Sketch
- $Name - Static variable in class com.actelion.research.util.Sketch
- $Nostruct_label - Static variable in class com.actelion.research.util.Sketch
- $Nostruct_regno - Static variable in class com.actelion.research.util.Sketch
- $Obj - Static variable in class com.actelion.research.util.Sketch
- $Obj_Atom - Static variable in class com.actelion.research.util.Sketch
- $Obj_Bond - Static variable in class com.actelion.research.util.Sketch
- $Obj_Chiral - Static variable in class com.actelion.research.util.Sketch
- $Obj_coords - Static variable in class com.actelion.research.util.Sketch
- $Obj_Mol - Static variable in class com.actelion.research.util.Sketch
- $Parent - Static variable in class com.actelion.research.util.Sketch
- $Pen_color - Static variable in class com.actelion.research.util.Sketch
- $Pen_RGB2Color - Static variable in class com.actelion.research.util.Sketch
- $Pen_style - Static variable in class com.actelion.research.util.Sketch
- $Pen_style_token - Static variable in class com.actelion.research.util.Sketch
- $Pen_width - Static variable in class com.actelion.research.util.Sketch
- $Pen_widthUnit - Static variable in class com.actelion.research.util.Sketch
- $Poly_points - Static variable in class com.actelion.research.util.Sketch
- $Poly_smoothed - Static variable in class com.actelion.research.util.Sketch
- $RGroupNo - Static variable in class com.actelion.research.util.Sketch
- $RLogic - Static variable in class com.actelion.research.util.Sketch
- $Roundrect_curve - Static variable in class com.actelion.research.util.Sketch
- $RxnAtch - Static variable in class com.actelion.research.util.Sketch
- $SGroupAtch - Static variable in class com.actelion.research.util.Sketch
- $SGroupAtchPt - Static variable in class com.actelion.research.util.Sketch
- $SGroupBracketLen - Static variable in class com.actelion.research.util.Sketch
- $SGroupContext - Static variable in class com.actelion.research.util.Sketch
- $SGroupLinkVal - Static variable in class com.actelion.research.util.Sketch
- $SGroupName - Static variable in class com.actelion.research.util.Sketch
- $SGroupNewAtch - Static variable in class com.actelion.research.util.Sketch
- $SGroupType - Static variable in class com.actelion.research.util.Sketch
- $Totobjs - Static variable in class com.actelion.research.util.Sketch
- $Transparent - Static variable in class com.actelion.research.util.Sketch
- $Version - Static variable in class com.actelion.research.util.Sketch
A
- a - Variable in class com.actelion.research.chem.forcefield.mmff.SortedPair
- a - Variable in class com.actelion.research.util.BurtleHasherABC
- A - Static variable in class com.actelion.research.chem.docking.scoring.plp.REPTerm
- a_i(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
-
Returns 'A-i' from the table.
- a1 - Variable in class com.actelion.research.chem.forcefield.mmff.AngleBend
- a1 - Variable in class com.actelion.research.chem.forcefield.mmff.BondStretch
- a1 - Variable in class com.actelion.research.chem.forcefield.mmff.Electrostatic
- a1 - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
- a1 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- a1 - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
- a1t - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- a1t - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
- a2 - Variable in class com.actelion.research.chem.forcefield.mmff.AngleBend
- a2 - Variable in class com.actelion.research.chem.forcefield.mmff.BondStretch
- a2 - Variable in class com.actelion.research.chem.forcefield.mmff.Electrostatic
- a2 - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
- a2 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- a2 - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
- a2t - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- a2t - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
- a3 - Variable in class com.actelion.research.chem.forcefield.mmff.AngleBend
- a3 - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
- a3 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- a3t - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- a4 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- a4t - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- AbstractDepictor - Class in com.actelion.research.chem
- AbstractDepictor(StereoMolecule) - Constructor for class com.actelion.research.chem.AbstractDepictor
- AbstractDepictor(StereoMolecule, int) - Constructor for class com.actelion.research.chem.AbstractDepictor
- AbstractDepictor.DepictorDot - Class in com.actelion.research.chem
- AbstractDepictor.DepictorLine - Class in com.actelion.research.chem
- AbstractDescriptorHandlerFP<U> - Class in com.actelion.research.chem.descriptor
- AbstractDescriptorHandlerFP() - Constructor for class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
- AbstractDescriptorHandlerLongFP<U> - Class in com.actelion.research.chem.descriptor
- AbstractDescriptorHandlerLongFP() - Constructor for class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
- AbstractDrawingObject - Class in com.actelion.research.chem
- AbstractDrawingObject() - Constructor for class com.actelion.research.chem.AbstractDrawingObject
- AbstractExtendedDepictor<T,C> - Class in com.actelion.research.share.gui.editor.chem
- AbstractExtendedDepictor(Reaction, List<IDrawingObject>, boolean, boolean, DrawConfig) - Constructor for class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- AbstractExtendedDepictor(StereoMolecule[], int, List<IDrawingObject>, boolean, DrawConfig) - Constructor for class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
-
Use this constructor for markush structures.
- AbstractExtendedDepictor(StereoMolecule[], List<IDrawingObject>, boolean, DrawConfig) - Constructor for class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- AbstractExtendedDepictor(StereoMolecule, List<IDrawingObject>, boolean, DrawConfig) - Constructor for class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- AbstractForceField - Class in com.actelion.research.chem.forcefield
- AbstractForceField(StereoMolecule) - Constructor for class com.actelion.research.chem.forcefield.AbstractForceField
- AbstractParser - Class in com.actelion.research.chem.io
-
A parser is used to load and save molecules from the filesystem.
- AbstractParser() - Constructor for class com.actelion.research.chem.io.AbstractParser
- AbstractScoringEngine - Class in com.actelion.research.chem.docking.scoring
- AbstractScoringEngine(StereoMolecule, Set<Integer>, MoleculeGrid) - Constructor for class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- accept(double, double) - Method in class com.actelion.research.chem.phesaflex.MetropolisMonteCarloHelper
- accept(File) - Method in class com.actelion.research.chem.io.CompoundFileFilter
-
Return true if this file should be shown in the directory pane, false if it shouldn't.
- ACCEPTOR - com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint.Functionality
- ACCEPTOR_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- AcceptorPoint - Class in com.actelion.research.chem.phesa.pharmacophore
- AcceptorPoint(AcceptorPoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
- AcceptorPoint(StereoMolecule, int, List<Integer>, int) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
- AcceptorPoint(StereoMolecule, int, List<Integer>, int, int) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
- Action - Interface in com.actelion.research.share.gui.editor.actions
-
Basic Interface for all editor actions
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.dock.DockableHeader
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.dock.JDockingPanel
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JAtomLabelDialog
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JAtomQueryFeatureDialog
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JBondQueryFeatureDialog
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JChemistryView
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JDrawArea
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JDrawDialog
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JStructureView
- actionPerformed(ActionEvent) - Method in class com.actelion.research.gui.JTextDrawingObjectDialog
- add(byte[]) - Method in class com.actelion.research.util.datamodel.IntArray
- add(byte, byte) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
-
Adds a pair of nodes to this solution.
- add(double) - Method in class com.actelion.research.calc.Matrix
- add(double) - Method in class com.actelion.research.util.Angle
- add(double) - Method in class com.actelion.research.util.datamodel.DoubleArray
- add(double[]) - Method in class com.actelion.research.util.datamodel.DoubleArray
- add(double, double, double) - Method in class com.actelion.research.chem.Coordinates
- add(float[]) - Method in class com.actelion.research.util.datamodel.DoubleArray
- add(int) - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
- add(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
-
Caution! After finishing all adding's realize() has to be called!
- add(int) - Method in class com.actelion.research.util.datamodel.IntArray
- add(int) - Method in class com.actelion.research.util.hash.HashSetInt
-
If the key is already present nothing will happen.
- add(int[]) - Method in class com.actelion.research.util.datamodel.IntArray
- add(int[]) - Method in class com.actelion.research.util.hash.HashSetInt
- add(int, int) - Method in class com.actelion.research.chem.coords.FragmentAssociation
- add(int, long) - Method in class com.actelion.research.chem.CanonizerBaseValue
- add(int, T) - Method in class com.actelion.research.util.UniqueList
- add(long) - Method in class com.actelion.research.chem.CanonizerBaseValue
- add(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- add(SubFlexophoreGenerator.ViolatedConditionsCount) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator.ViolatedConditionsCount
- add(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Adds two vectors together by component.
- add(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- add(IBitArray) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- add(ListWithIntVecIdCode) - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- add(Angle) - Method in class com.actelion.research.util.Angle
- add(ByteVec) - Method in class com.actelion.research.util.datamodel.ByteVec
- add(DoubleArray) - Method in class com.actelion.research.util.datamodel.DoubleArray
- add(IntVec) - Method in class com.actelion.research.util.datamodel.IntVec
- add(DoubleVec) - Method in class com.actelion.research.util.DoubleVec
- add(ErrorHashMap) - Method in class com.actelion.research.util.ErrorHashMap
- add(Point2D) - Method in interface com.actelion.research.share.gui.editor.geom.IPolygon
- add(Point2D) - Method in class com.actelion.research.share.gui.Polygon
- add(Exception) - Method in class com.actelion.research.util.ErrorHashMap
- add(String, int) - Method in class com.actelion.research.chem.prediction.ParameterizedStringList
- add(String, String) - Method in class com.actelion.research.util.CommandLineParser
- add(List<Integer>) - Method in class com.actelion.research.util.datamodel.IntArray
- add(List<Integer>) - Method in class com.actelion.research.util.hash.HashSetInt
- add(T) - Method in class com.actelion.research.util.SortedList
-
Adds object to the list provided that it doesn't contain an object being considered equal by compareTo().
- add(T) - Method in class com.actelion.research.util.UniqueList
- add2CompleteCol(Matrix) - Method in class com.actelion.research.calc.Matrix
-
The value in the col from the input matrix is added to all values in the corresponding col in the matrix.
- add2DCoordinatesColumn(int) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Creates a new column to hold encoded 2-dimensional atom coordinates for the structures stored in the associated structure column.
- add2Row(int, Matrix, int) - Method in class com.actelion.research.calc.Matrix
- add3DCoordinatesColumn(String, int) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Creates a new column to hold encoded 3-dimensional atom coordinates for the structures stored in the associated structure column.
- addAll(List<Exception>) - Method in class com.actelion.research.util.ErrorHashMap
- addAllBits(ListWithIntVec) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- addAlphanumericalColumn(String) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Creates a new standard column to hold any alphanumerical content.
- addArrOriginalAtomIndexRGroups(AtomIndexLinkerId) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- addAtom(double, double) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addAtom(double, double, double) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addAtom(int) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addAtom(int) - Method in class com.actelion.research.chem.Molecule3D
-
Add an atom with the given atomicNo
- addAtom(Molecule3D, int) - Method in class com.actelion.research.chem.Molecule3D
-
Add an atom by copying its properties from the given Molecule3D This has to be overriden by subclasses
- addAtom(String) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addAtomIndices(HashSetInt, List<SubGraphIndices>) - Static method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
-
Adds the atom indices to the hash set.
- addAtomList(StringBuilder) - Method in class org.openmolecules.chem.conf.so.ConformationRule
- addAtoms(PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
-
Only atoms are added that are not yet in the list, check PPAtom.equals for comparison.
- addAtoms(PPNodeViz) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
-
Only atoms are added that are not yet in the list, check PPAtom.equals for comparison.
- addBit(int) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
-
Dont't forget to calculate the hash!
- addBits(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- addBond(int, int) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addBond(int, int, int) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addC(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- addCatalyst(StereoMolecule) - Method in class com.actelion.research.chem.reaction.Reaction
- addCatalyst(StereoMolecule, int) - Method in class com.actelion.research.chem.reaction.Reaction
- addChangeListener(IChangeListener) - Method in class com.actelion.research.share.gui.editor.Model
- addColumnProperty(int, String, String) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
This method may be used to define column properties, e.g.
- addCompound(int, T) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- addCompound(int, T) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- addCompound(T) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- addCompound(T) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- addCompoundCollectionListener(CompoundCollectionListener) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- addCompoundCollectionListener(CompoundCollectionListener) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- addCompoundList(Collection<T>) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- addCompoundList(Collection<T>) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- addContent(Dockable, boolean) - Method in class com.actelion.research.gui.dock.TreeLeaf
- addCoord(Coordinates) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.MultCoordFragIndex
- addCore(StereoMolecule) - Method in class com.actelion.research.chem.MarkushStructure
- addData(List<T>) - Method in class com.actelion.research.util.Pipeline
- addData(T) - Method in class com.actelion.research.util.Pipeline
- addDescription(String) - Method in class com.actelion.research.chem.io.CompoundFileFilter
- addDescriptorColumn(String, String, int) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Creates a new column to hold a chemical descriptor for the structures stored in the associated structure column.
- addDrawAreaListener(DrawAreaListener) - Method in class com.actelion.research.gui.JDrawArea
- addDrawingObject(IDrawingObject) - Method in class com.actelion.research.share.gui.editor.Model
- addElement(String, double) - Method in class com.actelion.research.chem.prediction.IncrementTable
- addEnergyTerm(EnergyTerm) - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
- addExtension(String) - Method in class com.actelion.research.chem.io.CompoundFileFilter
-
Adds a filetype "dot" extension to filter against.
- addFacultative(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
-
The fragment is added if it is not already in the hash map.
- addFeatureMatch(TreeMatcher.FeatureMatch) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
- addFragment(ExtendedMolecule, int, int[]) - Method in class com.actelion.research.chem.ExtendedMolecule
-
This adds a fragment from sourceMol to this molecule by first copying rootAtom and then all connected atoms and bonds by traversing the graph breadth first.
- addGradient(double[]) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
- addHandle() - Method in class com.actelion.research.gui.wmf.WMF
- addHydrogenAtoms(StereoMolecule) - Static method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Adds explicit hydrogen atoms where they are implicit by filling valences and adapting for atom charges.
- addHydrogens(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Add the missing hydrogens for the ligand
- addHydrogens(Molecule3D, boolean) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Adds the missing hydrogens (no optimization)
- addHydrogensAroundLigand(Molecule3D, double) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- addImplicitHydrogens() - Method in class com.actelion.research.chem.conf.AtomAssembler
- addImplicitHydrogens(int) - Method in class com.actelion.research.chem.conf.AtomAssembler
- addImplicitHydrogens(StereoMolecule) - Static method in class com.actelion.research.chem.contrib.HydrogenHandler
- addImplicitHydrogens(StereoMolecule, int) - Static method in class com.actelion.research.chem.contrib.HydrogenHandler
- addIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- addIndex(int[]) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- addIndexOriginalAtom(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- addInevitablePharmacophorePoint(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- addInteraction(int, int, double) - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- addLayoutComponent(String, Component) - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Adds a feature to the LayoutComponent attribute of the VerticalFlowLayout object
- addListener(ForceFieldChangeListener) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
-
Return the variance across all atoms in a molecule for the specified coordinate.
- addListener(ForceFieldChangeListener) - Method in interface com.actelion.research.chem.forcefield.ForceField
- addMatching(TreeMatcher.TreeMatching) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
- addMissingChirality(StereoMolecule) - Static method in class com.actelion.research.chem.contrib.DiastereotopicAtomID
- addMissingChirality(StereoMolecule, int) - Static method in class com.actelion.research.chem.contrib.DiastereotopicAtomID
-
The problem is that sometimes we need to add chiral bond that was not planned because it is the same group This is the case for example for the valine where the 2 C of the methyl groups are diastereotopic
- addMolecule(int, StereoMolecule) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- addMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- addMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCode
- addMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCodeWithName
- addMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.Molecule
- addMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.Native
- addMolecule(Molecule) - Method in class com.actelion.research.chem.Molecule
-
Copies all atoms and bonds of mol to the end of this Molecule's atom and bond tables.
- addMolecule(StereoMolecule, double, double) - Method in class com.actelion.research.share.gui.editor.Model
- addMoleculeList(Collection<StereoMolecule>) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- addMoleculeList(Collection<StereoMolecule>) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- addNode(PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- addNode(PPNodeViz) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- addNode(PharmacophoreNode, List<PharmacophoreNode>, Map<Integer, List<Integer>>) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
- addNoise(double, double, double) - Method in class com.actelion.research.util.DoubleVec
- addOrChangeAtom(double, double, int, int, int, int, String) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addOrChangeBond(int, int, int) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addOriginalAtomIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- addOriginalAtomIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- addOriginalAtomIndex(int[]) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- addPoint(double, double) - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- addPoint(PointDouble) - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- addPoint(Point) - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
-
add a point to the vector of points
- addProduct(StereoMolecule) - Method in class com.actelion.research.chem.reaction.Reaction
- addProduct(StereoMolecule, int) - Method in class com.actelion.research.chem.reaction.Reaction
- addProgressListener(ProgressListener) - Method in class com.actelion.research.calc.DataProcessor
- addReactant(StereoMolecule) - Method in class com.actelion.research.chem.reaction.Reaction
- addReactant(StereoMolecule, int) - Method in class com.actelion.research.chem.reaction.Reaction
- addRenderingHints(Map<?, ?>) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- addResidue(Molecule3D) - Method in class com.actelion.research.chem.io.pdb.parser.ProteinSynthesizer
-
an amino acid is added to the protein structure and a peptide coupling is performed, if coupling cannot be performed, the function results false and the residue is not added
- addRGroup(StereoMolecule) - Method in class com.actelion.research.chem.MarkushStructure
-
This adds a substituent list representing one R-group as multiple fragments within one StereoMolecule.
- addRing(double, double, int, boolean) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- AddRingAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 2/1/13 Time: 4:03 PM
- AddRingAction(Model, int, boolean) - Constructor for class com.actelion.research.share.gui.editor.actions.AddRingAction
- addRingToAtom(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addRingToBond(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- addRNDvalue(double) - Method in class com.actelion.research.util.DoubleVec
-
Adds aor subtracts a random value to the original value.
- addRow(double[]) - Method in class com.actelion.research.calc.Matrix
- addRow(int[]) - Method in class com.actelion.research.calc.Matrix
- addShift(Coordinates) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- addStateInfo(ArrayList<String>, String) - Method in class com.actelion.research.gui.dock.TreeFork
- addStateInfo(ArrayList<String>, String) - Method in class com.actelion.research.gui.dock.TreeLeaf
-
adds docking state entries of this leaf's Dockables
- addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.AxialStereoRule
- addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.ConformationRule
- addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.DistanceRule
- addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.PlaneRule
- addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.StraightLineRule
- addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.TetrahedralStereoRule
- addStrain(Conformer, double[]) - Method in class org.openmolecules.chem.conf.so.TorsionRule
- addString(String) - Method in class com.actelion.research.chem.SortedStringList
- addString(String) - Method in class com.actelion.research.chem.UniqueStringList
- addStructureColumn(String, String) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
This adds a column to host canonical structure representations (idcodes).
- addStructureListener(StructureListener) - Method in class com.actelion.research.gui.JChemistryView
- addStructureListener(StructureListener) - Method in class com.actelion.research.gui.JDrawDialog
- addStructureListener(StructureListener) - Method in class com.actelion.research.gui.JStructureView
- addSubstituent(Molecule, int) - Method in class com.actelion.research.chem.Molecule
-
Adds and connects the substituent molecule to the connectionAtom of this molecule.
- addSubstituent(Molecule, int, boolean) - Method in class com.actelion.research.chem.Molecule
-
Adds and connects the substituent molecule to the connectionAtom of this molecule.
- addToElement(int, int, double) - Method in class com.actelion.research.calc.Matrix
- addToExistingSet(long[]) - Method in class com.actelion.research.chem.DiversitySelector
- addToIntArray(int[], int) - Static method in class com.actelion.research.chem.CanonizerMesoHelper
- addValidationListener(IValidationListener) - Method in class com.actelion.research.share.gui.editor.Model
- advanceToNext() - Method in class com.actelion.research.chem.io.CompoundFileParser
-
Dont't call this method directly.
- advanceToNext() - Method in class com.actelion.research.chem.io.DWARFileParser
- advanceToNext() - Method in class com.actelion.research.chem.io.ODEFileParser
- advanceToNext() - Method in class com.actelion.research.chem.io.SDFileParser
- align() - Method in class com.actelion.research.chem.alignment3d.KabschAlignment
- align() - Method in class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
- align(Coordinates, Matrix, Coordinates) - Method in class com.actelion.research.chem.alignment3d.KabschAlignment
- align(PheSAMolecule, MolecularVolume, MolecularVolume, StereoMolecule, double) - Static method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer
- align(PheSAMolecule, PheSAMolecule, StereoMolecule[], double, boolean) - Static method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer
- AlignmentResult(double, double[][], int, int) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.PPTriangleMatcher.AlignmentResult
- alignTwoMolsInPlace(StereoMolecule, StereoMolecule) - Static method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer
- alignTwoMolsInPlace(StereoMolecule, StereoMolecule, double) - Static method in class com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer
- allFieldsEquals(int) - Method in class com.actelion.research.util.datamodel.IntVec
- allowDrag(boolean) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- allowDrag(boolean) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- ALMOST_ZERO - Static variable in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
- alpha - Variable in class com.actelion.research.chem.phesa.Gaussian3D
- ALPHA - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- alpha_i(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
-
Returns 'alpha-i' from the table.
- alpha_pref - Static variable in class com.actelion.research.chem.phesa.MolecularVolume
- ALTERNATE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- AMemorizedObject - Class in com.actelion.research.util.graph.complete
-
AMemorizedObject
- AMemorizedObject() - Constructor for class com.actelion.research.util.graph.complete.AMemorizedObject
- AMERICAN - com.actelion.research.util.Formatter.LocaleFormat
- AMIDE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- AMIDINE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- AMINO_ACIDS - Static variable in enum com.actelion.research.chem.io.pdb.converter.AminoAcidsLabeledContainer
- AminoAcidLabeled - Class in com.actelion.research.chem.io.pdb.converter
-
AminoAcidLabeled
- AminoAcidLabeled(StereoMolecule, String, String) - Constructor for class com.actelion.research.chem.io.pdb.converter.AminoAcidLabeled
- AminoAcidsLabeledContainer - Enum in com.actelion.research.chem.io.pdb.converter
-
AminoAcidsLabeledContainer The txt file was generated with com.actelion.research.chem.parsers.pdb.ProcessLabeledAminoAcids
- analyse(String) - Method in class com.actelion.research.util.DateAnalysis
-
Checks, whether entry consists of three elements separated by one or more non-word characters (neither digit nor letter) that might be day, month and year.
- analyzeFragmentMembership() - Method in class com.actelion.research.share.gui.editor.Model
- analyzeMolecule(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- analyzeReaction() - Method in class com.actelion.research.share.gui.editor.Model
- AND(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Makes an logical AND and calculates the hash code.
- angle - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- angle(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Returns the angle between this vector and that vector.
- Angle - Class in com.actelion.research.chem.forcefield.mmff.table
-
Angle table, corresponds to the MMFFANG.PAR parameters table provided in the MMFF literature.
- Angle - Class in com.actelion.research.chem.forcefield.mmff.type
-
The angle type class provides static functions for getting angle and stretch bend MMFF type.
- Angle - Class in com.actelion.research.util
-
This class provides various operations on angles, while making sure that the values is always in the rangle from -pi >= v > pi.
- Angle() - Constructor for class com.actelion.research.chem.forcefield.mmff.type.Angle
- Angle() - Constructor for class com.actelion.research.util.Angle
- Angle(double) - Constructor for class com.actelion.research.util.Angle
- Angle(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Angle
- Angle(Angle) - Constructor for class com.actelion.research.util.Angle
- AngleBend - Class in com.actelion.research.chem.forcefield.mmff
-
Angle bending energy term class.
- AngleBend(Tables, MMFFMolecule, int, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.AngleBend
-
Construct a new angle bend energy term.
- AngleConstraint - Class in com.actelion.research.chem.potentialenergy
- AngleConstraint(Conformer, int[], double) - Constructor for class com.actelion.research.chem.potentialenergy.AngleConstraint
- ANSI_CHARSET - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- append(String) - Method in class com.actelion.research.util.datamodel.ByteVec
- apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.AxialStereoRule
- apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.ConformationRule
- apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.DistanceRule
- apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.PlaneRule
- apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.StraightLineRule
- apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.TetrahedralStereoRule
- apply(Conformer, double) - Method in class org.openmolecules.chem.conf.so.TorsionRule
- apply(DistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.SlidingWindowDistHist
- applyTo(AbstractDrawingObject) - Method in class com.actelion.research.chem.DepictorTransformation
- applyTo(DepictorTransformation) - Method in class com.actelion.research.chem.DepictorTransformation
- applyTo(Molecule) - Method in class com.actelion.research.chem.DepictorTransformation
- applyTo(Point2D.Double) - Method in class com.actelion.research.chem.DepictorTransformation
- applyTo(Rectangle2D.Double) - Method in class com.actelion.research.chem.DepictorTransformation
- applyTransformation(DepictorTransformation) - Method in class com.actelion.research.chem.AbstractDepictor
- approveSelection() - Method in class com.actelion.research.gui.JFileChooserOverwrite
- arc(int, int, int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- arc(int, int, int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMF
- arccos(double) - Static method in class com.actelion.research.util.Angle
- arcsin(double) - Static method in class com.actelion.research.util.Angle
- arctan(double, double) - Static method in class com.actelion.research.util.Angle
- area - Variable in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- areAtomsSimilar(int, int) - Method in class com.actelion.research.chem.SSSearcher
- areBonded(Residue) - Method in class com.actelion.research.chem.io.pdb.parser.Residue
- areBondsSimilar(int, int) - Method in class com.actelion.research.chem.SSSearcher
- areNodesMapping(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
-
Dynamic calculation of similarity threshold.
- areNodesMapping(int, int) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- areRowsEqual(int, int) - Method in class com.actelion.research.calc.Matrix
- arom(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
-
Returns the Arom bool of an atom given its MMFF type.
- AROM - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- AROM_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- AROM_RING - com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint.Functionality
- AROM_RING_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- AromaticityResolver - Class in com.actelion.research.chem
- AromaticityResolver(ExtendedMolecule) - Constructor for class com.actelion.research.chem.AromaticityResolver
-
Creates a new AromaticityResolver for molecule mol.
- aromatize(Molecule3D, ArrayList<Integer>[], RingCollection, Set<Integer>, Set<Integer>) - Static method in class com.actelion.research.chem.io.pdb.converter.BondsCalculator
- aromatize(Molecule3D, Set<Integer>, Set<Integer>) - Static method in class com.actelion.research.chem.io.pdb.converter.BondsCalculator
- AromRingPoint - Class in com.actelion.research.chem.phesa.pharmacophore
- AromRingPoint(AromRingPoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
- AromRingPoint(StereoMolecule, int, List<Integer>) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
- ARR_TAGS - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- arrange(double, boolean) - Method in class com.actelion.research.chem.coords.FragmentAssociation
- arrangeReaction(Reaction, Dimension) - Static method in class com.actelion.research.chem.ChemistryHelper
- arrangeWith(InventorFragment) - Method in class com.actelion.research.chem.coords.InventorFragment
- arrAtomLabelRGroups - Static variable in class com.actelion.research.util.ConstantsDWAR
- ArrayUtils - Class in com.actelion.research.util
- ArrayUtils() - Constructor for class com.actelion.research.util.ArrayUtils
- ArrayUtilsCalc - Class in com.actelion.research.calc
- ArrayUtilsCalc() - Constructor for class com.actelion.research.calc.ArrayUtilsCalc
- arrDistHists - Variable in class com.actelion.research.chem.descriptor.flexophore.DistHist
- Arrow - Class in com.actelion.research.share.gui
- Arrow(DrawConfig, double, double, double, double) - Constructor for class com.actelion.research.share.gui.Arrow
- ArrowAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 5/16/13 Time: 3:46 PM
- ArrowAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.ArrowAction
- arrRGroupsAtomicNo - Static variable in class com.actelion.research.chem.ExtendedMoleculeFunctions
- arrRGroupsSymbol - Static variable in class com.actelion.research.chem.ExtendedMoleculeFunctions
- aspec(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
-
Returns the ASPEC type of an atom given its MMFF type.
- assemble() - Method in class com.actelion.research.chem.io.pdb.parser.StructureAssembler
- assessCLogP(StereoMolecule) - Method in class com.actelion.research.chem.prediction.CLogPPredictor
-
Ambiguous bonds are normalized.
- assessDruglikeness(StereoMolecule, ThreadMaster) - Method in class com.actelion.research.chem.prediction.DruglikenessPredictor
- assessPSA(StereoMolecule) - Method in class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
-
Calculates the topological polar surface area (TPSA) of a molecule as a sum of contributions of its polar atom-types.
- assessRisk(StereoMolecule, int, ThreadMaster) - Method in class com.actelion.research.chem.prediction.ToxicityPredictor
- assessSolubility(StereoMolecule) - Method in class com.actelion.research.chem.prediction.SolubilityPredictor
- ASSIGN_PARITIES_TO_TETRAHEDRAL_N - Static variable in class com.actelion.research.chem.Canonizer
- assignCol(int, Matrix) - Method in class com.actelion.research.calc.Matrix
- assignCol(int, Matrix, int) - Method in class com.actelion.research.calc.Matrix
- assignRow(int, double[]) - Method in class com.actelion.research.calc.Matrix
- assignRow(int, int[]) - Method in class com.actelion.research.calc.Matrix
- assignRow(int, DoubleVec) - Method in class com.actelion.research.calc.Matrix
- assignRow(int, Vector<Double>) - Method in class com.actelion.research.calc.Matrix
- atom - Variable in class com.actelion.research.chem.coords.InventorCharge
- atom - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- Atom - Class in com.actelion.research.chem.forcefield.mmff.table
-
Atom table, corresponds to the MMFFPROP.PAR parameters table provided in the MMFF literature.
- Atom - Class in com.actelion.research.chem.forcefield.mmff.type
-
The Atom type class provides static functions to perform atom typing on atoms in a Molecule.
- Atom() - Constructor for class com.actelion.research.chem.forcefield.mmff.type.Atom
- Atom(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Atom
- ATOM_LABEL_R1 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R10 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R11 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R12 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R13 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R14 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R15 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R16 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R2 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R3 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R4 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R5 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R6 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R7 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R8 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_LABEL_R9 - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATOM_TYPE - Static variable in class com.actelion.research.chem.prediction.CLogPPredictor
- AtomAssembler - Class in com.actelion.research.chem.conf
- AtomAssembler(StereoMolecule) - Constructor for class com.actelion.research.chem.conf.AtomAssembler
- atomAtomSubStrucMatch(StereoMolecule, int, StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- AtomComparator - Class in com.actelion.research.chem
- AtomComparator() - Constructor for class com.actelion.research.chem.AtomComparator
- AtomFunctionAnalyzer - Class in com.actelion.research.chem
- AtomFunctionAnalyzer() - Constructor for class com.actelion.research.chem.AtomFunctionAnalyzer
- AtomHighlightAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 2/1/13 Time: 4:13 PM
- ATOMIC_NO - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- AtomicFloat - Class in com.actelion.research.util.concurrent
- AtomicFloat() - Constructor for class com.actelion.research.util.concurrent.AtomicFloat
- AtomicFloat(float) - Constructor for class com.actelion.research.util.concurrent.AtomicFloat
- AtomicGaussian - Class in com.actelion.research.chem.phesa
- AtomicGaussian(int, int, Coordinates) - Constructor for class com.actelion.research.chem.phesa.AtomicGaussian
- AtomicGaussian(AtomicGaussian) - Constructor for class com.actelion.research.chem.phesa.AtomicGaussian
- atomicNo - Variable in class com.actelion.research.chem.phesa.Gaussian3D
- atomId - Variable in class com.actelion.research.chem.phesa.Gaussian3D
- AtomIndexLinkerId - Class in com.actelion.research.chem.descriptor.flexophore.entity
-
AtomIndexLinkerId
- AtomIndexLinkerId() - Constructor for class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
- AtomIndexLinkerId(int, int, int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
- AtomMapAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 5/22/13 Time: 4:00 PM
- AtomMapAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.AtomMapAction
- AtomRecord - Class in com.actelion.research.chem.io.pdb.parser
-
ModelAtom
- AtomRecord(int, String, String, String, String, int, String, double, double, double, double, double, String) - Constructor for class com.actelion.research.chem.io.pdb.parser.AtomRecord
- AtomTypeCalculator - Class in com.actelion.research.chem
- AtomTypeCalculator() - Constructor for class com.actelion.research.chem.AtomTypeCalculator
- AtomTypeList - Class in com.actelion.research.chem
- AtomTypeList(int) - Constructor for class com.actelion.research.chem.AtomTypeList
-
Creates an empty AtomTypeList, which must be populated by multiply calling processMolecule() and finally calling finalizeProcessMolecules() once.
- AtomTypeList(String, int) - Constructor for class com.actelion.research.chem.AtomTypeList
-
Creates a new AtomTypeList from a given file using the given mode.
- AtomTypeMap - Class in com.actelion.research.chem.descriptor.flexophore.generator
- ATTACHED_HYDROGEN_COUNT - Static variable in class com.actelion.research.chem.Molecule3D
- ATTACHED_HYDROGEN_COUNT_SHIFT - Static variable in class com.actelion.research.chem.Molecule3D
- ATTR_ACCEPTOR - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
- ATTR_ALIPHATIC - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
- ATTR_AROMATIC - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
- ATTR_DONOR - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
- ATTR_NEGATIVE_CHARGE - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
- ATTR_NO - Static variable in class com.actelion.research.util.ConstantsDWAR
- ATTR_POSITIVE_CHARGE - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
- ATTR_YES - Static variable in class com.actelion.research.util.ConstantsDWAR
- autoMap() - Method in interface com.actelion.research.chem.reaction.AutoMapper
- autoMap() - Method in class com.actelion.research.chem.reaction.MoleculeAutoMapper
- AutoMapper - Interface in com.actelion.research.chem.reaction
-
Project: User: rufenec Date: 6/17/2014 Time: 10:04 AM
- autoScroll() - Method in class com.actelion.research.gui.ScrollPaneAutoScrollerWhenDragging
- avr() - Method in class com.actelion.research.util.datamodel.DoubleArray
- AxialStereoRule - Class in org.openmolecules.chem.conf.so
-
Handles attropisomery as well as chiral allenes
- AxialStereoRule(StereoMolecule, int[], int[], boolean, boolean) - Constructor for class org.openmolecules.chem.conf.so.AxialStereoRule
B
- b - Variable in class com.actelion.research.chem.forcefield.mmff.SortedPair
- b - Variable in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
- b - Variable in class com.actelion.research.util.BurtleHasherABC
- B - Static variable in class com.actelion.research.chem.docking.scoring.plp.REPTerm
- B_sq - Static variable in class com.actelion.research.chem.docking.scoring.plp.REPTerm
- back(ListWithIntVec) - Method in class com.actelion.research.chem.mcs.ContainerListWithIntVec
- back(S) - Method in class com.actelion.research.util.graph.complete.ContainerMemory
- BACKBONE - com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
- BACKBONE - Static variable in class com.actelion.research.chem.Molecule3D
- BadAtomTypeException - Exception in com.actelion.research.chem.forcefield.mmff
-
The BadAtomTypeException is thrown when there is a bad atom type in a molecule.
- BadAtomTypeException() - Constructor for exception com.actelion.research.chem.forcefield.mmff.BadAtomTypeException
- BadAtomTypeException(String) - Constructor for exception com.actelion.research.chem.forcefield.mmff.BadAtomTypeException
- BadRingAromException - Exception in com.actelion.research.chem.forcefield.mmff
-
The BadRingAromException is thrown when there is a problem with the MMFF ring aromaticity assignment.
- BadRingAromException() - Constructor for exception com.actelion.research.chem.forcefield.mmff.BadRingAromException
- BadRingAromException(String) - Constructor for exception com.actelion.research.chem.forcefield.mmff.BadRingAromException
- BASE_LOG - Static variable in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
- BASIC - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- BASIC_ATOM_FLAG_COUNT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomFlagCount
- bcc() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.Graph
- bccutil(int, int[], int[], LinkedList<Graph.Edge>, int[]) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.Graph
- bci_binary_search(int, int, int, int, boolean) - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
-
Binary search in the bci table.
- beta - Variable in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
- between(Coordinates, Coordinates, double) - Method in class com.actelion.research.chem.Coordinates
-
Updates this to contain a point on the straight line through c1 and c2.
- BiGramInt(int[]) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
- BiGramInt(int[], int) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
- BiGramInt(int, int) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
- BIN_SIZE - Static variable in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
- BIN_SIZE - Static variable in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- binary(int[], int[], Searchable) - Static method in class com.actelion.research.chem.forcefield.mmff.Search
-
Binary search on a collection of values in columns in a table.
- binary(int, int, int, int, boolean, Searchable) - Static method in class com.actelion.research.chem.forcefield.mmff.Search
-
Binary searches for a value and returns the index to it.
- binary(int, int, Searchable) - Static method in class com.actelion.research.chem.forcefield.mmff.Search
-
Helper function that acts like Search.binary(int[], int[], Searchable) but takes a single int for cols and vals to search just one column.
- BinaryDecoder - Class in com.actelion.research.util
- BinaryDecoder(BufferedReader) - Constructor for class com.actelion.research.util.BinaryDecoder
- BinaryDecoder(BufferedReader, int, int) - Constructor for class com.actelion.research.util.BinaryDecoder
- bindingSiteAtoms - Variable in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- BINS_HISTOGRAM - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
-
Defines the resolution for the range.
- BitArray128 - Class in com.actelion.research.chem.properties.complexity
- BitArray128() - Constructor for class com.actelion.research.chem.properties.complexity.BitArray128
- BitArray128(int) - Constructor for class com.actelion.research.chem.properties.complexity.BitArray128
- BitArray128(BitArray128) - Constructor for class com.actelion.research.chem.properties.complexity.BitArray128
-
Deep copy
- BitArray128Factory - Class in com.actelion.research.chem.properties.complexity
- BitArray128Factory() - Constructor for class com.actelion.research.chem.properties.complexity.BitArray128Factory
- bitCount(int) - Static method in class com.actelion.research.util.BitUtils
-
Deprecated.use Integer.bitCount() instead.
- bitCount(long) - Static method in class com.actelion.research.util.BitUtils
- BitUtils - Class in com.actelion.research.util
- BitUtils() - Constructor for class com.actelion.research.util.BitUtils
- BLACK - Static variable in class com.actelion.research.gui.hidpi.ColorUtils
- BLACK - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
- BLACKNESS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- BLUE - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
- blurrSingleBinHistograms() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- bndk - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- Bndk - Class in com.actelion.research.chem.forcefield.mmff.table
-
Bndk table, corresponds to the MMFFBNDK.PAR parameters table provided in the MMFF literature.
- Bndk(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Bndk
- BOMSkipper - Class in com.actelion.research.io
- BOMSkipper() - Constructor for class com.actelion.research.io.BOMSkipper
- bond - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- Bond - Class in com.actelion.research.chem.forcefield.mmff.table
-
Bond table, corresponds to the MMFFBOND.PAR parameters table provided in the MMFF literature.
- Bond - Class in com.actelion.research.chem.forcefield.mmff.type
-
The bond type class provides static functions for getting the MMFF bond type (either by bond or by the atoms of a bond).
- Bond() - Constructor for class com.actelion.research.chem.forcefield.mmff.type.Bond
- Bond(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Bond
- BOND_CUTOFF_SQ - Static variable in class com.actelion.research.chem.io.pdb.parser.Residue
- BondAngleSet - Class in com.actelion.research.chem.conf
- BondAngleSet(StereoMolecule, BondLengthSet) - Constructor for class com.actelion.research.chem.conf.BondAngleSet
-
Calculates and caches a list of bond angle estimates for any two neighbours of any atom of the molecule.
- BondBaseAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 1/28/13 Time: 1:07 PM
- BondBaseAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.BondBaseAction
- BondConstraint - Class in com.actelion.research.chem.potentialenergy
- BondConstraint(Conformer, int[], double) - Constructor for class com.actelion.research.chem.potentialenergy.BondConstraint
- BondHighlightAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 1/28/13 Time: 1:07 PM
- BondHighlightAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.BondHighlightAction
- BondLengthSet - Class in com.actelion.research.chem.conf
- BondLengthSet(StereoMolecule) - Constructor for class com.actelion.research.chem.conf.BondLengthSet
-
Calculates and caches a list of bond length estimates from molecule.
- BondRotationHelper - Class in com.actelion.research.chem.conf
- BondRotationHelper(StereoMolecule) - Constructor for class com.actelion.research.chem.conf.BondRotationHelper
- bondsAreParallel(double, double) - Method in class com.actelion.research.chem.ExtendedMolecule
- BondsCalculator - Class in com.actelion.research.chem.io.pdb.converter
-
BondsCalculator is used to recreate the bonds and / or calculate the bonds orders based on the 3D coordinates of the atoms
- BondsCalculator() - Constructor for class com.actelion.research.chem.io.pdb.converter.BondsCalculator
- BondStretch - Class in com.actelion.research.chem.forcefield.mmff
-
Bond stretching energy term class.
- BondStretch(Tables, MMFFMolecule, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.BondStretch
-
Creates a new bond stretch given a force field and a bond.
- BondStretch(Tables, MMFFMolecule, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.BondStretch
-
Creates a new bond stretch given a force field and two bonded atoms.
- BondVector2IdCode - Class in com.actelion.research.chem.mcs
- BondVector2IdCode(StereoMolecule) - Constructor for class com.actelion.research.chem.mcs.BondVector2IdCode
- borrowContent() - Method in class com.actelion.research.gui.dock.Dockable
-
Removes the content temporarily to be added to another container Must be followed later by a endBorrowContent() call.
- BOTTOM - Static variable in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Field
- brighter(Color, float) - Static method in class com.actelion.research.util.ColorHelper
-
Creates a new
Color
that is a brighter version of thisColor
. - Bromine - Static variable in class com.actelion.research.chem.PeriodicTable
- BS_DIBPATTERN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- BS_HATCHED - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- BS_HOLLOW - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- BS_NULL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- BS_PATTERN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- BS_SOLID - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- build() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- BURIED_TERM - Static variable in class com.actelion.research.chem.docking.scoring.plp.PLPTerm
- BurtleHasher - Class in com.actelion.research.util
-
http://burtleburtle.net/bob/c/lookup3.c ------------------------------------------------------------------------------- lookup3.c, by Bob Jenkins, May 2006, Public Domain.
- BurtleHasher() - Constructor for class com.actelion.research.util.BurtleHasher
- BurtleHasherABC - Class in com.actelion.research.util
- BurtleHasherABC(long, long, long) - Constructor for class com.actelion.research.util.BurtleHasherABC
- buttonPressed(int) - Method in class com.actelion.research.gui.JDrawArea
- ByteArray - Class in com.actelion.research.util
- ByteArrayComparator - Class in com.actelion.research.util
- ByteArrayComparator() - Constructor for class com.actelion.research.util.ByteArrayComparator
- byteArrayToDouble(byte[]) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
- byteArrayToDoubleArray(byte[]) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
- byteArrayToInt(byte[]) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
- byteArrayToIntArray(byte[]) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
- ByteVec - Class in com.actelion.research.util.datamodel
-
ByteVec:
- ByteVec(byte[]) - Constructor for class com.actelion.research.util.datamodel.ByteVec
- ByteVec(int) - Constructor for class com.actelion.research.util.datamodel.ByteVec
- ByteVec(int[]) - Constructor for class com.actelion.research.util.datamodel.ByteVec
- ByteVec(ByteVec) - Constructor for class com.actelion.research.util.datamodel.ByteVec
-
Deep copy
- ByteVec(String) - Constructor for class com.actelion.research.util.datamodel.ByteVec
-
Hash code is calculated.
C
- c - Variable in class com.actelion.research.util.BurtleHasherABC
- C - Static variable in class com.actelion.research.chem.docking.scoring.plp.REPTerm
- CacheEntry(Coordinates[][], double[]) - Constructor for class org.openmolecules.chem.conf.gen.RigidFragmentCache.CacheEntry
- calcFeatureSim(int[], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- calcMin(StereoMolecule) - Method in class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
- calculate() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- calculate() - Method in class com.actelion.research.chem.conf.SymmetryCorrectedRMSDCalculator
- calculate() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- calculate() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.FeatureCalculator
- calculate() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
-
calculates the total volume and size of the node from its elements
- calculate() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
- calculate(double, double, double, double, int[]) - Static method in class com.actelion.research.chem.prediction.DrugScoreCalculator
- calculate(StereoMolecule) - Method in class com.actelion.research.chem.properties.complexity.MolecularComplexityCalculator
- calculate(List<PharmacophoreNode>, List<PharmacophoreNode>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
- calculateAverageBondLength() - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- calculateBondOrders(Molecule3D) - Static method in class com.actelion.research.chem.io.pdb.converter.BondsCalculator
-
Calculate the bond orders of the molecule (without knowing the hydrogens).
- calculateCollisionTolerance() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- calculateCorrelation(INumericalDataColumn, INumericalDataColumn, int) - Method in class com.actelion.research.calc.CorrelationCalculator
-
Calculates the correlation coefficient between two columns of data.
- calculateDescriptor(int[]) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
-
Calculates the torsion descriptor for the current coordinates.
- calculateHash() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- calculateHash(BitArray128) - Method in class com.actelion.research.chem.properties.complexity.BitArray128Factory
- calculateHash(BitArray128) - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsHasher
- calculateHash(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- calculateHash(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- calculateHash(T) - Method in interface com.actelion.research.chem.properties.complexity.IBitArrayFactory
-
Stores the hash in f.
- calculateHashCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- calculateHashCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- calculateHashCode() - Method in class com.actelion.research.util.datamodel.IntArray
- calculateHashCode() - Method in class com.actelion.research.util.datamodel.IntVec
- calculateHashCode(IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- calculateHeight() - Method in class com.actelion.research.chem.phesa.AtomicGaussian
- calculateHeight() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- calculateHeight() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
- calculateHeight() - Method in class com.actelion.research.chem.phesa.pharmacophore.SimplePPGaussian
- calculateHeight() - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- calculateMassCovarianceMatrix(Conformer) - Static method in class com.actelion.research.chem.docking.DockingUtils
- calculateMatrix(INumericalDataColumn[], int) - Method in class com.actelion.research.calc.CorrelationCalculator
-
Calculates a half correlation matrix of all passed numerical columns
- calculatePreferredAttachmentAngle(double, double, int, double) - Method in class com.actelion.research.chem.coords.InventorFragment
- calculateProbabilities() - Method in class com.actelion.research.chem.AtomTypeList
- calculateRules(ArrayList<ConformationRule>, StereoMolecule) - Static method in class org.openmolecules.chem.conf.so.AxialStereoRule
- calculateRules(ArrayList<ConformationRule>, StereoMolecule) - Static method in class org.openmolecules.chem.conf.so.DistanceRule
- calculateRules(ArrayList<ConformationRule>, StereoMolecule) - Static method in class org.openmolecules.chem.conf.so.PlaneRule
- calculateRules(ArrayList<ConformationRule>, StereoMolecule) - Static method in class org.openmolecules.chem.conf.so.StraightLineRule
- calculateRules(ArrayList<ConformationRule>, StereoMolecule) - Static method in class org.openmolecules.chem.conf.so.TetrahedralStereoRule
- calculateRules(ArrayList<ConformationRule>, StereoMolecule) - Static method in class org.openmolecules.chem.conf.so.TorsionRule
- calculateScore(ResultFragmentsStatistic) - Method in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
-
28.08.2013
- calculateSimilarity() - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- calculateStrain(ArrayList<ConformationRule>) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- calculateTorsion(int[]) - Method in class com.actelion.research.chem.conf.Conformer
-
Calculates a signed torsion as an exterior spherical angle from a valid 4-atom strand.
- calculateTorsion(int[]) - Method in class com.actelion.research.chem.Molecule
-
Calculates a signed torsion as an exterior spherical angle from a valid 4-atom strand.
- calculateTorsionExtended(Conformer, int[]) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Calculates a signed torsion like calculateTorsion().
- calculateTorsionExtended(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Calculates a signed torsion like calculateTorsion().
- calculateVolume() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- calculateWidth() - Method in class com.actelion.research.chem.phesa.AtomicGaussian
- calculateWidth() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- calculateWidth() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
- calculateWidth() - Method in class com.actelion.research.chem.phesa.pharmacophore.SimplePPGaussian
- calculateWidth() - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- calculationFailed(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- calculationFailed(int[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
- calculationFailed(int[][]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- calculationFailed(long[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
- calculationFailed(PharmacophoreTree) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- calculationFailed(PheSAMolecule) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- calculationFailed(Object) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- calculationFailed(T) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
- cAllowedAtomicNo - Static variable in class com.actelion.research.chem.Mutation
- cAllowLogModeForNegativeOrZeroValues - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- candidatePose - Variable in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- canDrop() - Method in class com.actelion.research.gui.JChemistryView
- canDrop() - Method in class com.actelion.research.gui.JStructureView
- canonize() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- canonizeCharge(boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Normalizes charge distribution in single- and multifragment molecules.
- canonizeCharge(boolean, boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Normalizes charge distribution in single- and multifragment molecules.
- Canonizer - Class in com.actelion.research.chem
- Canonizer(StereoMolecule) - Constructor for class com.actelion.research.chem.Canonizer
-
Runs a canonicalization procedure for the given molecule that creates unique atom ranks, which takes stereo features, ESR settings and query features into account.
- Canonizer(StereoMolecule, int) - Constructor for class com.actelion.research.chem.Canonizer
-
Runs a canonicalization procedure for the given molecule that creates unique atom ranks, which takes stereo features, ESR settings and query features into account.
- CanonizerBaseValue - Class in com.actelion.research.chem
- CanonizerBaseValue(int) - Constructor for class com.actelion.research.chem.CanonizerBaseValue
- CanonizerMesoHelper - Class in com.actelion.research.chem
- CanonizerMesoHelper(ExtendedMolecule, int[], boolean[], byte[], byte[], byte[], byte[], byte[], byte[], boolean[], boolean[], boolean[]) - Constructor for class com.actelion.research.chem.CanonizerMesoHelper
- CanonizerUtil - Class in com.actelion.research.chem
- CanonizerUtil() - Constructor for class com.actelion.research.chem.CanonizerUtil
- CanonizerUtil.IDCODE_TYPE - Enum in com.actelion.research.chem
- CanonizerUtil.StrongHasher - Class in com.actelion.research.chem
-
64 bit hash, derived from numerical recipes Will move this class later to dd_core.
- canWriteAndDeleteInPath(File) - Static method in class com.actelion.research.util.IO
- CAPACITY_INEVITABLE_PPPOINTS - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- Carbon - Static variable in class com.actelion.research.chem.PeriodicTable
- CARBOXYL - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- cartesianProduct(List<List<T>>) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
-
https://en.wikipedia.org/wiki/Cartesian_product generates all possible combinations of elements from a list of lists
- cat(int[], int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- CATALYST_DELIMITER - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- cAtomCIPParityNone - Static variable in class com.actelion.research.chem.Molecule
- cAtomCIPParityProblem - Static variable in class com.actelion.research.chem.Molecule
- cAtomCIPParityRorM - Static variable in class com.actelion.research.chem.Molecule
- cAtomCIPParitySorP - Static variable in class com.actelion.research.chem.Molecule
- cAtomColorBlue - Static variable in class com.actelion.research.chem.Molecule
- cAtomColorDarkGreen - Static variable in class com.actelion.research.chem.Molecule
- cAtomColorDarkRed - Static variable in class com.actelion.research.chem.Molecule
- cAtomColorGreen - Static variable in class com.actelion.research.chem.Molecule
- cAtomColorMagenta - Static variable in class com.actelion.research.chem.Molecule
- cAtomColorNone - Static variable in class com.actelion.research.chem.Molecule
- cAtomColorOrange - Static variable in class com.actelion.research.chem.Molecule
- cAtomColorRed - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagAllylic - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagAromatic - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagConfigurationUnknown - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagMarked - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlags2RingBonds - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlags3RingBonds - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlags4RingBonds - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagsESR - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagsHelper - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagsHelper2 - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagsHelper3 - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagSmallRing - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagsParity - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagsRingBonds - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagStabilized - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagStereoProblem - Static variable in class com.actelion.research.chem.Molecule
- cAtomFlagsValence - Static variable in class com.actelion.research.chem.Molecule
- cAtomLabel - Static variable in class com.actelion.research.chem.Molecule
- cAtomParity1 - Static variable in class com.actelion.research.chem.Molecule
- cAtomParity2 - Static variable in class com.actelion.research.chem.Molecule
- cAtomParityIsPseudo - Static variable in class com.actelion.research.chem.Molecule
- cAtomParityNone - Static variable in class com.actelion.research.chem.Molecule
- cAtomParityUnknown - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFAny - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFAromatic - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFAromState - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFAromStateBits - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFAromStateShift - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFCharge - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFChargeBits - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFChargeShift - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFExcludeGroup - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFFlatNitrogen - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFHydrogen - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFHydrogenBits - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFHydrogenShift - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFMatchStereo - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFMoreNeighbours - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNarrowing - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNeighbourBits - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNeighbours - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNeighbourShift - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNoMoreNeighbours - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNoOfBits - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot0Hydrogen - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot0Neighbours - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot0PiElectrons - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot1Hydrogen - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot1Neighbour - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot1PiElectron - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot2Hydrogen - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot2Neighbours - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot2PiElectrons - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot2RingBonds - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot3Hydrogen - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot3Neighbours - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot3RingBonds - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot4Neighbours - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNot4RingBonds - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNotAromatic - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNotChain - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNotCharge0 - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNotChargeNeg - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFNotChargePos - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFPiElectronBits - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFPiElectrons - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFPiElectronShift - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRingSize - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRingSizeBits - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRingSizeShift - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRingState - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRingStateBits - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRingStateShift - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRxnParityBits - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRxnParityHint - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRxnParityInvert - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRxnParityRacemize - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRxnParityRetain - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFRxnParityShift - Static variable in class com.actelion.research.chem.Molecule
- cAtomQFSimpleFeatures - Static variable in class com.actelion.research.chem.Molecule
- cAtomRadicalState - Static variable in class com.actelion.research.chem.Molecule
- cAtomRadicalStateD - Static variable in class com.actelion.research.chem.Molecule
- cAtomRadicalStateNone - Static variable in class com.actelion.research.chem.Molecule
- cAtomRadicalStateS - Static variable in class com.actelion.research.chem.Molecule
- cAtomRadicalStateShift - Static variable in class com.actelion.research.chem.Molecule
- cAtomRadicalStateT - Static variable in class com.actelion.research.chem.Molecule
- cAtomValence - Static variable in class com.actelion.research.chem.Molecule
- cAutoStartMacro - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cBondCIPParityEorP - Static variable in class com.actelion.research.chem.Molecule
- cBondCIPParityNone - Static variable in class com.actelion.research.chem.Molecule
- cBondCIPParityProblem - Static variable in class com.actelion.research.chem.Molecule
- cBondCIPParityZorM - Static variable in class com.actelion.research.chem.Molecule
- cBondFlagAromatic - Static variable in class com.actelion.research.chem.Molecule
- cBondFlagDelocalized - Static variable in class com.actelion.research.chem.Molecule
- cBondFlagRing - Static variable in class com.actelion.research.chem.Molecule
- cBondFlagsCIPParityShift - Static variable in class com.actelion.research.chem.Molecule
- cBondFlagsESR - Static variable in class com.actelion.research.chem.Molecule
- cBondFlagsHelper2 - Static variable in class com.actelion.research.chem.Molecule
- cBondFlagsHelper3 - Static variable in class com.actelion.research.chem.Molecule
- cBondFlagSmallRing - Static variable in class com.actelion.research.chem.Molecule
- cBondFlagsParity - Static variable in class com.actelion.research.chem.Molecule
- cBondParityEor1 - Static variable in class com.actelion.research.chem.Molecule
- cBondParityNone - Static variable in class com.actelion.research.chem.Molecule
- cBondParityUnknown - Static variable in class com.actelion.research.chem.Molecule
- cBondParityZor2 - Static variable in class com.actelion.research.chem.Molecule
- cBondQFAllFeatures - Static variable in class com.actelion.research.chem.Molecule
- cBondQFAromatic - Static variable in class com.actelion.research.chem.Molecule
- cBondQFAromState - Static variable in class com.actelion.research.chem.Molecule
- cBondQFAromStateBits - Static variable in class com.actelion.research.chem.Molecule
- cBondQFAromStateShift - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBondTypes - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBondTypesBits - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBondTypesShift - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBridge - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBridgeBits - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBridgeMin - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBridgeMinBits - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBridgeMinShift - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBridgeShift - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBridgeSpan - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBridgeSpanBits - Static variable in class com.actelion.research.chem.Molecule
- cBondQFBridgeSpanShift - Static variable in class com.actelion.research.chem.Molecule
- cBondQFDelocalized - Static variable in class com.actelion.research.chem.Molecule
- cBondQFDouble - Static variable in class com.actelion.research.chem.Molecule
- cBondQFMatchStereo - Static variable in class com.actelion.research.chem.Molecule
- cBondQFMetalLigand - Static variable in class com.actelion.research.chem.Molecule
- cBondQFNarrowing - Static variable in class com.actelion.research.chem.Molecule
- cBondQFNoOfBits - Static variable in class com.actelion.research.chem.Molecule
- cBondQFNotAromatic - Static variable in class com.actelion.research.chem.Molecule
- cBondQFNotRing - Static variable in class com.actelion.research.chem.Molecule
- cBondQFRing - Static variable in class com.actelion.research.chem.Molecule
- cBondQFRingSize - Static variable in class com.actelion.research.chem.Molecule
- cBondQFRingSizeBits - Static variable in class com.actelion.research.chem.Molecule
- cBondQFRingSizeShift - Static variable in class com.actelion.research.chem.Molecule
- cBondQFRingState - Static variable in class com.actelion.research.chem.Molecule
- cBondQFRingStateBits - Static variable in class com.actelion.research.chem.Molecule
- cBondQFRingStateShift - Static variable in class com.actelion.research.chem.Molecule
- cBondQFSimpleFeatures - Static variable in class com.actelion.research.chem.Molecule
- cBondQFSingle - Static variable in class com.actelion.research.chem.Molecule
- cBondQFTriple - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeCross - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeDeleted - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeDelocalized - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeDouble - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeDown - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeIncreaseOrder - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeMaskSimple - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeMaskStereo - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeMetalLigand - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeSingle - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeTriple - Static variable in class com.actelion.research.chem.Molecule
- cBondTypeUp - Static variable in class com.actelion.research.chem.Molecule
- cButtonCleanStructure - Static variable in class com.actelion.research.gui.JDrawToolbar
- cButtonClear - Static variable in class com.actelion.research.gui.JDrawToolbar
- cButtonsPerColumn - Static variable in class com.actelion.research.gui.JDrawToolbar
- cButtonUndo - Static variable in class com.actelion.research.gui.JDrawToolbar
- cChainCursor - Static variable in class com.actelion.research.util.CursorHelper
- cChiralityDiastereomers - Static variable in class com.actelion.research.chem.Molecule
- cChiralityEpimers - Static variable in class com.actelion.research.chem.Molecule
- cChiralityIsomerCountMask - Static variable in class com.actelion.research.chem.Molecule
- cChiralityKnownEnantiomer - Static variable in class com.actelion.research.chem.Molecule
- cChiralityMeso - Static variable in class com.actelion.research.chem.Molecule
- cChiralityNotChiral - Static variable in class com.actelion.research.chem.Molecule
- cChiralityRacemic - Static variable in class com.actelion.research.chem.Molecule
- cChiralityUnknown - Static variable in class com.actelion.research.chem.Molecule
- cChiralityUnknownEnantiomer - Static variable in class com.actelion.research.chem.Molecule
- cCLogPUnknown - Static variable in class com.actelion.research.chem.prediction.CLogPPredictor
- cColorGray - Static variable in class com.actelion.research.chem.AbstractDepictor
- cColumnName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnNameRowList - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnProperty - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyBinBase - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyBinIsDate - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyBinIsLog - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyBinSize - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyCommentDepartment - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyCommentUploadStatus - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyCyclicDataMax - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyDataMax - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyDataMin - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyDescriptorVersion - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyDetailCount - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyDetailName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyDetailSeparator - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyDetailSource - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyDetailType - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyDisplayGroup - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyFormula - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyGroupName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyImagePath - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyIsClusterNo - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyIsDisplayable - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyIsFragment - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLaunchAllowMultiple - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLaunchCommand - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLaunchCount - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLaunchDecoration - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLaunchName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLaunchOption - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLookupCount - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLookupDetailURL - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLookupEncode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLookupFilter - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLookupFilterRemoveMinus - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLookupName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyLookupURL - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyOpenExternalName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyOpenExternalPath - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyOrbitType - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyParentColumn - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyReactionPart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyReferencedColumn - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyReferenceStrengthColumn - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyReferenceType - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyReferenceTypeRedundant - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyReferenceTypeTopDown - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyRelatedCatalystColumn - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyRelatedIdentifierColumn - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertySpecialType - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertySuperpose - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertySuperposeAlign - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertySuperposeMolecule - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnPropertyUseThumbNail - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnRelationTypes - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnType2DCoordinates - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnType3DCoordinates - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnTypeAtomColorInfo - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnTypeIDCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnTypeReactionMapping - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnTypeReactionObjects - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnTypeRXNCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnUnassignedCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cColumnUnassignedItemText - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cCommonOxidationState - Static variable in class com.actelion.research.chem.Molecule
- cCountModeExistance - Static variable in class com.actelion.research.chem.SSSearcher
- cCountModeFirstMatch - Static variable in class com.actelion.research.chem.SSSearcher
- cCountModeOverlapping - Static variable in class com.actelion.research.chem.SSSearcher
- cCountModeRigorous - Static variable in class com.actelion.research.chem.SSSearcher
- cCountModeSeparated - Static variable in class com.actelion.research.chem.SSSearcher
- cDataDependentPropertiesEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDataDependentPropertiesStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDataTypeAutomatic - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDataTypeCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDataTypeDate - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDataTypeNumerical - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDataTypeString - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDataTypeText - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDefaultAtomValence - Static variable in class com.actelion.research.chem.Molecule
- cDefaultDetailSeparator - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDefaultMatchMode - Static variable in class com.actelion.research.chem.SSSearcher
- cDeleteCursor - Static variable in class com.actelion.research.util.CursorHelper
- cDetailDataEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDetailDataStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDetailID - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDetailIndexSeparator - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cDModeAtomNo - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeBondNo - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeHiliteAllQueryFeatures - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeNoColorOnESRAndCIP - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeNoImplicitAtomLabelColors - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeNoStereoProblem - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeNoTabus - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeShowMapping - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeShowSymmetryDiastereotopic - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeShowSymmetryEnantiotopic - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeShowSymmetrySimple - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeSuppressChiralText - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeSuppressCIPParity - Static variable in class com.actelion.research.chem.AbstractDepictor
- cDModeSuppressESR - Static variable in class com.actelion.research.chem.AbstractDepictor
- CDPBondAttach(int, int) - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondAttach
- CDPBondBegin(int) - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondBegin
- CDPBondEnd(int) - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondEnd
- CDPElement(short) - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPElement
- CDPPoint2D(int, int) - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPPoint2D
- cDruglikenessUnknown - Static variable in class com.actelion.research.chem.prediction.DruglikenessPredictor
- CDXConstants - Class in com.actelion.research.gui.clipboard.external
- CDXConstants() - Constructor for class com.actelion.research.gui.clipboard.external.CDXConstants
- CDXDocument() - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXDocument
- CDXPage() - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXPage
- CDXReactionStep(int[], int[]) - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXReactionStep
- center - Variable in class com.actelion.research.chem.phesa.Gaussian3D
- center() - Method in class com.actelion.research.chem.conf.Conformer
-
Translate this conformer's coordinates such that its center of gravity is moved to P(0,0,0) assuming all atoms have the same mass.
- center() - Method in class com.actelion.research.chem.Molecule
-
Translate this molecule's 3D-coordinates such that its center of gravity is moved to P(0,0,0) assuming all atoms have the same mass.
- center(Coordinates) - Method in class com.actelion.research.chem.Coordinates
-
Calculates the center point between this and c and sets this to the center point.
- center(Coordinates, Coordinates) - Method in class com.actelion.research.chem.Coordinates
-
Updates this to contains the center between c1 and c2.
- CENTER - Static variable in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Field
- cEntrySeparator - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cEntrySeparatorBytes - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cESRGroupBits - Static variable in class com.actelion.research.chem.Molecule
- cESRMaxGroups - Static variable in class com.actelion.research.chem.Molecule
- cESRTypeAbs - Static variable in class com.actelion.research.chem.Molecule
- cESRTypeAnd - Static variable in class com.actelion.research.chem.Molecule
- cESRTypeOr - Static variable in class com.actelion.research.chem.Molecule
- cExtensionNameFileExplanation - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cExtensionNameMacroList - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cFileExplanationEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cFileExplanationStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cFileTypeDataWarrior - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeDataWarriorCompatibleData - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeDataWarriorMacro - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeDataWarriorQuery - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeDataWarriorTemplate - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeDataWarriorTemplateContaining - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeDirectory - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeGIF - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeJPG - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeMask - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeMOL - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeMOL2 - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypePDB - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypePictureFile - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypePNG - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeRD - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeRDV2 - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeRDV3 - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeRXN - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeSD - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeSDV2 - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeSDV3 - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeSOM - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeSVG - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeText - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeTextCommaSeparated - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeTextTabDelimited - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFileTypeUnknown - Static variable in class com.actelion.research.chem.io.CompoundFileHelper
- cFistCursor - Static variable in class com.actelion.research.util.CursorHelper
- chainHiliteColor() - Static method in class com.actelion.research.gui.JDrawArea
- cHandCursor - Static variable in class com.actelion.research.util.CursorHelper
- cHandPlusCursor - Static variable in class com.actelion.research.util.CursorHelper
- changeAtom(int, int, int, int, int) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- ChangeAtomAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 2/1/13 Time: 4:13 PM
- ChangeAtomAction(Model, int) - Constructor for class com.actelion.research.share.gui.editor.actions.ChangeAtomAction
- changeAtomCharge(double, double, boolean) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- changeAtomCharge(int, boolean) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- ChangeAtomPropertiesAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 2/1/13 Time: 4:13 PM
- ChangeAtomPropertiesAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.ChangeAtomPropertiesAction
- changeBond(int, int) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- ChangeChargeAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 2/1/13 Time: 4:13 PM
- ChangeChargeAction(Model, boolean) - Constructor for class com.actelion.research.share.gui.editor.actions.ChangeChargeAction
- changed() - Method in class com.actelion.research.share.gui.editor.Model
- changed(Action) - Method in interface com.actelion.research.share.gui.editor.actions.ToolbarSelectionChange
- changeTitle(String, String) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
changes a title of a docked Dockable
- changeTitle(String, String) - Method in class com.actelion.research.gui.dock.TreeLeaf
- charge - Variable in class com.actelion.research.chem.coords.InventorCharge
- Charge - Class in com.actelion.research.chem.forcefield.mmff.table
- Charge - Class in com.actelion.research.chem.forcefield.mmff.type
-
The charge class provides static functions for calculating formal and partial charges on a molecule.
- Charge() - Constructor for class com.actelion.research.chem.forcefield.mmff.type.Charge
- Charge(Tables, String, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Charge
- CHARGE_NEG_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- CHARGE_POS_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- charge_term - Variable in class com.actelion.research.chem.forcefield.mmff.Electrostatic
- ChargePoint - Class in com.actelion.research.chem.phesa.pharmacophore
- ChargePoint(ChargePoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- ChargePoint(StereoMolecule, int, List<Integer>, int) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- CHARSET_ENCODING - Static variable in class com.actelion.research.util.ConstantsDWAR
- check() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- check() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- check(String, String) - Method in interface com.actelion.research.chem.forcefield.mmff.Sdf.OnMolecule
- checkBiggestFragmentForUnwanted(StereoMolecule, List<Integer>) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- checkCommandWithValue(String) - Method in class com.actelion.research.util.CommandLineParser
- checkHiliting(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
- checkHiliting(double, double) - Method in class com.actelion.research.chem.reaction.ReactionArrow
- checkHiliting(double, double) - Method in class com.actelion.research.chem.TextDrawingObject
- cHelperBitCIP - Static variable in class com.actelion.research.chem.Molecule
- cHelperBitIncludeNitrogenParities - Static variable in class com.actelion.research.chem.Molecule
- cHelperBitNeighbours - Static variable in class com.actelion.research.chem.Molecule
- cHelperBitParities - Static variable in class com.actelion.research.chem.Molecule
- cHelperBitRings - Static variable in class com.actelion.research.chem.Molecule
- cHelperBitRingsSimple - Static variable in class com.actelion.research.chem.Molecule
- cHelperBitsStereo - Static variable in class com.actelion.research.chem.Molecule
- cHelperBitSymmetryDiastereotopic - Static variable in class com.actelion.research.chem.Molecule
- cHelperBitSymmetryEnantiotopic - Static variable in class com.actelion.research.chem.Molecule
- cHelperBitSymmetrySimple - Static variable in class com.actelion.research.chem.Molecule
- cHelperCIP - Static variable in class com.actelion.research.chem.Molecule
- cHelperNeighbours - Static variable in class com.actelion.research.chem.Molecule
- cHelperNone - Static variable in class com.actelion.research.chem.Molecule
- cHelperParities - Static variable in class com.actelion.research.chem.Molecule
- cHelperRings - Static variable in class com.actelion.research.chem.Molecule
- cHelperRingsSimple - Static variable in class com.actelion.research.chem.Molecule
- cHelperSymmetryDiastereotopic - Static variable in class com.actelion.research.chem.Molecule
- cHelperSymmetryEnantiotopic - Static variable in class com.actelion.research.chem.Molecule
- cHelperSymmetrySimple - Static variable in class com.actelion.research.chem.Molecule
- CHEM_SIM_WEIGHT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- ChemDrawCDX - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX() - Constructor for class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- ChemDrawCDX.CDPAtomCharge - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPAtomCIP - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPAtomEnhGroup - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPAtomEnhStereoType - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPAtomIsotope - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPAtomRadical - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPBondAttach - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPBondBegin - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPBondDisplay - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPBondEnd - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPBondType - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPElement - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPPoint2D - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPProducts - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPReactants - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPShowAtomStereo - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPShowBondStereo - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPShowEnhAtomStereo - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDPText - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDXDocument - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDXPage - Class in com.actelion.research.gui.clipboard.external
- ChemDrawCDX.CDXReactionStep - Class in com.actelion.research.gui.clipboard.external
- ChemistryDataFormats - Class in com.actelion.research.chem.dnd
- ChemistryDataFormats() - Constructor for class com.actelion.research.chem.dnd.ChemistryDataFormats
- ChemistryFlavors - Class in com.actelion.research.chem.dnd
- ChemistryFlavors() - Constructor for class com.actelion.research.chem.dnd.ChemistryFlavors
- ChemistryHelper - Class in com.actelion.research.chem
- ChemPLP - Class in com.actelion.research.chem.docking.scoring
-
Implementation of ChemPLP scoring function as described in: doi: 10.1021/ci800298z THIS SCORING FUNCTION REQUIRES EXPLICIT HYDROGENS TO BE PRESENT!
- ChemPLP(Molecule3D, Set<Integer>, MoleculeGrid) - Constructor for class com.actelion.research.chem.docking.scoring.ChemPLP
- CHEMPLP - com.actelion.research.chem.docking.DockingEngine.ScoringFunction
- chge - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- chi(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.CovRad
-
Returns the 'chi' (or pauEle) parameter from the table at the given index.
- CHI - Static variable in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
- CHI - Static variable in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- cHighRisk - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- cHitlistData - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cHitlistDataEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cHitlistDataStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cHitlistName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- Chlorine - Static variable in class com.actelion.research.chem.PeriodicTable
- chooseDropFlavor(DropTargetDropEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- chooseDropFlavor(DropTargetDropEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- chooseDropFlavor(DropTargetDropEvent) - Method in class com.actelion.research.gui.dnd.SDFileMoleculeDropAdapter
- cIDCodeCurrentVersion - Static variable in class com.actelion.research.chem.Canonizer
- cIDCodeVersion2 - Static variable in class com.actelion.research.chem.Canonizer
- cIDCodeVersion3 - Static variable in class com.actelion.research.chem.Canonizer
- cIndexMatchMode - Static variable in class com.actelion.research.chem.SSSearcher
- cIndexVersion - Static variable in class com.actelion.research.chem.SSSearcherWithIndex
- cInvisibleCursor - Static variable in class com.actelion.research.util.CursorHelper
- cKeyIDCode - Static variable in class com.actelion.research.chem.SSSearcherWithIndex
- ClassificationData - Class in com.actelion.research.chem.reaction
- classify(StereoMolecule, int) - Method in class com.actelion.research.chem.conf.TorsionDetail
-
Determines uniquely an identifying name for the rotatable bond and its vicinity.
- cLassoCursor - Static variable in class com.actelion.research.util.CursorHelper
- cLassoPlusCursor - Static variable in class com.actelion.research.util.CursorHelper
- CleanAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 1/28/13 Time: 10:09 AM
- CleanAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.CleanAction
- cleanDate(String) - Static method in class com.actelion.research.util.Formatter
- cleanDateTime(String) - Static method in class com.actelion.research.util.Formatter
- cleanMolecule(boolean, boolean) - Method in class com.actelion.research.share.gui.editor.Model
- cleanReaction(boolean) - Method in class com.actelion.research.share.gui.editor.Model
- cleanStructure() - Method in class com.actelion.research.gui.JDrawPanel
- cleanupCoordinates(boolean, boolean) - Method in class com.actelion.research.share.gui.editor.Model
- clear() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- clear() - Method in class com.actelion.research.chem.DepictorTransformation
- clear() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
- clear() - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- clear() - Method in class com.actelion.research.chem.Molecule
-
Empties the molecule to serve as container for constructing a new molecule, e.g.
- clear() - Method in class com.actelion.research.chem.Molecule3D
- clear() - Method in class com.actelion.research.chem.reaction.Reaction
- clear() - Method in interface com.actelion.research.gui.CompoundCollectionModel
- clear() - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- clear() - Method in class com.actelion.research.util.datamodel.DoubleArray
- clear() - Method in class com.actelion.research.util.datamodel.IntArray
- clear() - Method in class com.actelion.research.util.datamodel.IntVec
- clear() - Method in class com.actelion.research.util.ErrorHashMap
- clear() - Method in class com.actelion.research.util.hash.HashSetInt
- clear() - Method in class com.actelion.research.util.IntQueue
- clear() - Method in class com.actelion.research.util.Pipeline
- clear() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- ClearAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 1/24/13 Time: 5:09 PM
- ClearAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.ClearAction
- clearAll() - Method in class com.actelion.research.gui.JDrawArea
- clearCovers(int[], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- clearHiliting() - Method in class com.actelion.research.chem.AbstractDrawingObject
- clearHiliting() - Method in class com.actelion.research.chem.reaction.ReactionArrow
- clearHiliting() - Method in class com.actelion.research.chem.TextDrawingObject
- clearInfo() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- clearOriginalAtomIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- clearRect(double, double, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- clearRect(double, double, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- clearRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- clearRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- clearStateInfo() - Method in class com.actelion.research.gui.dock.TreeElement
- clearStateInfo() - Method in class com.actelion.research.gui.dock.TreeFork
- clearStateInfo() - Method in class com.actelion.research.gui.dock.TreeLeaf
- clearStateInfo() - Method in class com.actelion.research.gui.dock.TreeRoot
- cLineSeparator - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cLineSeparatorByte - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- clip(Shape) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- CLIP_CHARACTER_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- CLIP_DEFAULT_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- CLIP_LH_ANGLES - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- CLIP_MASK - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- CLIP_STROKE_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- CLIP_TT_ALWAYS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- ClipboardHandler - Class in com.actelion.research.gui.clipboard
-
Title: Actelion Library
- ClipboardHandler() - Constructor for class com.actelion.research.gui.clipboard.ClipboardHandler
- ClipboardHelper - Class in com.actelion.research.jfx.gui.misc
-
Created by baerr on 7/28/14.
- clipRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- clipRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- CLogPPredictor - Class in com.actelion.research.chem.prediction
- CLogPPredictor() - Constructor for class com.actelion.research.chem.prediction.CLogPPredictor
- clone() - Method in class com.actelion.research.chem.AbstractDrawingObject
- clone() - Method in class com.actelion.research.chem.phesa.EvaluableOverlap
- clone() - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- clone() - Method in class com.actelion.research.chem.reaction.ReactionArrow
- clone() - Method in class com.actelion.research.chem.TextDrawingObject
- clone() - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
- clone() - Method in class com.actelion.research.util.DoubleVec
- close() - Method in class com.actelion.research.chem.io.CompoundFileParser
-
Closes the underlying reader.
- close() - Method in class com.actelion.research.io.StringReadChannel
- close() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- close() - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- cLowRisk - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- ClusterNode - Class in com.actelion.research.chem.descriptor.flexophore
- ClusterNode(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.ClusterNode
- cMacroListEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cMacroListStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cMatchAromDBondToDelocalized - Static variable in class com.actelion.research.chem.SSSearcher
- cMatchAtomCharge - Static variable in class com.actelion.research.chem.SSSearcher
- cMatchAtomMass - Static variable in class com.actelion.research.chem.SSSearcher
- cMatchDBondToDelocalized - Static variable in class com.actelion.research.chem.SSSearcher
- cMaxAtomicNo - Static variable in class com.actelion.research.chem.Molecule
- cMaxConnAtoms - Static variable in class com.actelion.research.chem.ExtendedMolecule
- cMaxDateOrDoubleCategoryCount - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cMaxTextCategoryCount - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- CMNT_FIELD - Static variable in class com.actelion.research.chem.SDFileMolecule
- cModeChiralTextAboveMolecule - Static variable in class com.actelion.research.chem.AbstractDepictor
- cModeChiralTextBelowMolecule - Static variable in class com.actelion.research.chem.AbstractDepictor
- cModeChiralTextOnFrameBottom - Static variable in class com.actelion.research.chem.AbstractDepictor
- cModeChiralTextOnFrameTop - Static variable in class com.actelion.research.chem.AbstractDepictor
- cModeInflateToAVBL - Static variable in class com.actelion.research.chem.AbstractDepictor
- cModeInflateToHighResAVBL - Static variable in class com.actelion.research.chem.AbstractDepictor
- cModeInflateToMaxAVBL - Static variable in class com.actelion.research.chem.AbstractDepictor
- cModeMaxBondLength - Static variable in class com.actelion.research.chem.AbstractDepictor
- cMoleculeColorDefault - Static variable in class com.actelion.research.chem.Molecule
- cMoleculeColorNeutral - Static variable in class com.actelion.research.chem.Molecule
- cNativeFileCreated - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cNativeFileHeaderEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cNativeFileHeaderStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cNativeFileRowCount - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cNativeFileVersion - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cNewLineString - Static variable in class com.actelion.research.chem.io.RDFileParser
- cNewLineString - Static variable in class com.actelion.research.chem.io.SDFileParser
- cNoRisk - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- coeff - Variable in class com.actelion.research.chem.phesa.Gaussian3D
- collectionUpdated(int, int) - Method in interface com.actelion.research.gui.CompoundCollectionListener
- collectionUpdated(int, int) - Method in class com.actelion.research.gui.CompoundCollectionPane
- color - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorDot
- COLOR_BLUE - Static variable in class com.actelion.research.chem.AbstractDepictor
- COLOR_DARK_GREEN - Static variable in class com.actelion.research.chem.AbstractDepictor
- COLOR_DARK_RED - Static variable in class com.actelion.research.chem.AbstractDepictor
- COLOR_FOR_CENTER_SELECTION - Static variable in class com.actelion.research.chem.ExtendedMoleculeFunctions
- COLOR_GREEN - Static variable in class com.actelion.research.chem.AbstractDepictor
- COLOR_MAGENTA - Static variable in class com.actelion.research.chem.AbstractDepictor
- COLOR_ORANGE - Static variable in class com.actelion.research.chem.AbstractDepictor
- COLOR_RED - Static variable in class com.actelion.research.chem.AbstractDepictor
- ColorHelper - Class in com.actelion.research.util
- ColorHelper() - Constructor for class com.actelion.research.util.ColorHelper
- COLORS - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
Colors for visualization of the Flexophore mapping.
- colorToString(Color) - Static method in class com.actelion.research.gui.hidpi.ColorUtils
- ColorUtils - Class in com.actelion.research.gui.hidpi
-
Defines a color with some utility methods.
- ColorUtils() - Constructor for class com.actelion.research.gui.hidpi.ColorUtils
- cols() - Method in class com.actelion.research.calc.Matrix
- com.actelion.research.calc - package com.actelion.research.calc
- com.actelion.research.calc.combinatorics - package com.actelion.research.calc.combinatorics
- com.actelion.research.calc.filter - package com.actelion.research.calc.filter
- com.actelion.research.calc.geometry - package com.actelion.research.calc.geometry
- com.actelion.research.calc.graph - package com.actelion.research.calc.graph
- com.actelion.research.calc.histogram - package com.actelion.research.calc.histogram
- com.actelion.research.calc.regression.linear.simple - package com.actelion.research.calc.regression.linear.simple
- com.actelion.research.calc.statistics.median - package com.actelion.research.calc.statistics.median
- com.actelion.research.chem - package com.actelion.research.chem
- com.actelion.research.chem.alignment3d - package com.actelion.research.chem.alignment3d
- com.actelion.research.chem.conf - package com.actelion.research.chem.conf
- com.actelion.research.chem.conf.torsionstrain - package com.actelion.research.chem.conf.torsionstrain
- com.actelion.research.chem.contrib - package com.actelion.research.chem.contrib
- com.actelion.research.chem.coords - package com.actelion.research.chem.coords
- com.actelion.research.chem.descriptor - package com.actelion.research.chem.descriptor
- com.actelion.research.chem.descriptor.flexophore - package com.actelion.research.chem.descriptor.flexophore
- com.actelion.research.chem.descriptor.flexophore.calculator - package com.actelion.research.chem.descriptor.flexophore.calculator
- com.actelion.research.chem.descriptor.flexophore.completegraphmatcher - package com.actelion.research.chem.descriptor.flexophore.completegraphmatcher
- com.actelion.research.chem.descriptor.flexophore.entity - package com.actelion.research.chem.descriptor.flexophore.entity
- com.actelion.research.chem.descriptor.flexophore.example - package com.actelion.research.chem.descriptor.flexophore.example
- com.actelion.research.chem.descriptor.flexophore.generator - package com.actelion.research.chem.descriptor.flexophore.generator
- com.actelion.research.chem.descriptor.flexophore.redgraph - package com.actelion.research.chem.descriptor.flexophore.redgraph
- com.actelion.research.chem.descriptor.pharmacophoregraph - package com.actelion.research.chem.descriptor.pharmacophoregraph
- com.actelion.research.chem.descriptor.pharmacophoretree - package com.actelion.research.chem.descriptor.pharmacophoretree
- com.actelion.research.chem.dnd - package com.actelion.research.chem.dnd
- com.actelion.research.chem.docking - package com.actelion.research.chem.docking
- com.actelion.research.chem.docking.scoring - package com.actelion.research.chem.docking.scoring
- com.actelion.research.chem.docking.scoring.chemscore - package com.actelion.research.chem.docking.scoring.chemscore
- com.actelion.research.chem.docking.scoring.idoscore - package com.actelion.research.chem.docking.scoring.idoscore
- com.actelion.research.chem.docking.scoring.plp - package com.actelion.research.chem.docking.scoring.plp
- com.actelion.research.chem.forcefield - package com.actelion.research.chem.forcefield
- com.actelion.research.chem.forcefield.mmff - package com.actelion.research.chem.forcefield.mmff
- com.actelion.research.chem.forcefield.mmff.table - package com.actelion.research.chem.forcefield.mmff.table
- com.actelion.research.chem.forcefield.mmff.type - package com.actelion.research.chem.forcefield.mmff.type
- com.actelion.research.chem.interactionstatistics - package com.actelion.research.chem.interactionstatistics
- com.actelion.research.chem.io - package com.actelion.research.chem.io
- com.actelion.research.chem.io.pdb.converter - package com.actelion.research.chem.io.pdb.converter
- com.actelion.research.chem.io.pdb.parser - package com.actelion.research.chem.io.pdb.parser
- com.actelion.research.chem.mcs - package com.actelion.research.chem.mcs
- com.actelion.research.chem.name - package com.actelion.research.chem.name
- com.actelion.research.chem.optimization - package com.actelion.research.chem.optimization
- com.actelion.research.chem.phesa - package com.actelion.research.chem.phesa
- com.actelion.research.chem.phesa.pharmacophore - package com.actelion.research.chem.phesa.pharmacophore
- com.actelion.research.chem.phesaflex - package com.actelion.research.chem.phesaflex
- com.actelion.research.chem.potentialenergy - package com.actelion.research.chem.potentialenergy
- com.actelion.research.chem.prediction - package com.actelion.research.chem.prediction
- com.actelion.research.chem.properties.complexity - package com.actelion.research.chem.properties.complexity
- com.actelion.research.chem.properties.fractaldimension - package com.actelion.research.chem.properties.fractaldimension
- com.actelion.research.chem.reaction - package com.actelion.research.chem.reaction
- com.actelion.research.chem.shredder - package com.actelion.research.chem.shredder
- com.actelion.research.gui - package com.actelion.research.gui
- com.actelion.research.gui.clipboard - package com.actelion.research.gui.clipboard
- com.actelion.research.gui.clipboard.external - package com.actelion.research.gui.clipboard.external
- com.actelion.research.gui.dnd - package com.actelion.research.gui.dnd
- com.actelion.research.gui.dock - package com.actelion.research.gui.dock
- com.actelion.research.gui.hidpi - package com.actelion.research.gui.hidpi
- com.actelion.research.gui.wmf - package com.actelion.research.gui.wmf
- com.actelion.research.io - package com.actelion.research.io
- com.actelion.research.jfx.dataformat - package com.actelion.research.jfx.dataformat
- com.actelion.research.jfx.gui - package com.actelion.research.jfx.gui
- com.actelion.research.jfx.gui.chem - package com.actelion.research.jfx.gui.chem
- com.actelion.research.jfx.gui.misc - package com.actelion.research.jfx.gui.misc
- com.actelion.research.share.gui - package com.actelion.research.share.gui
- com.actelion.research.share.gui.editor - package com.actelion.research.share.gui.editor
- com.actelion.research.share.gui.editor.actions - package com.actelion.research.share.gui.editor.actions
- com.actelion.research.share.gui.editor.chem - package com.actelion.research.share.gui.editor.chem
- com.actelion.research.share.gui.editor.dialogs - package com.actelion.research.share.gui.editor.dialogs
- com.actelion.research.share.gui.editor.geom - package com.actelion.research.share.gui.editor.geom
- com.actelion.research.share.gui.editor.io - package com.actelion.research.share.gui.editor.io
- com.actelion.research.share.gui.editor.listeners - package com.actelion.research.share.gui.editor.listeners
- com.actelion.research.util - package com.actelion.research.util
- com.actelion.research.util.concurrent - package com.actelion.research.util.concurrent
- com.actelion.research.util.convert - package com.actelion.research.util.convert
- com.actelion.research.util.datamodel - package com.actelion.research.util.datamodel
- com.actelion.research.util.datamodel.table - package com.actelion.research.util.datamodel.table
- com.actelion.research.util.graph.complete - package com.actelion.research.util.graph.complete
- com.actelion.research.util.hash - package com.actelion.research.util.hash
- CombinationGenerator - Class in com.actelion.research.calc.combinatorics
-
CombinationGenerator
- CombinationGenerator() - Constructor for class com.actelion.research.calc.combinatorics.CombinationGenerator
- combineIntsToLong(int, int) - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- CommandAction - Class in com.actelion.research.share.gui.editor.actions
-
Abstract class for handling of all the actions which handle single type of actions: the action is executed when pressing the button and the current drawing action will remain unchanged
- CommandAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.CommandAction
- CommandLineParser - Class in com.actelion.research.util
-
CommandLineParser Simple command line parser.
- CommandLineParser() - Constructor for class com.actelion.research.util.CommandLineParser
- CommandLineParser(String[]) - Constructor for class com.actelion.research.util.CommandLineParser
- CommandLineParser(String, String) - Constructor for class com.actelion.research.util.CommandLineParser
- CommonSubGraphHelper - Class in com.actelion.research.chem.reaction
- CommonSubGraphHelper() - Constructor for class com.actelion.research.chem.reaction.CommonSubGraphHelper
- compact() - Method in class com.actelion.research.chem.Molecule3D
- compare(byte[], byte[]) - Method in class com.actelion.research.util.ByteArrayComparator
- compare(int[], int[]) - Method in class com.actelion.research.util.IntArrayComparator
- compareAndSet(float, float) - Method in class com.actelion.research.util.concurrent.AtomicFloat
- compareArrays(byte[], byte[]) - Static method in class com.actelion.research.util.ByteArray
- compareArrays(byte[], byte[], int) - Static method in class com.actelion.research.util.ByteArray
- compareTo(CanonizerBaseValue) - Method in class com.actelion.research.chem.CanonizerBaseValue
- compareTo(Conformer) - Method in class com.actelion.research.chem.conf.Conformer
- compareTo(TorsionDescriptor) - Method in class com.actelion.research.chem.conf.TorsionDescriptor
-
Returns 0, if none of the torsion angles are more different than TORSION_EQUIVALENCE_TOLERANCE; Returns -1 if the first non-equivalent torsion angle is smaller for this than for the passed TorsionDescriptor td.
- compareTo(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- compareTo(ClusterNode) - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
- compareTo(PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- compareTo(PPNodeVizTriangle) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- compareTo(SortedPair) - Method in class com.actelion.research.chem.forcefield.mmff.SortedPair
-
Compares this object with another.
- compareTo(Molecule3D) - Method in class com.actelion.research.chem.Molecule3D
- compareTo(Fragment3D) - Method in class com.actelion.research.chem.shredder.Fragment3D
- compareTo(ByteVec) - Method in class com.actelion.research.util.datamodel.ByteVec
- compareTo(IdentifiedObject<T>) - Method in class com.actelion.research.util.datamodel.IdentifiedObject
- compareTo(IntVec) - Method in class com.actelion.research.util.datamodel.IntVec
- compareTo(DoubleVec) - Method in class com.actelion.research.util.DoubleVec
- compareTo(SolutionCompleteGraph) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- compareTo(RigidFragmentCache.CacheEntry) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache.CacheEntry
- compareTo(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSet
-
Allows to order TorsionSets in a unique way for quick uniqueness checking against a TreeSet.
- CompleteGraphMatcher<T extends ICompleteGraph> - Class in com.actelion.research.util.graph.complete
-
CompleteGraphMatcher
- CompleteGraphMatcher(IObjectiveCompleteGraph<T>) - Constructor for class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- CompoundCollectionListener - Interface in com.actelion.research.gui
- CompoundCollectionModel<T> - Interface in com.actelion.research.gui
- CompoundCollectionPane<T> - Class in com.actelion.research.gui
- CompoundCollectionPane(CompoundCollectionModel<T>, boolean) - Constructor for class com.actelion.research.gui.CompoundCollectionPane
-
This is a visual component to display and edit a compound collection maintained by a CompoundCollectionModel.
- CompoundCollectionPane(CompoundCollectionModel<T>, boolean, int, int, int) - Constructor for class com.actelion.research.gui.CompoundCollectionPane
- CompoundFileFilter - Class in com.actelion.research.chem.io
-
A convenience implementation of FileFilter that filters out all files except for those type extensions that it knows about.
- CompoundFileFilter() - Constructor for class com.actelion.research.chem.io.CompoundFileFilter
-
Creates a file filter.
- CompoundFileFilter(String) - Constructor for class com.actelion.research.chem.io.CompoundFileFilter
-
Creates a file filter that accepts files with the given extension.
- CompoundFileFilter(String[]) - Constructor for class com.actelion.research.chem.io.CompoundFileFilter
-
Creates a file filter from the given string array.
- CompoundFileFilter(String[], String) - Constructor for class com.actelion.research.chem.io.CompoundFileFilter
-
Creates a file filter from the given string array and description.
- CompoundFileFilter(String, String) - Constructor for class com.actelion.research.chem.io.CompoundFileFilter
-
Creates a file filter that accepts the given file type.
- CompoundFileHelper - Class in com.actelion.research.chem.io
- CompoundFileHelper() - Constructor for class com.actelion.research.chem.io.CompoundFileHelper
- CompoundFileParser - Class in com.actelion.research.chem.io
- CompoundFileParser() - Constructor for class com.actelion.research.chem.io.CompoundFileParser
- CompoundTableConstants - Interface in com.actelion.research.chem.io
- compressMolTable() - Method in class com.actelion.research.chem.Molecule
- compressMolTable() - Method in class com.actelion.research.chem.Molecule3D
- cond() - Method in class com.actelion.research.calc.SingularValueDecomposition
-
Two norm condition number
- CONF_GIVEN_SINGLE_CONFORMATION - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- ConformationRule - Class in org.openmolecules.chem.conf.so
- ConformationRule(int[]) - Constructor for class org.openmolecules.chem.conf.so.ConformationRule
- ConformationSelfOrganizer - Class in org.openmolecules.chem.conf.so
- ConformationSelfOrganizer(StereoMolecule, boolean) - Constructor for class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
-
Generates a new ConformationSelfOrganizer from the given molecule.
- Conformer - Class in com.actelion.research.chem.conf
- Conformer(Conformer) - Constructor for class com.actelion.research.chem.conf.Conformer
-
Creates a new conformer as an exact copy of the given one.
- Conformer(Conformer, StereoMolecule) - Constructor for class com.actelion.research.chem.conf.Conformer
-
Use at own risk!! Initializes the conformer as a copy of c but replaces the StereoMolecule by the supplied molecule.
- Conformer(StereoMolecule) - Constructor for class com.actelion.research.chem.conf.Conformer
-
Creates a Conformer, i.e.
- ConformerGenerator - Class in org.openmolecules.chem.conf.gen
-
This class generates 3D-conformers of a given molecule using the following strategy: All rotatable, non-ring bonds are determined.
- ConformerGenerator() - Constructor for class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Instantiates a ConformerGenerator for creating non-reproducible conformers.
- ConformerGenerator(boolean) - Constructor for class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Instantiates a ConformerGenerator for creating non-reproducible conformers.
- ConformerGenerator(long, boolean) - Constructor for class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Instantiates a ConformerGenerator for creating reproducible conformers unless seed is 0L.
- ConformerGenerator(long, RigidFragmentCache, boolean) - Constructor for class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Instantiates a ConformerGenerator for creating reproducible conformers unless seed is 0L.
- ConformerGenerator(long, RigidFragmentProvider) - Constructor for class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Instantiates a ConformerGenerator for creating reproducible conformers unless seed is 0L.
- ConformerSet - Class in com.actelion.research.chem.conf
- ConformerSet() - Constructor for class com.actelion.research.chem.conf.ConformerSet
- ConformerSet(String) - Constructor for class com.actelion.research.chem.conf.ConformerSet
- ConformerSetGenerator - Class in com.actelion.research.chem.conf
- ConformerSetGenerator() - Constructor for class com.actelion.research.chem.conf.ConformerSetGenerator
-
STRATEGY_LIKELY_RANDOM was evaluated to be the best strategy for reproducing bioactive conformers (J.W.
- ConformerSetGenerator(boolean) - Constructor for class com.actelion.research.chem.conf.ConformerSetGenerator
- ConformerSetGenerator(boolean, long) - Constructor for class com.actelion.research.chem.conf.ConformerSetGenerator
- ConformerSetGenerator(int, int, boolean, long) - Constructor for class com.actelion.research.chem.conf.ConformerSetGenerator
- connected(Molecule3D, int, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Returns the rotatable bonds (sorted).
- connected(StereoMolecule, int, int, int) - Static method in class com.actelion.research.chem.io.pdb.converter.BondsCalculator
- connectFragments(Conformer, boolean[], int[]) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
-
Checks both rigid fragments that are connected by this bond, whether they have been attached to the conformer yet, i.e.
- ConnectionPoint - Static variable in class com.actelion.research.chem.PeriodicTable
- CONSIDER_DIASTEREOTOPICITY - Static variable in class com.actelion.research.chem.Canonizer
- CONSIDER_ENANTIOTOPICITY - Static variable in class com.actelion.research.chem.Canonizer
- CONSIDER_STEREOHETEROTOPICITY - Static variable in class com.actelion.research.chem.Canonizer
- Constants - Class in com.actelion.research.chem.forcefield.mmff
-
The Constants class holds numerical constants that are reused in multiple classes.
- ConstantsAminoAcidsLabeled - Class in com.actelion.research.chem.io.pdb.converter
-
ConstantsAminoAcidsLabeled
- ConstantsAminoAcidsLabeled() - Constructor for class com.actelion.research.chem.io.pdb.converter.ConstantsAminoAcidsLabeled
- ConstantsDWAR - Class in com.actelion.research.util
-
ConstantsDWAR
- ConstantsDWAR() - Constructor for class com.actelion.research.util.ConstantsDWAR
- ConstantsFlexophore - Class in com.actelion.research.chem.descriptor.flexophore
- ConstantsFlexophore() - Constructor for class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophore
- ConstantsFlexophoreGenerator - Class in com.actelion.research.chem.descriptor.flexophore.generator
- ConstantsFlexophoreGenerator() - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
- ConstantsFlexophoreHardPPPoints - Class in com.actelion.research.chem.descriptor.flexophore
- ConstantsFlexophoreHardPPPoints() - Constructor for class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
- ConstantsHistogram - Class in com.actelion.research.calc.histogram
-
ConstantsHistogram
- ConstantsHistogram() - Constructor for class com.actelion.research.calc.histogram.ConstantsHistogram
- ContainerBitArray - Class in com.actelion.research.chem.properties.complexity
- ContainerBitArray(int, int) - Constructor for class com.actelion.research.chem.properties.complexity.ContainerBitArray
- ContainerFragBondsSolutions - Class in com.actelion.research.chem.properties.complexity
- ContainerFragBondsSolutions(int, int) - Constructor for class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
-
Fragments are represented as bit arrays.
- ContainerListWithIntVec - Class in com.actelion.research.chem.mcs
- ContainerListWithIntVec(int, int) - Constructor for class com.actelion.research.chem.mcs.ContainerListWithIntVec
- ContainerMemory<S extends AMemorizedObject> - Class in com.actelion.research.util.graph.complete
-
ContainerMemory
- ContainerMemory(int, IFactory<S>) - Constructor for class com.actelion.research.util.graph.complete.ContainerMemory
- contains(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
-
Checks, whether this drawing object contains the point at x,y
- contains(double, double) - Method in class com.actelion.research.chem.reaction.ReactionArrow
- contains(double, double) - Method in class com.actelion.research.chem.TextDrawingObject
- contains(double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IPolygon
- contains(double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
- contains(double, double) - Method in class com.actelion.research.share.gui.Polygon
- contains(int) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- contains(int) - Method in class com.actelion.research.util.hash.HashSetInt
- contains(int[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- contains(Point2D) - Method in class com.actelion.research.share.gui.Polygon
- contains(String) - Method in class com.actelion.research.chem.SortedStringList
- contains(String) - Method in class com.actelion.research.util.CommandLineParser
- contains(List<int[]>, int[]) - Static method in class com.actelion.research.util.ArrayUtils
- contains(T) - Method in class com.actelion.research.util.SortedList
- contains(T) - Method in class com.actelion.research.util.UniqueList
- containsAtLeastOneAtomicNumbersFromHashSet(ExtendedMolecule, HashSet<Integer>) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- containsColumn(String) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- containsFragmentOpenRing(IBitArray) - Method in class com.actelion.research.chem.mcs.BondVector2IdCode
- containsHeteroAtom(ExtendedMolecule, int[]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- containsInteractionID(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- containsLowerCase(String) - Static method in class com.actelion.research.util.StringFunctions
- containsRow(DoubleVec) - Method in class com.actelion.research.calc.Matrix
- containsSolelyAtomicNumbersFromHashSet(ExtendedMolecule, HashSet<Integer>) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- containsUpperCase(String) - Static method in class com.actelion.research.util.StringFunctions
- contentChanged(DrawAreaEvent) - Method in interface com.actelion.research.gui.DrawAreaListener
- convert(String) - Static method in class com.actelion.research.util.convert.String2DoubleArray
- convert(ArrayList) - Static method in class com.actelion.research.util.convert.String2DoubleArray
- convertDataToPrimitiveTypes(List<Molecule3D>) - Static method in class com.actelion.research.chem.io.AbstractParser
- convertPath(int[][], int[][], int) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- convertStereoBondsToSingleBonds(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Converts any stereo bond attached with its pointed tip to this atom into a single bond.
- convertToValidFileNameCharacters(String) - Static method in class com.actelion.research.util.StringFunctions
-
Not allowed are: \ / : * ? < > |
- CoordinateInventor - Class in com.actelion.research.chem.coords
- CoordinateInventor() - Constructor for class com.actelion.research.chem.coords.CoordinateInventor
-
Creates an CoordinateInventor, which removes unneeded hydrogen atoms and creates new atom coordinates for all(!) atoms.
- CoordinateInventor(int) - Constructor for class com.actelion.research.chem.coords.CoordinateInventor
-
Creates an CoordinateInventor, which removes unneeded hydrogens, if mode flags include MODE_REMOVE_HYDROGEN.
- coordinates - Variable in class com.actelion.research.util.datamodel.IDCodeCoord
- Coordinates - Class in com.actelion.research.chem
-
Class to encapsulate 3D coordinates
- Coordinates() - Constructor for class com.actelion.research.chem.Coordinates
- Coordinates(double, double, double) - Constructor for class com.actelion.research.chem.Coordinates
- Coordinates(Coordinates) - Constructor for class com.actelion.research.chem.Coordinates
- coordinatesAre3D(byte[], byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- coordinatesAre3D(byte[], byte[], int, int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- coordinatesAre3D(String, String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- coordinatesAreAbsolute(byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- coordinatesAreAbsolute(byte[], int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- coordinatesAreAbsolute(String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- COORDS_ARE_3D - Static variable in class com.actelion.research.chem.Canonizer
- coordVariance(int) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
- cOptAvBondLen - Static variable in class com.actelion.research.chem.AbstractDepictor
- copy() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- copy() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- copy() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
- copy(byte[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- copy(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- copy(Matrix) - Method in class com.actelion.research.calc.Matrix
-
Copies a matrix ma into this, the pointer to ma1 is not changed.
- copy(DistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- copy(MolDistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- copy(MolDistHistViz) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- copy(PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
-
Copy of node into this.
- copy(PPNodeViz) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
-
Copy of node into this
- copy(StereoMolecule) - Static method in class com.actelion.research.jfx.gui.misc.ClipboardHelper
- copy(IntVec) - Method in class com.actelion.research.util.datamodel.IntVec
- copy(Object) - Static method in class com.actelion.research.util.ArrayUtils
-
Copy an array
- copy(Object[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- CopyAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 5/16/13 Time: 3:31 PM
- CopyAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.CopyAction
- copyArea(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- copyArea(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- copyAtom(Molecule, int, int, int) - Method in class com.actelion.research.chem.Molecule
-
Creates a new atom in destMol and copies all source atom properties including atom list, custom label, flags, and mapNo to it.
- copyAtom(Molecule, int, int, int) - Method in class com.actelion.research.chem.Molecule3D
- copyAtoms(Molecule3D, Molecule3D, List<Integer>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- copyBond(Molecule, int, int, int, int[], boolean) - Method in class com.actelion.research.chem.Molecule
- copyBond(Molecule, int, int, int, int, int, boolean) - Method in class com.actelion.research.chem.Molecule
- copyColumn(Matrix, int, int) - Method in class com.actelion.research.calc.Matrix
- copyFrom(Conformer) - Method in class com.actelion.research.chem.conf.Conformer
-
Copies the conformer's atom coordinates to this Conformer.
- copyFrom(StereoMolecule) - Method in class com.actelion.research.chem.conf.Conformer
-
Copies the molecule's atom coordinates to this Conformer.
- copyImage(Image) - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Copies an Image to the clipboard
- copyImage(Image) - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- copyImage(Image) - Static method in class com.actelion.research.gui.clipboard.ImageClipboardHandler
- copyIntArray(List<int[]>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- copyIntoThis(ListWithIntVec) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- copyIntoThis(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
-
Deep copy The index is not copied
- copyIntoThis(IBitArray) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- copyIntoThis(AMemorizedObject) - Method in class com.actelion.research.util.graph.complete.AMemorizedObject
-
Has to be a deep copy
- copyIntoThis(AMemorizedObject) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- copyMetaFile(byte[]) - Static method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Copy a windows enhance metafile to the Windows clipboard
- copyMolecule(boolean) - Method in class com.actelion.research.share.gui.editor.actions.CopyAction
- copyMolecule(boolean) - Method in class com.actelion.research.share.gui.editor.Model
- copyMolecule(Molecule) - Method in class com.actelion.research.chem.Molecule
-
Copies this molecule including parity settings, if valid.
- copyMolecule(StereoMolecule) - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Copies a molecule to the clipboard in various formats: ENHMETAFILE with an embedded sketch MDLSK Sketch MDLCT MDL molfile
- copyMolecule(StereoMolecule) - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- copyMolecule(String) - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
- copyMolecule(String) - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- copyMoleculeByAtoms(ExtendedMolecule, boolean[], boolean, int[]) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Clears destmol and then copies a part of this Molecule into destMol, being defined by a mask of atoms to be included.
- copyMoleculeByBonds(ExtendedMolecule, boolean[], boolean, int[]) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Clears destmol and then copies a part of this Molecule into destMol, being defined by a mask of bonds to be included.
- copyMoleculeProperties(Molecule) - Method in class com.actelion.research.chem.Molecule
-
Copies name,isFragment,chirality and validity of parity & CIP flags.
- copyMoleculeProperties(Molecule) - Method in class com.actelion.research.chem.StereoMolecule
-
Copies name, isFragment, chirality.
- copyMoleculeToClipboard(String, byte[], byte[]) - Static method in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- copyOf(double[][]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- copyPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
- copyPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
- copyPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- copyPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
- copyPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
- copyPharmacophorePoint() - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
- copyReaction(boolean) - Method in class com.actelion.research.share.gui.editor.actions.CopyAction
- copyReaction(boolean) - Method in class com.actelion.research.share.gui.editor.Model
- copyReaction(Reaction) - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Copies a reaction to the clipboard in various formats: MDLSK Sketch MDLCT MDL molfile
- copyReaction(Reaction) - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- copyReaction(String) - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Copies a reaction to the clipboard in various formats: CTAB with an embedded sketch MDLSK Sketch serialized
- copyReaction(String) - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- copyReactionToClipboard(byte[], byte[], byte[]) - Static method in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- copySizedMoleculeToClipboard(String, byte[], byte[], int, int) - Static method in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- copyText(String) - Static method in class com.actelion.research.gui.clipboard.TextClipboardHandler
- copyTo(StereoMolecule) - Method in class com.actelion.research.chem.conf.Conformer
-
Copies this conformer's atom coordinates to mol.
- coreToOriginalAtom(int) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- correlation() - Method in class com.actelion.research.calc.Matrix
-
Generate a correlation matrix, each column contains values of a pulling.
- CorrelationCalculator - Class in com.actelion.research.calc
- CorrelationCalculator() - Constructor for class com.actelion.research.calc.CorrelationCalculator
- cos() - Method in class com.actelion.research.util.Angle
- cosAngle(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- cosAngle(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Returns the cosine of the angle between this vector and that vector.
- Cosine(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
-
Vectors have to be normed!
- COSINE - Static variable in class com.actelion.research.util.datamodel.ByteVec
- COSINE - Static variable in class com.actelion.research.util.DoubleVec
- countIntegerInText(String) - Static method in class com.actelion.research.util.StringFunctions
- countOccurence(String, char) - Static method in class com.actelion.research.util.StringFunctions
- countWordInText(String) - Static method in class com.actelion.research.util.StringFunctions
- COVALENT_RADIUS - Static variable in interface com.actelion.research.chem.conf.VDWRadii
-
These covalent single bond radii values were taken from the following source: 'Molecular Double-Bond Covalent Radii for Elements Li–E112', 2009, Pyykkö and Atsumi, doi: 10.1002/chem.200901472
- covariance() - Method in class com.actelion.research.calc.Matrix
-
Generate a covariance matrix, each column contains values of a pulling.
- covrad - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- CovRad - Class in com.actelion.research.chem.forcefield.mmff.table
-
CovRad table, used in the bond stretch empirical calculations of 'kb' and 'r0'.
- CovRad(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.CovRad
- cParentSpecialColumnTypes - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cParity1And - Static variable in class com.actelion.research.chem.Canonizer
- cParity1Or - Static variable in class com.actelion.research.chem.Canonizer
- cParity2And - Static variable in class com.actelion.research.chem.Canonizer
- cParity2Or - Static variable in class com.actelion.research.chem.Canonizer
- cPointedHandCursor - Static variable in class com.actelion.research.util.CursorHelper
- cPointerCursor - Static variable in class com.actelion.research.util.CursorHelper
- cPolarAtomTypeName - Static variable in class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
- cPropertiesAll - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesAtomAllylic - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesAtomAromatic - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesAtomCharged - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesAtomRingCount - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesAtomRingSize - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesAtomSmallRing - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesAtomStabilized - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesBasicType - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesConnAtomAromatic - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesConnAtomNeighbours - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesConnAtomNeighboursExact - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesConnAtomSmallRing - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesConnAtomStabilized - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesConnAtomType - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesConnAtomTypeSimple - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesConnBondOrder - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cPropertiesForCLogP - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesForCLogPCharges - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesForMutator - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesForSolubility - Static variable in class com.actelion.research.chem.AtomTypeCalculator
- cPropertiesStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cPSAUnknown - Static variable in class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
- cRangeNotAvailable - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cRangeSeparation - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- crd(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
-
Returns the CRD type of an atom given its MMFF type.
- cReactionHiliteModeCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cReactionHiliteModeNone - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cReactionHiliteModeReactionCenter - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cReactionHiliteModeText - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cReactionPartDelimiter - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cReactionPartProducts - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cReactionPartReactants - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cReactionPartReaction - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- create() - Static method in class com.actelion.research.gui.hidpi.ScaledEditorKit
- create() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- create() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- create(Conformer, int[], String) - Static method in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionTerm
- create(Conformer, int, int[], Coordinates, double) - Static method in class com.actelion.research.chem.docking.scoring.chemscore.MetalTerm
- create(Conformer, Conformer, int, int) - Static method in class com.actelion.research.chem.docking.scoring.plp.REPTerm
- create(Conformer, Conformer, int, int, int[], double) - Static method in class com.actelion.research.chem.docking.scoring.chemscore.SimpleMetalTerm
- create(Conformer, Conformer, int, int, int[], int[]) - Static method in class com.actelion.research.chem.docking.scoring.idoscore.InteractionTerm
- create(Conformer, Conformer, int, int, int, boolean, boolean, int[], double) - Static method in class com.actelion.research.chem.docking.scoring.chemscore.HBTerm
- create(Conformer, Conformer, int, int, Map<String, Double>) - Static method in class com.actelion.research.chem.docking.scoring.plp.PLPTerm
- create(IDCodeParser, DescriptorHandlerFlexophore, String) - Static method in class com.actelion.research.chem.descriptor.flexophore.example.MatchFlexophoreNodesMain
- create(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- create(StereoMolecule, int) - Method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
-
Creates a list with ModelExhaustiveStatistics.
- create(IDCodeCoord) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.FlexophoreCreateFunctions
- create(String) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandlerFactory
- create(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerStandard2DFactory
- create(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerStandardFactory
- create(String) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.FlexophoreCreateFunctions
- create(String) - Method in interface com.actelion.research.chem.descriptor.ISimilarityHandlerFactory
- create(String, String) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.FlexophoreCreateFunctions
- create(List<PPGaussian>, Coordinates) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangleCreator
- CREATE_PSEUDO_STEREO_GROUPS - Static variable in class com.actelion.research.chem.Canonizer
- CREATE_SYMMETRY_RANK - Static variable in class com.actelion.research.chem.Canonizer
- createArrow(Rectangle2D) - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- createAtomPropertiesDialog(StereoMolecule, int) - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- createAtomQueryFeatureDialog(StereoMolecule, int, boolean) - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- createBarycenter(Coordinates...) - Static method in class com.actelion.research.chem.Coordinates
- createBondFeaturesDialog(StereoMolecule, int) - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- createBonds(Molecule3D, boolean) - Static method in class com.actelion.research.chem.io.pdb.converter.BondsCalculator
-
Calculates the bonds of a molecule by checking the distance between all atoms.
- createBrushIndirect(int, Color, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- createBrushIndirect(int, Color, int) - Method in class com.actelion.research.gui.wmf.WMF
- createCache(String[], String, int, boolean, int, RigidFragmentProvider) - Static method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
-
This is a helper method to generate a custom cache and optionally a set of cache files from one or more compound files.
- createCanonicalOrientation(Conformer, MolecularVolume) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- createColor(double, double, double, double) - Method in class com.actelion.research.share.gui.DrawConfig
- createColor(long) - Static method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- createColor(Color, float) - Static method in class com.actelion.research.util.ColorHelper
-
Creates a new color with the hue taken from color
c
, but adjusted in brightness to match the desired perceived brightness. - createColor(Color, int) - Static method in class com.actelion.research.gui.hidpi.ColorUtils
- createCursor(int) - Static method in class com.actelion.research.util.CursorHelper
- createDefaultDocument() - Method in class com.actelion.research.gui.hidpi.ScaledEditorKit
- createDepictor(StereoMolecule) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- createDepictor(StereoMolecule) - Method in class com.actelion.research.share.gui.editor.Model
- createDepictor(StereoMolecule, boolean, DrawConfig) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- createDescriptor(ConformerSet) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- createDescriptor(Reaction) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
-
This descriptor contains non-hashed counts of predefined overlapping small fragments of organic functional groups.
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
-
This descriptor requires proper up/down bonds, because it encodes stereo parities.
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedPharmSphere
-
This descriptor requires proper up/down bonds, because it encodes stereo parities.
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
-
This descriptor requires proper up/down bonds, because it encodes stereo parities.
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPharmPath
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
-
This descriptor requires proper up/down bonds, because it encodes stereo parities.
- createDescriptor(StereoMolecule) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.FlexophoreCreateFunctions
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- createDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
-
the ShapeDescriptor consists of a whole ensemble of MolecularVolumes (MolecularGaussians), obtained from a conformational search algorithm
- createDescriptor(Object) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- createDescriptor(U) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
- createDescriptorSingleConf(ConformerSet) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- createDescriptorSingleConf(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- createDisabledIcon(String, int) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
- createExtendedDepictor() - Method in class com.actelion.research.share.gui.editor.Model
- createFileFilter(int, boolean) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
- createFont(int, int, int, int, int, boolean, boolean, boolean, byte, byte, byte, byte, byte, String) - Method in class com.actelion.research.gui.wmf.MetaFile
- createFont(int, int, int, int, int, boolean, boolean, boolean, byte, byte, byte, byte, byte, String) - Method in class com.actelion.research.gui.wmf.WMF
- createFont(Font, int, boolean, boolean) - Method in class com.actelion.research.gui.wmf.MetaFile
- createFont(Font, int, boolean, boolean) - Method in class com.actelion.research.gui.wmf.WMF
- createFragment(StereoMolecule, int[], int) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentProvider
- createFromDataFlavor(DataFlavor, Object) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- createFromDataFlavor(DataFlavor, Object) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- createFromDataFlavor(DataFlavor, Object) - Method in class com.actelion.research.gui.dnd.SDFileMoleculeDropAdapter
- createFromGivenConformation(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- createGenericTautomer() - Method in class com.actelion.research.chem.TautomerHelper
-
If no tautomers can be formed then a copy of the original molecule is returned.
- createHandles() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- createHTMLView(JComponent, String) - Static method in class com.actelion.research.gui.hidpi.ScaledHTML
-
Create an html renderer for the given component and string of html.
- createIcon(String, int) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
- createImage(String) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
-
Creates an image from the fileName.
- createImage(String) - Static method in class com.actelion.research.gui.JDrawToolbar
- createIndex(StereoMolecule) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- createIndexTables() - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- createInitialOrientation(Conformer) - Static method in class com.actelion.research.chem.docking.DockingUtils
- createInstance(String) - Static method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- createLaFCompatibleImage(String) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
-
Creates an image from the fileName.
- createLongIndex(StereoMolecule) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- createMolecule(int, int) - Method in class com.actelion.research.chem.StereoMolecule
- createMolFromSketchBuffer(StereoMolecule, byte[]) - Static method in class com.actelion.research.util.Sketch
- createMolFromSketchFile(StereoMolecule, String) - Static method in class com.actelion.research.util.Sketch
- createMostCentralRingSystem(StereoMolecule) - Static method in class com.actelion.research.chem.ScaffoldHelper
-
Modifies mol in-place to represent the most central ring system of the original mol.
- createMultipleConformations(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
-
Conformation generator of Thomas Sander
- createMurckoScaffold(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.ScaffoldHelper
-
Modifies mol in-place to represent the Murcko scaffold from the original mol.
- createNodeIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
This index is used to track the fate of the nodes MvK 17.07.2007
- createObject() - Method in class com.actelion.research.util.graph.complete.FactorySolution
- createObject() - Method in interface com.actelion.research.util.graph.complete.IFactory
- createObject(String) - Static method in class com.actelion.research.chem.DrawingObjectFactory
- createParser(String) - Static method in class com.actelion.research.chem.io.CompoundFileParser
-
Creates the proper parser for the given type of compound file (currently SD or DWAR).
- createPatternBrush(int[], int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- createPatternBrush(int[], int, int) - Method in class com.actelion.research.gui.wmf.WMF
- createPenIndirect(int, int, Color) - Method in class com.actelion.research.gui.wmf.MetaFile
- createPenIndirect(int, int, Color) - Method in class com.actelion.research.gui.wmf.WMF
- createPolygon() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- createPopupMenu(String, boolean) - Method in interface com.actelion.research.gui.dock.PopupProvider
- createPreview(Dockable, Dockable, int, JDockingPanel) - Method in class com.actelion.research.gui.dock.GhostPreview
- createReactionFromSketchBuffer(Reaction, byte[]) - Static method in class com.actelion.research.util.Sketch
- createReactionFromSketchFile(Reaction, String) - Static method in class com.actelion.research.util.Sketch
- createReactionSmiles(Reaction) - Static method in class com.actelion.research.chem.IsomericSmilesCreator
- createResidue(Map<String, AtomRecord>) - Method in class com.actelion.research.chem.io.pdb.converter.AminoAcidLabeled
- createSketchFromMol(Molecule) - Static method in class com.actelion.research.util.Sketch
- createSketchFromReaction(Reaction) - Static method in class com.actelion.research.util.Sketch
- createSketchFromReactionOLd(Reaction) - Static method in class com.actelion.research.util.Sketch
- createStateInfo() - Method in class com.actelion.research.gui.dock.TreeRoot
- createTorsionSet(int[], int[]) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
-
Creates a new TorsionSet object from a torsion index array.
- createTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
-
Provide the next set of torsion angles using a specific strategy and considering, which angle combinations were already tried, which had failed, and (depending on the strategy) considering the likelyhoods of particular torsions.
- createTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategyAdaptiveRandom
- createTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategyLikelySystematic
-
Determine the next likely set of torsion angles and return the TorsionSet containing an array of indexes referring to the torsion value in the RotatableBond and containing the contribution of this conformer to all non colliding ones.
- createTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategyRandom
-
Build a new set of torsion angles by pure or biased random picking.
- createVisualDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
-
This descriptor contains the molecule used for construction.
- createVisualDescriptor(StereoMolecule) - Method in interface com.actelion.research.chem.descriptor.flexophore.IDescriptorHandlerFlexophore
- createVisualDescriptorSingleConf(ConformerSet) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- creatorMolDistHistViz - Variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- CreatorMolDistHistViz - Class in com.actelion.research.chem.descriptor.flexophore.generator
-
CreatorMolDistHistViz
- CreatorMolDistHistViz() - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- cRiskNameA - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- cRiskNameN - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- cRiskTypeIrritant - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- cRiskTypeMutagenic - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- cRiskTypeReproductiveEffective - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- cRiskTypes - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- cRiskTypeTumorigenic - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- crop(Molecule3D, Coordinates, double) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- cropLigand(Molecule3D, double) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- cross(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- cross(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Computes the vector cross product between this vector and that vector.
- CROSSHAIR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- cRoundedMass - Static variable in class com.actelion.research.chem.Molecule
- cSelectRectCursor - Static variable in class com.actelion.research.util.CursorHelper
- cSelectRectPlusCursor - Static variable in class com.actelion.research.util.CursorHelper
- cSolubilityUnknown - Static variable in class com.actelion.research.chem.prediction.SolubilityPredictor
- cStringTypeDouble - Static variable in class com.actelion.research.chem.prediction.ParameterizedStringList
- cStringTypeIDCode - Static variable in class com.actelion.research.chem.prediction.ParameterizedStringList
- cStringTypeText - Static variable in class com.actelion.research.chem.prediction.ParameterizedStringList
- cStructureHiliteModeCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cStructureHiliteModeCurrentRow - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cStructureHiliteModeFilter - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cStructureHiliteModeNone - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cStructureHiliteModeText - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSummaryModeCode - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSummaryModeMaximum - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSummaryModeMean - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSummaryModeMedian - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSummaryModeMinimum - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSummaryModeNormal - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSummaryModeSum - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSummaryModeText - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSuperposeAlignValueShape - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cSuperposeValueReferenceRow - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- Csv - Class in com.actelion.research.chem.forcefield.mmff
-
Basic CSV parser.
- Csv() - Constructor for class com.actelion.research.chem.forcefield.mmff.Csv
- cTemplateTagName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cTextCursor - Static variable in class com.actelion.research.util.CursorHelper
- cTextExclusionTypeContains - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cTextExclusionTypeEndsWith - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cTextExclusionTypeEquals - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cTextExclusionTypeRegEx - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cTextExclusionTypeStartsWith - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cTextMultipleCategories - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cTool3Ring - Static variable in class com.actelion.research.gui.JDrawToolbar
- cTool4Ring - Static variable in class com.actelion.research.gui.JDrawToolbar
- cTool5Ring - Static variable in class com.actelion.research.gui.JDrawToolbar
- cTool6Ring - Static variable in class com.actelion.research.gui.JDrawToolbar
- cTool7Ring - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolAromRing - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolAtomBr - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolAtomC - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolAtomCl - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolAtomF - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolAtomH - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolAtomI - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolAtomN - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolAtomO - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolAtomOther - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolAtomP - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolAtomS - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolAtomSi - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolChain - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolDelete - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolDownBond - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolESR - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolESRAbs - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolESRAnd - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolESROr - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolLassoPointer - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolMapper - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolNegCharge - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolPosCharge - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolStdBond - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolText - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolUnknownParity - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolUpBond - Static variable in class com.actelion.research.gui.JDrawToolbar
- cToolZoom - Static variable in class com.actelion.research.gui.JDrawToolbar
- cubicDistance(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
- cubicDistance(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- cubicDistance(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
- cUnknownRisk - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- CursorHelper - Class in com.actelion.research.util
- CursorHelper() - Constructor for class com.actelion.research.util.CursorHelper
- cut(double[], int, int) - Static method in class com.actelion.research.util.ArrayUtils
-
Resize an array of Object
- CUT_LEFT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- CUT_NONE - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- CUT_RIGHT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- CutAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 5/16/13 Time: 3:43 PM
- CutAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.CutAction
- CUTOFF_RADIUS - Static variable in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- cVersion - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- cViewConfigTagName - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cViewNameEnd - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cViewNameStart - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- cZoomCursor - Static variable in class com.actelion.research.util.CursorHelper
D
- d - Variable in class com.actelion.research.util.LittleEndianDataInputStream
- D - Static variable in class com.actelion.research.chem.docking.scoring.plp.REPTerm
- da(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
-
Returns 'DA' from the table.
- da1 - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
- da2 - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
- daeps - Variable in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
- darad - Variable in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
- darker(Color, float) - Static method in class com.actelion.research.util.ColorHelper
-
Creates a new
Color
that is a darker version of thisColor
. - DATA_FORMATS - Static variable in class com.actelion.research.jfx.dataformat.MoleculeDataFormats
-
Deprecated.
- DataProcessor - Class in com.actelion.research.calc
- DataProcessor() - Constructor for class com.actelion.research.calc.DataProcessor
- DATE_FORMAT - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- DateAnalysis - Class in com.actelion.research.util
- DateAnalysis() - Constructor for class com.actelion.research.util.DateAnalysis
- debug - Static variable in class com.actelion.research.chem.MolfileParser
- debug - Static variable in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- debug - Static variable in class com.actelion.research.gui.dnd.ReactionDropAdapter
- DEBUG - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- DEBUG - Static variable in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes a binary fingerprint from a String into an int[].
- decode(byte[]) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistEncoder
- decode(byte[]) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- decode(byte[]) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- decode(byte[], byte[], byte[], String, byte[], boolean) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
-
Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class.
- decode(String) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
- decode(String) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
- decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes a binary fingerprint from a String into an int[].
- decode(String) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
- decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
- decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
- decode(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- decode(String) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistEncoder
- decode(String) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- decode(String) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- decode(String) - Method in class com.actelion.research.chem.phesa.AtomicGaussian
- decode(String) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- decode(String) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- decode(String) - Static method in class com.actelion.research.util.EncoderFloatingPointNumbers
- decode(String) - Static method in class com.actelion.research.util.EncoderIntegerNumbers
- decode(String, boolean) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
- decode(String, boolean, Reaction) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
-
Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class and are passed OBJECT_DELIMITER-delimited within one string.
- decode(String, int, Reaction) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
-
Creates a Reaction object by interpreting a reaction string encoded by this class.
- decode(String, StereoMolecule) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
- decode(String, String, String, String, String, boolean, Reaction) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
-
Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class.
- decodeCatalysts(byte[]) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
-
Generates an array of all catalysts of the encoded reaction string as bytes.
- decodeCoordsOnly(String, MolecularVolume) - Static method in class com.actelion.research.chem.phesa.MolecularVolume
- decodeCounts(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes a list of fragment/has-value counts from an encoded byte sequence into a byte[].
- decodeCounts(String) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes a list of fragment/has-value counts from an encoded String.
- decodeFull(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.MolecularVolume
- decodeHistograms(String, MolDistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHistEncoder
- decodeIntArray(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes an int[] without upper limit.
- decodeIntArray(String) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes an int[] without upper limit.
- decodeLong(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes a binary fingerprint from a String into a long[].
- decodeLong(String) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes a binary fingerprint from a String into a long[].
- decodeMolecules(byte[], byte[], byte[], boolean, boolean) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
-
Generates an array of all reactants and/or products of the encoded reaction string as bytes.
- decodeMolecules(String, boolean, boolean, boolean, boolean) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
-
Generates an array of all reactants and/or products of the encoded reaction string as bytes.
- decodeNodes(String) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistEncoder
- decodePairs(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes pairs of identifying integer with corresponding count values in the form of an int[n][2], where n is the number of pairs, index=0 refers to the ID value and index=1 refers to the count value.
- decodePairs(String) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Decodes pairs of identifying integer with corresponding count values in the form of an int[n][2], where n is the number of pairs, index=0 refers to the ID value and index=1 refers to the count value.
- def - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- Def - Class in com.actelion.research.chem.forcefield.mmff.table
-
Equivalence table, corresponds to MMFFDEF.PAR parameters table provided in the MMFF literature.
- Def(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Def
- DEFAULT - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- DEFAULT_BG - Static variable in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- DEFAULT_BOND_LENGTH - Static variable in class com.actelion.research.chem.conf.BondLengthSet
- DEFAULT_BOND_STDDEV - Static variable in class com.actelion.research.chem.conf.BondLengthSet
- DEFAULT_CAPACITY - Static variable in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- DEFAULT_CHARSET - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- DEFAULT_ELEM_WIDTH - Static variable in class com.actelion.research.chem.SVGDepictor
- DEFAULT_IMAGE_HEIGHT - Static variable in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- DEFAULT_IMAGE_WIDTH - Static variable in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- DEFAULT_MERGE_SPAN - Static variable in class com.actelion.research.chem.conf.TorsionDB
- DEFAULT_PITCH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- DEFAULT_QUALITY - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- DEFAULT_SIZE - Static variable in class com.actelion.research.chem.TextDrawingObject
- DEFAULT_STYLE - Static variable in class com.actelion.research.chem.TextDrawingObject
- DEFAULT_VAL - Static variable in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- DefaultCompoundCollectionModel<T> - Class in com.actelion.research.gui
- DefaultCompoundCollectionModel() - Constructor for class com.actelion.research.gui.DefaultCompoundCollectionModel
- DefaultCompoundCollectionModel.IDCode - Class in com.actelion.research.gui
-
This version of the DefaultCompoundCollectionModel collects molecules as IDCodes.
- DefaultCompoundCollectionModel.IDCodeWithName - Class in com.actelion.research.gui
-
This version of the DefaultCompoundCollectionModel collects molecules as String[2] with idcodes & idcoords (index 0) and molecule name (index 1).
- DefaultCompoundCollectionModel.Molecule - Class in com.actelion.research.gui
-
This version of the DefaultCompoundCollectionModel collects molecules as StereoMolecules.
- DefaultCompoundCollectionModel.Native - Class in com.actelion.research.gui
-
This version of the DefaultCompoundCollectionModel collects IDCodes and StereoMolecules without conversion into their native type.
- DEG2RAD - Static variable in class com.actelion.research.chem.forcefield.mmff.Constants
- degree(MMFFMolecule, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
-
Returns the total number of atoms connected to an atom, including implicit and explicit hydrogens.
- degree(MMFFMolecule, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Charge
- Delegator<T> - Class in com.actelion.research.share.gui
- Delegator(T) - Constructor for class com.actelion.research.share.gui.Delegator
- DeleteAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 3/26/13 Time: 4:15 PM
- DeleteAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.DeleteAction
- deleteAtom(int) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- deleteAtom(int) - Method in class com.actelion.research.chem.Molecule3D
-
High level function for constructing a molecule.
- deleteAtomOrBond(double, double) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- deleteAtoms(boolean[]) - Method in class com.actelion.research.chem.conf.Conformer
-
Removes atoms Coordinates objects from those atoms that are marked in the given array.
- deleteAtoms(boolean[]) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- deleteAtoms(int[]) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- deleteAtoms(List<Integer>) - Method in class com.actelion.research.chem.Molecule3D
- deleteBond(int) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- deleteBond(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- deleteBondAndSurrounding(int) - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- deleteHandles() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- deleteHydrogens(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- deleteMarkedAtomsAndBonds() - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- deleteMolecule() - Method in class com.actelion.research.chem.Molecule
-
Deprecated.
- deleteMolecule(StereoMolecule) - Method in class com.actelion.research.share.gui.editor.Model
- deleteObject(int) - Method in class com.actelion.research.gui.wmf.MetaFile
- deleteObject(int) - Method in class com.actelion.research.gui.wmf.WMF
- deleteSelectedAtoms() - Method in class com.actelion.research.chem.Molecule
-
High level function for constructing a molecule.
- DELTA_BONDS - Static variable in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
- DENSITY_FIELD - Static variable in class com.actelion.research.chem.SDFileMolecule
- Depictor - Class in com.actelion.research.chem
- Depictor(StereoMolecule) - Constructor for class com.actelion.research.chem.Depictor
- Depictor(StereoMolecule, int) - Constructor for class com.actelion.research.chem.Depictor
- Depictor2D - Class in com.actelion.research.chem
- Depictor2D(StereoMolecule) - Constructor for class com.actelion.research.chem.Depictor2D
- Depictor2D(StereoMolecule, int) - Constructor for class com.actelion.research.chem.Depictor2D
- DepictorLine() - Constructor for class com.actelion.research.chem.AbstractDepictor.DepictorLine
- DepictorLine(double, double, double, double) - Constructor for class com.actelion.research.chem.AbstractDepictor.DepictorLine
- DepictorTransformation - Class in com.actelion.research.chem
- DepictorTransformation() - Constructor for class com.actelion.research.chem.DepictorTransformation
- DepictorTransformation(double, double, double) - Constructor for class com.actelion.research.chem.DepictorTransformation
- DepictorTransformation(DepictorTransformation) - Constructor for class com.actelion.research.chem.DepictorTransformation
- DepictorTransformation(Rectangle2D.Double, Rectangle2D.Double, double, int) - Constructor for class com.actelion.research.chem.DepictorTransformation
- derivative() - Method in class com.actelion.research.util.FastSpline
-
Returns the derivative of the polynomial spline function as a PolynomialSplineFunction
- derivative() - Method in class com.actelion.research.util.FastSpline.Polynome
- DESCRIBE_ALL - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- DESCRIBE_MAPPED - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
Only mapped atoms are described.
- DESCRIPTOR_BINARY_SKELETONSPHERES - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_CenteredSkeletonFragments - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_END - Static variable in class com.actelion.research.chem.AbstractDrawingObject
- DESCRIPTOR_EXTENDED_LIST - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_FFP512 - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_Flexophore - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_FULL_FRAGMENT_SET - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_HashedCFp - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_IntegerVector - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_LIST - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_MAX_COMMON_SUBSTRUCT - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_OrganicFunctionalGroups - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_PFP512 - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_PhysicoChemicalProperties - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_PTREE - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_ReactionFP - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_ShapeAlign - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_ShapeAlignSingleConf - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_SkeletonSpheres - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_START - Static variable in class com.actelion.research.chem.AbstractDrawingObject
- DESCRIPTOR_SUBSTRUCT_QUERY_IN_BASE - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_TopoPPHistDist - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_TYPE - Static variable in class com.actelion.research.chem.AbstractDrawingObject
- DESCRIPTOR_TYPE_MOLECULE - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_TYPE_REACTION - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DESCRIPTOR_TYPE_UNKNOWN - Static variable in interface com.actelion.research.chem.descriptor.DescriptorConstants
- DescriptorConstants - Interface in com.actelion.research.chem.descriptor
- DescriptorEncoder - Class in com.actelion.research.chem.descriptor
-
DescriptorEncoder encodes int[] based descriptors into byte arrays that may be used to instantiate Strings
- DescriptorEncoder() - Constructor for class com.actelion.research.chem.descriptor.DescriptorEncoder
- DescriptorHandler<T,U> - Interface in com.actelion.research.chem.descriptor
-
DescriptorHandler is the base Interface for any molecular descriptor handling StereoMolecules or Reactions
- DescriptorHandlerFactory - Interface in com.actelion.research.chem.descriptor
- DescriptorHandlerFFP512 - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerFFP512() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
- DescriptorHandlerFlexophore - Class in com.actelion.research.chem.descriptor
-
DescriptorHandlerFlexophore
- DescriptorHandlerFlexophore() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- DescriptorHandlerFlexophore(int, int, double, double, boolean) - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- DescriptorHandlerFlexophore(String) - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- DescriptorHandlerFunctionalGroups - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerFunctionalGroups() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- DescriptorHandlerHashedCFp - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerHashedCFp() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
- DescriptorHandlerHashedPharmSphere - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerHashedPharmSphere() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerHashedPharmSphere
- DescriptorHandlerLongCFP - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerLongCFP() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
- DescriptorHandlerLongFFP512 - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerLongFFP512() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
- DescriptorHandlerLongPFP512 - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerLongPFP512() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
- DescriptorHandlerPFP512 - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerPFP512() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
- DescriptorHandlerPharmPath - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerPharmPath() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerPharmPath
- DescriptorHandlerPTree - Class in com.actelion.research.chem.descriptor.pharmacophoretree
- DescriptorHandlerPTree() - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- DescriptorHandlerReactionFP - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerReactionFP() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- DescriptorHandlerShape - Class in com.actelion.research.chem.phesa
- DescriptorHandlerShape() - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShape
- DescriptorHandlerShape(boolean) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShape
- DescriptorHandlerShape(boolean, double) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShape
- DescriptorHandlerShape(boolean, int, double) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShape
- DescriptorHandlerShape(double) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShape
- DescriptorHandlerShape(int, double) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShape
- DescriptorHandlerShapeOneConf - Class in com.actelion.research.chem.phesa
- DescriptorHandlerShapeOneConf() - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShapeOneConf
- DescriptorHandlerShapeOneConf(double) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShapeOneConf
- DescriptorHandlerShapeOneConf(int, double) - Constructor for class com.actelion.research.chem.phesa.DescriptorHandlerShapeOneConf
- DescriptorHandlerSkeletonSpheres - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerSkeletonSpheres() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- DescriptorHandlerStandard2DFactory - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerStandard2DFactory() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerStandard2DFactory
- DescriptorHandlerStandardFactory - Class in com.actelion.research.chem.descriptor
- DescriptorHandlerStandardFactory() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHandlerStandardFactory
- DescriptorHelper - Class in com.actelion.research.chem.descriptor
- DescriptorHelper() - Constructor for class com.actelion.research.chem.descriptor.DescriptorHelper
- DescriptorInfo - Class in com.actelion.research.chem.descriptor
- DescriptorInfo(String, String, String, int, boolean, boolean, boolean, boolean) - Constructor for class com.actelion.research.chem.descriptor.DescriptorInfo
- det() - Method in class com.actelion.research.calc.LUDecomposition
-
Determinant
- det() - Method in class com.actelion.research.calc.Matrix
-
Matrix determinant
- detect() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.IonizableGroupDetector2D
- detect() - Method in class com.actelion.research.chem.phesa.pharmacophore.IonizableGroupDetector
- determineAromaticity(boolean[], boolean[], int[], boolean) - Method in class com.actelion.research.chem.RingCollection
- devide(double) - Method in class com.actelion.research.calc.Matrix
- devide(Matrix) - Method in class com.actelion.research.calc.Matrix
- devide(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
- devide(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- devide(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
- devideCols(Matrix) - Method in class com.actelion.research.calc.Matrix
- devideDivisorBigger(Matrix) - Method in class com.actelion.research.calc.Matrix
- devideRow(int, double) - Method in class com.actelion.research.calc.Matrix
- DF_IDCODE - Static variable in class com.actelion.research.chem.dnd.ChemistryDataFormats
- DF_IDCODE - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
- DF_MDLMOLFILE - Static variable in class com.actelion.research.chem.dnd.ChemistryDataFormats
- DF_MDLMOLFILE - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
- DF_MDLMOLFILE - Static variable in class com.actelion.research.jfx.dataformat.MoleculeDataFormats
-
Deprecated.
- DF_MDLMOLFILEV3 - Static variable in class com.actelion.research.chem.dnd.ChemistryDataFormats
- DF_MDLMOLFILEV3 - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
- DF_MDLMOLFILEV3 - Static variable in class com.actelion.research.jfx.dataformat.MoleculeDataFormats
-
Deprecated.
- DF_REACTION_SMILES - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
- DF_SERIALIZED_MOLECULE - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
- DF_SERIALIZED_OBJECT - Static variable in class com.actelion.research.chem.dnd.ChemistryDataFormats
- DF_SERIALIZED_REACTION - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
- DF_SERIALIZEDMOLECULE - Static variable in class com.actelion.research.jfx.dataformat.MoleculeDataFormats
-
Deprecated.
- DF_SERIALIZEDREACTANT - Static variable in class com.actelion.research.jfx.dataformat.MoleculeDataFormats
-
Deprecated.
- DF_SERIALIZEDSTRUCTURETRANSFERDATA - Static variable in class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
- DF_SMILES - Static variable in class com.actelion.research.chem.dnd.ChemistryDataFormats
- DF_SMILES - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
- DF_SMILES - Static variable in class com.actelion.research.jfx.dataformat.MoleculeDataFormats
-
Deprecated.
- dfI2 - Static variable in class com.actelion.research.util.Formatter
- dfI3 - Static variable in class com.actelion.research.util.Formatter
- dfs(Molecule3D, int, Set<Integer>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- dfs(Molecule3D, int, Set<Integer>, int, boolean) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- dfsb - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- Dfsb - Class in com.actelion.research.chem.forcefield.mmff.table
- Dfsb(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Dfsb
- diagonalize() - Method in class com.actelion.research.calc.Matrix
- DialogResult - Enum in com.actelion.research.share.gui
-
Return values from Dialog calls
- DiastereoIDTest - Class in com.actelion.research.chem.contrib
- DiastereoIDTest() - Constructor for class com.actelion.research.chem.contrib.DiastereoIDTest
- DiastereotopicAtomID - Class in com.actelion.research.chem.contrib
- DiastereotopicAtomID() - Constructor for class com.actelion.research.chem.contrib.DiastereotopicAtomID
- DIB_PAL_COLORS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- DIB_RGB_COLORS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- difference(double, double) - Static method in class com.actelion.research.util.Angle
-
Determines the normalized difference between a2 and a1, i.e.
- difference(Angle, Angle) - Static method in class com.actelion.research.util.Angle
-
Determines the normalized difference between a2 and a1, i.e.
- disableCollidingTorsionRules(SelfOrganizedConformer) - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- disableIfColliding(SelfOrganizedConformer) - Method in class org.openmolecules.chem.conf.so.TorsionRule
- disablePlaneRules() - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- disableTorsionRules() - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- dispose() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- dispose() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- dispose() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- dist() - Method in class com.actelion.research.chem.Coordinates
- dist(InteractionSimilarityTable.InteractionDescriptor) - Method in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable.InteractionDescriptor
- DIST_CUTOFF - Static variable in class com.actelion.research.chem.phesa.Gaussian3D
- distance(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- distance(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Computes the euclidean distance between two Vector3s.
- distance(ByteVec, ByteVec, int) - Static method in class com.actelion.research.util.datamodel.ByteVec
- distance(DoubleVec, DoubleVec, int) - Static method in class com.actelion.research.util.DoubleVec
- DistanceRule - Class in org.openmolecules.chem.conf.so
- DistanceRule() - Constructor for class org.openmolecules.chem.conf.so.DistanceRule
-
Creates a dummy rule to be neglected
- DistanceRule(int[], double, double, int) - Constructor for class org.openmolecules.chem.conf.so.DistanceRule
- DistanceRule(int[], int[], double, double, int) - Constructor for class org.openmolecules.chem.conf.so.DistanceRule
- DistanceRule(int[], int[], double, int) - Constructor for class org.openmolecules.chem.conf.so.DistanceRule
-
Constructor for 2 bonds in between.
- distanceSquared(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- DistHist - Class in com.actelion.research.chem.descriptor.flexophore
- DistHist() - Constructor for class com.actelion.research.chem.descriptor.flexophore.DistHist
- DistHist(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.DistHist
- DistHist(DistHist) - Constructor for class com.actelion.research.chem.descriptor.flexophore.DistHist
- DistHistEncoder - Class in com.actelion.research.chem.descriptor.flexophore
- DistHistEncoder() - Constructor for class com.actelion.research.chem.descriptor.flexophore.DistHistEncoder
- DistHistHelper - Class in com.actelion.research.chem.descriptor.flexophore
-
DistHistHelper
- DistHistHelper() - Constructor for class com.actelion.research.chem.descriptor.flexophore.DistHistHelper
- DistHistHelper.RangeStatistics - Class in com.actelion.research.chem.descriptor.flexophore
- DISTINGUISH_RACEMIC_OR_GROUPS - Static variable in class com.actelion.research.chem.Canonizer
- distModel - Variable in class com.actelion.research.chem.forcefield.mmff.Electrostatic
- distSq() - Method in class com.actelion.research.chem.Coordinates
- distSquareTo(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- DiversitySelector - Class in com.actelion.research.chem
- DiversitySelector() - Constructor for class com.actelion.research.chem.DiversitySelector
- DiversitySelector.DiversitySelectorRecord - Class in com.actelion.research.chem
- dock(Dockable) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
Dock the dockable to the center of the selected view.
- dock(Dockable, int) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
Dock the Dockable at the given position to the selected view.
- dock(Dockable, String) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
Dock the dockable either as a new root dockable or to the treeElement that contains dockable specified as part dockInfo.
- DOCK_BOTTOM - Static variable in class com.actelion.research.gui.dock.JDockingPanel
- DOCK_CENTER - Static variable in class com.actelion.research.gui.dock.JDockingPanel
- DOCK_LEFT - Static variable in class com.actelion.research.gui.dock.JDockingPanel
- DOCK_RIGHT - Static variable in class com.actelion.research.gui.dock.JDockingPanel
- DOCK_TOP - Static variable in class com.actelion.research.gui.dock.JDockingPanel
- Dockable - Class in com.actelion.research.gui.dock
-
A lightweight component derived from JPanel that features certain subcomponents that make it look similar to a frame or internal frame.
- Dockable(JDockingPanel, JComponent, String, ActionListener, boolean) - Constructor for class com.actelion.research.gui.dock.Dockable
-
Constructs a
TitledComponent
with the specified title and content panel. - Dockable(JDockingPanel, JComponent, String, ActionListener, boolean, boolean) - Constructor for class com.actelion.research.gui.dock.Dockable
-
Constructs a
TitledComponent
with the specified title and content panel. - DockableHeader - Class in com.actelion.research.gui.dock
- DockableHeader(Dockable, String, ActionListener, boolean, boolean) - Constructor for class com.actelion.research.gui.dock.DockableHeader
- DockingEngine - Class in com.actelion.research.chem.docking
- DockingEngine(Molecule3D, Molecule3D) - Constructor for class com.actelion.research.chem.docking.DockingEngine
- DockingEngine(Molecule3D, Molecule3D, int, int, DockingEngine.ScoringFunction, DockingEngine.StartPosition) - Constructor for class com.actelion.research.chem.docking.DockingEngine
- DockingEngine.DockingResult - Class in com.actelion.research.chem.docking
- DockingEngine.ScoringFunction - Enum in com.actelion.research.chem.docking
- DockingEngine.StartPosition - Enum in com.actelion.research.chem.docking
- DockingFailedException - Exception in com.actelion.research.chem.docking
- DockingFailedException(String) - Constructor for exception com.actelion.research.chem.docking.DockingFailedException
- DockingResult(StereoMolecule, double) - Constructor for class com.actelion.research.chem.docking.DockingEngine.DockingResult
- DockingUtils - Class in com.actelion.research.chem.docking
- dockMolecule(StereoMolecule) - Method in class com.actelion.research.chem.docking.DockingEngine
- doModal() - Method in interface com.actelion.research.share.gui.editor.dialogs.IDialog
- doModalAt(double, double) - Method in interface com.actelion.research.share.gui.editor.dialogs.IDialog
- DONOR - com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint.Functionality
- DONOR_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- DonorPoint - Class in com.actelion.research.chem.phesa.pharmacophore
- DonorPoint(DonorPoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
- DonorPoint(StereoMolecule, int, int, int) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
- dot(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- dot(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Computes the vector dot product between this vector and that vector.
- DoubleArray - Class in com.actelion.research.util.datamodel
-
DoubleArray 26 Jun 2010 MvK: Start implementation
- DoubleArray() - Constructor for class com.actelion.research.util.datamodel.DoubleArray
- DoubleArray(double[]) - Constructor for class com.actelion.research.util.datamodel.DoubleArray
-
Deep constructor
- DoubleArray(int) - Constructor for class com.actelion.research.util.datamodel.DoubleArray
- DoubleArray(int[]) - Constructor for class com.actelion.research.util.datamodel.DoubleArray
- DoubleArray(IntArray) - Constructor for class com.actelion.research.util.datamodel.DoubleArray
- doubleArrayToByteArray(double[]) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
- DoubleFormat - Class in com.actelion.research.util
- DoubleFormat() - Constructor for class com.actelion.research.util.DoubleFormat
- doubleToByteArray(double) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
- doubleValue() - Method in class com.actelion.research.util.concurrent.AtomicFloat
- DoubleVec - Class in com.actelion.research.util
- DoubleVec(double[]) - Constructor for class com.actelion.research.util.DoubleVec
- DoubleVec(double[], boolean) - Constructor for class com.actelion.research.util.DoubleVec
- DoubleVec(int) - Constructor for class com.actelion.research.util.DoubleVec
- DoubleVec(int[]) - Constructor for class com.actelion.research.util.DoubleVec
- DoubleVec(DoubleVec) - Constructor for class com.actelion.research.util.DoubleVec
- DoubleVec(DoubleVec, boolean) - Constructor for class com.actelion.research.util.DoubleVec
- DoubleVec(Vector<Double>) - Constructor for class com.actelion.research.util.DoubleVec
- DoubleVec(Vector<Double>, boolean) - Constructor for class com.actelion.research.util.DoubleVec
- DownBondAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 1/28/13 Time: 1:51 PM
- DownBondAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.DownBondAction
- DRAFT_QUALITY - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- dragDropEnd(DragSourceDropEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- dragDropEnd(DragSourceDropEvent) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- dragDropEnd(DragSourceDropEvent) - Method in class com.actelion.research.gui.JChemistryView
- dragEnter(DragSourceDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- dragEnter(DragSourceDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- dragEnter(DragSourceDragEvent) - Method in class com.actelion.research.gui.JChemistryView
- dragEnter(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- dragEnter(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- dragExit(DragSourceEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- dragExit(DragSourceEvent) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- dragExit(DragSourceEvent) - Method in class com.actelion.research.gui.JChemistryView
- dragExit(DropTargetEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- dragExit(DropTargetEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- dragGestureRecognized(DragGestureEvent) - Method in class com.actelion.research.gui.JChemistryView
- DragGlassPane - Class in com.actelion.research.jfx.gui.chem
-
Project: User: rufenec Date: 2/21/14 Time: 6:14 PM
- DragGlassPane() - Constructor for class com.actelion.research.jfx.gui.chem.DragGlassPane
- dragIsValidAndStarts() - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- dragOver(DragSourceDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- dragOver(DragSourceDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- dragOver(DragSourceDragEvent) - Method in class com.actelion.research.gui.JChemistryView
- dragOver(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- dragOver(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- draw() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- draw(IDrawContext) - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
- draw(IDrawContext, DepictorTransformation) - Method in class com.actelion.research.share.gui.Arrow
- draw(IDrawContext, DepictorTransformation) - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
- draw(Graphics, DepictorTransformation) - Method in class com.actelion.research.chem.AbstractDrawingObject
- draw(Graphics, DepictorTransformation) - Method in class com.actelion.research.chem.reaction.ReactionArrow
- draw(Graphics, DepictorTransformation) - Method in class com.actelion.research.chem.TextDrawingObject
- draw(Shape) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- draw2D(Graphics2D, DepictorTransformation) - Method in class com.actelion.research.chem.AbstractDrawingObject
- draw2D(Graphics2D, DepictorTransformation) - Method in class com.actelion.research.chem.reaction.ReactionArrow
- draw2D(Graphics2D, DepictorTransformation) - Method in class com.actelion.research.chem.TextDrawingObject
- DrawAction - Class in com.actelion.research.share.gui.editor.actions
-
Basic class which handles all actions which interact with the drawing surface
- DrawAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.DrawAction
- drawArc(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawArc(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- DrawAreaEvent - Class in com.actelion.research.gui
- DrawAreaEvent(Object, int, boolean) - Constructor for class com.actelion.research.gui.DrawAreaEvent
- DrawAreaListener - Interface in com.actelion.research.gui
- drawAtomHighlight(IDrawContext, StereoMolecule, int) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- drawAtomKeyStrokes(IDrawContext, StereoMolecule, int) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- drawBlackLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.AbstractDepictor
- drawBlackLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.Depictor
- drawBlackLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.Depictor2D
- drawBlackLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.SVGDepictor
- drawBlackLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- drawBondHighlight(IDrawContext, StereoMolecule, int) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- DrawConfig - Class in com.actelion.research.share.gui
-
User: rufenec Creation Date: 8/24/2016
- DrawConfig() - Constructor for class com.actelion.research.share.gui.DrawConfig
- drawDashedLine(double, double, double, double, int[]) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- drawDashedLine(double, double, double, double, int[]) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- drawDot(double, double) - Method in class com.actelion.research.chem.AbstractDepictor
- drawDottedLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.AbstractDepictor
- drawDottedLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.Depictor
- drawDottedLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.Depictor2D
- drawDottedLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.chem.SVGDepictor
- drawDottedLine(AbstractDepictor.DepictorLine) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- drawDragImage(Transferable, int, int) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- drawDragImage(Transferable, int, int) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- drawGlyphVector(GlyphVector, float, float) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawImage(BufferedImage, BufferedImageOp, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawImage(Image, int, int, int, int, int, int, int, int, Color, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawImage(Image, int, int, int, int, int, int, int, int, Color, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawImage(Image, int, int, int, int, int, int, int, int, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawImage(Image, int, int, int, int, int, int, int, int, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawImage(Image, int, int, int, int, Color, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawImage(Image, int, int, int, int, Color, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawImage(Image, int, int, int, int, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawImage(Image, int, int, int, int, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawImage(Image, int, int, Color, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawImage(Image, int, int, Color, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawImage(Image, int, int, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawImage(Image, int, int, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawImage(Image, AffineTransform, ImageObserver) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- DrawingObject - Class in com.actelion.research.share.gui.editor.chem
-
Project: User: rufenec Date: 5/16/13 Time: 12:31 PM
- DrawingObject() - Constructor for class com.actelion.research.share.gui.editor.chem.DrawingObject
- DrawingObjectFactory - Class in com.actelion.research.chem
- DrawingObjectList - Class in com.actelion.research.chem
- DrawingObjectList() - Constructor for class com.actelion.research.chem.DrawingObjectList
- DrawingObjectList(DrawingObjectList) - Constructor for class com.actelion.research.chem.DrawingObjectList
- DrawingObjectList(String) - Constructor for class com.actelion.research.chem.DrawingObjectList
- drawLine(double, double, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- drawLine(double, double, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- drawLine(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawLine(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawOval(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawOval(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawPolygon(double[], double[], int) - Method in class com.actelion.research.chem.AbstractDepictor
- drawPolygon(double[], double[], int) - Method in class com.actelion.research.chem.Depictor
- drawPolygon(double[], double[], int) - Method in class com.actelion.research.chem.Depictor2D
- drawPolygon(double[], double[], int) - Method in class com.actelion.research.chem.SVGDepictor
- drawPolygon(double[], double[], int) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- drawPolygon(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawPolygon(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawPolygon(IPolygon) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- drawPolygon(IPolygon) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- drawPolyline(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawPolyline(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawPreview(Graphics2D) - Method in class com.actelion.research.gui.dock.GhostPreview
- drawRect(double, double, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- drawRect(double, double, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- drawRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawRenderableImage(RenderableImage, AffineTransform) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawRenderedImage(RenderedImage, AffineTransform) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawRoundRect(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawRoundRect(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawString(String, double, double) - Method in class com.actelion.research.chem.AbstractDepictor
- drawString(String, double, double) - Method in class com.actelion.research.chem.Depictor
- drawString(String, double, double) - Method in class com.actelion.research.chem.Depictor2D
- drawString(String, double, double) - Method in class com.actelion.research.chem.SVGDepictor
- drawString(String, double, double) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- drawString(String, float, float) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawString(String, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawString(String, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawString(AttributedCharacterIterator, float, float) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawString(AttributedCharacterIterator, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- drawString(AttributedCharacterIterator, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- drawText(String, double, double, boolean, boolean) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- drawText(String, double, double, boolean, boolean) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- driver1() - Static method in class com.actelion.research.util.BurtleHasher
- driver3() - Static method in class com.actelion.research.util.BurtleHasher
- drop(DropTargetDropEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- drop(DropTargetDropEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- dropActionChanged(DragSourceDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- dropActionChanged(DragSourceDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- dropActionChanged(DragSourceDragEvent) - Method in class com.actelion.research.gui.JChemistryView
- dropActionChanged(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- dropActionChanged(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- DruglikenessPredictor - Class in com.actelion.research.chem.prediction
- DruglikenessPredictor() - Constructor for class com.actelion.research.chem.prediction.DruglikenessPredictor
- DrugScoreCalculator - Class in com.actelion.research.chem.prediction
-
Created by rufenec on 26/10/15.
- DrugScoreCalculator() - Constructor for class com.actelion.research.chem.prediction.DrugScoreCalculator
- DSTINVERT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- DUMMY_INTERACT_ID - Static variable in class com.actelion.research.chem.descriptor.flexophore.PPNode
- dump(ChemDrawCDX.CDXNode) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- DW_FRAGMENTS_FILE - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- DWAQ_EXTENSION - Static variable in class com.actelion.research.util.ConstantsDWAR
- DWAR_EXTENSION - Static variable in class com.actelion.research.util.ConstantsDWAR
- DWARFileCreator - Class in com.actelion.research.chem.io
- DWARFileCreator(BufferedWriter) - Constructor for class com.actelion.research.chem.io.DWARFileCreator
-
Use a DWARFileCreator for writing native DataWarrior files without a CompoundTableModel.
- DWARFileParser - Class in com.actelion.research.chem.io
- DWARFileParser(File) - Constructor for class com.actelion.research.chem.io.DWARFileParser
-
Constructs a DWARFileParser from a File with coordinate mode MODE_COORDINATES_PREFER_2D.
- DWARFileParser(File, int) - Constructor for class com.actelion.research.chem.io.DWARFileParser
-
Constructs a DWARFileParser from a File with the specified coordinate mode.
- DWARFileParser(Reader) - Constructor for class com.actelion.research.chem.io.DWARFileParser
-
Constructs a DWARFileParser from a Reader with coordinate mode MODE_COORDINATES_PREFER_2D.
- DWARFileParser(Reader, int) - Constructor for class com.actelion.research.chem.io.DWARFileParser
-
Constructs a DWARFileParser from a Reader with the specified coordinate mode.
- DWARFileParser(String) - Constructor for class com.actelion.research.chem.io.DWARFileParser
-
Constructs a DWARFileParser from a file name with coordinate mode MODE_COORDINATES_PREFER_2D.
- DWARFileParser(String, int) - Constructor for class com.actelion.research.chem.io.DWARFileParser
-
Constructs a DWARFileParser from a file name with the specified coordinate mode.
- DWARFileParser.SpecialField - Class in com.actelion.research.chem.io
E
- edge - Variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
- editableProperty() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- Electrostatic - Class in com.actelion.research.chem.forcefield.mmff
-
Nonbonded electrostatic energy term class.
- Electrostatic(MMFFMolecule, int, int, Separation.Relation, double, double) - Constructor for class com.actelion.research.chem.forcefield.mmff.Electrostatic
-
Constructor with default values for distModel and dielConst.
- Electrostatic(MMFFMolecule, int, int, Separation.Relation, double, double, boolean, double) - Constructor for class com.actelion.research.chem.forcefield.mmff.Electrostatic
-
Construct a new electrostatic energy term.
- Element - Class in com.actelion.research.chem
- Element() - Constructor for class com.actelion.research.chem.Element
- Element(int, String, String, double, double, double, double) - Constructor for class com.actelion.research.chem.Element
- eliminationRuleString(TorsionSetEliminationRule) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- ellipse(int, int, int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- ellipse(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMF
- ELUSIVE - Static variable in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- EmpiricalLigandStrain - Class in com.actelion.research.chem.potentialenergy
- EmpiricalLigandStrain(Conformer, int[], BondRotationHelper) - Constructor for class com.actelion.research.chem.potentialenergy.EmpiricalLigandStrain
- enableTorsionRules() - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- encode() - Method in class com.actelion.research.chem.phesa.AtomicGaussian
- encode() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
- encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
- encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
- encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
- encode() - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
- encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
- encode() - Method in class com.actelion.research.chem.phesa.pharmacophore.SimplePPGaussian
- encode() - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- encode(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- encode(double[], int) - Static method in class com.actelion.research.util.EncoderFloatingPointNumbers
-
Convenience method to encode a array with a given precision.
- encode(float[], int) - Static method in class com.actelion.research.util.EncoderFloatingPointNumbers
- encode(int[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
- encode(int[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Encodes a binary fingerprint stored as int[].
- encode(int[]) - Static method in class com.actelion.research.util.EncoderIntegerNumbers
-
Convenience method to encode a array with a given precision.
- encode(int[][]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- encode(long[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
- encode(MolDistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistEncoder
- encode(PharmacophoreNode) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- encode(PharmacophoreTree) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- encode(PheSAMolecule) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- encode(Reaction, boolean) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
-
Creates a String containing a unique reaction code by creating idcodes of every reactant and product and concatenating them in lexical order.
- encode(Reaction, boolean, int) - Static method in class com.actelion.research.chem.reaction.ReactionEncoder
-
Creates a String containing a reaction code by creating idcodes of every reactant and product and concatenating them in original (if mode includes RETAIN_REACTANT_AND_PRODUCT_ORDER) or in lexical order.
- encode(Object) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- encode(T) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
- ENCODE_ATOM_CUSTOM_LABELS - Static variable in class com.actelion.research.chem.Canonizer
- ENCODE_ATOM_SELECTION - Static variable in class com.actelion.research.chem.Canonizer
- encodeCoordsOnly() - Method in class com.actelion.research.chem.phesa.MolecularVolume
- encodeCounts(byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Encodes a fragment/hash-value count list.
- encodeFull() - Method in class com.actelion.research.chem.phesa.MolecularVolume
- EncodeFunctions - Class in com.actelion.research.chem.phesa
-
February 2018 Author: J.
- EncodeFunctions() - Constructor for class com.actelion.research.chem.phesa.EncodeFunctions
- encodeHistograms(DistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHistEncoder
- encodeHTML(String) - Static method in class com.actelion.research.util.StringFunctions
- encodeIntArray(int[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Encodes an int[] containing positive values without upper limit.
- encodeLong(long[]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Encodes a binary fingerprint stored as long[].
- encodePairs(int[][]) - Method in class com.actelion.research.chem.descriptor.DescriptorEncoder
-
Encodes pairs of identifying integer with corresponding count values in the form of an int[n][2], where n is the number of pairs, index=0 refers to the ID value and index=1 refers to the count value.
- EncoderFloatingPointNumbers - Class in com.actelion.research.util
- EncoderFloatingPointNumbers(double[], int) - Constructor for class com.actelion.research.util.EncoderFloatingPointNumbers
-
More values can be added after the constructor was called.
- EncoderFloatingPointNumbers(float[], int) - Constructor for class com.actelion.research.util.EncoderFloatingPointNumbers
- EncoderIntegerNumbers - Class in com.actelion.research.util
-
Encodes integer numbers into a string.
- EncoderIntegerNumbers(int[]) - Constructor for class com.actelion.research.util.EncoderIntegerNumbers
-
More values can be added after the constructor was called.
- end() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXDocument
- end() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXPage
- end() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXReactionStep
- endBorrowContent() - Method in class com.actelion.research.gui.dock.Dockable
-
Returns the content from temporarily adding it to another copntainer.
- ENERGY_CUTOFF - Static variable in class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
- EnergyTerm - Interface in com.actelion.research.chem.forcefield.mmff
-
Interface class for energy terms.
- ENOL - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- ensure2DCoordinates() - Method in class com.actelion.research.chem.IDCodeParser
- ensure2DCoordinates() - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- ensureHelperArrays(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
While the Molecule class covers all primary molecule information, its derived class ExtendedMolecule handles secondary, i.e.
- ensureHelperArrays(int) - Method in class com.actelion.research.chem.StereoMolecule
-
ensureHelperArrays() is the essential method when working with molecules.
- enumerateExtensionCutFast(int, int[], List<Integer>, Set<Integer>, Set<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
-
retrieve nodes that are part of extension match ("extension nodes") as well as the nodes that are part of a cut subtree (source nodes) from a cut-string
- enumerateExtensionCutFull(int, int[], List<Integer>, List<Integer>, List<List<Integer>>, List<List<Integer>>, List<Integer>, Set<Integer>, List<Integer>, List<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
-
retrieves nodes that are part of extension match ("extension nodes") as well as the different subtrees resulting from the cuts with a list of their edges (in bfs order) as well as the parents of the edges
- EPS - Static variable in class com.actelion.research.chem.forcefield.AbstractForceField
- equal(byte[], byte[]) - Static method in class com.actelion.research.util.StringFunctions
- equal(Matrix) - Method in class com.actelion.research.calc.Matrix
- equal(Matrix, double) - Method in class com.actelion.research.calc.Matrix
- equal(ByteVec) - Method in class com.actelion.research.util.datamodel.ByteVec
- equal(IntVec) - Method in class com.actelion.research.util.datamodel.IntVec
- equal(DoubleVec) - Method in class com.actelion.research.util.DoubleVec
- equalAtoms(PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
-
realize() may be called first.
- equalDimension(Matrix) - Method in class com.actelion.research.calc.Matrix
-
Checks two matrices for equal dimensions.
- equals(int[], int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- equals(int[], int[]) - Static method in class com.actelion.research.util.ArrayUtils
- equals(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntArray
- equals(int, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
-
Checks if this OutOfPlane's atoms are the same as a given set of 4 atoms, it checks all possible permutations of a1, a2 and a3.
- equals(Conformer) - Method in class com.actelion.research.chem.conf.Conformer
- equals(TorsionDescriptor) - Method in class com.actelion.research.chem.conf.TorsionDescriptor
-
Returns true, if none of the torsion angles are more different than TORSION_EQUIVALENCE_TOLERANCE;
- equals(Fragment3D) - Method in class com.actelion.research.chem.shredder.Fragment3D
- equals(SortedStringList) - Method in class com.actelion.research.chem.SortedStringList
- equals(DoubleVec) - Method in class com.actelion.research.util.DoubleVec
- equals(SortedList<T>) - Method in class com.actelion.research.util.SortedList
- equals(Object) - Method in class com.actelion.research.chem.Coordinates
- equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
- equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- equals(Object) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- equals(Object) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
- equals(Object) - Method in class com.actelion.research.chem.forcefield.mmff.SortedPair
-
Returns true if this SortedPair is equal with another object.
- equals(Object) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Checks for equality between two vectors.
- equals(Object) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- equals(Object) - Method in class com.actelion.research.chem.MolecularFormula
- equals(Object) - Method in class com.actelion.research.chem.Molecule3D
- equals(Object) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- equals(Object) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- equals(Object) - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- equals(Object) - Method in class com.actelion.research.chem.shredder.Fragment
- equals(Object) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondType
- equals(Object) - Method in class com.actelion.research.util.datamodel.ByteVec
- equals(Object) - Method in class com.actelion.research.util.datamodel.IntArray
- equals(Object) - Method in class com.actelion.research.util.datamodel.IntVec
- equals(Object) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- equals(Object) - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- equals(SelfOrganizedConformer) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
-
Returns true, if none of the torsion angles between both conformers are more different than TorsionDescriptor.TORSION_EQUIVALENCE_TOLERANCE; Calling this method requires that calculateDescriptor() has been called earlier.
- erasePrimes(int[][]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- ErrorHashMap - Class in com.actelion.research.util
-
ErrorHashMap 2005 MvK: Start implementation
- ErrorHashMap() - Constructor for class com.actelion.research.util.ErrorHashMap
- errors - Variable in class com.actelion.research.chem.io.AbstractParser
- escape(int, byte[]) - Method in class com.actelion.research.gui.wmf.MetaFile
- escape(int, byte[]) - Method in class com.actelion.research.gui.wmf.WMF
- escapeDanglingMetaCharacters(String) - Static method in class com.actelion.research.util.StringFunctions
-
Escapes the meta characters in a regular expression pattern with \\.
- esrTypeFromRow(int) - Static method in class com.actelion.research.share.gui.editor.Model
- ESTER - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- ETO_CLIPPED - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- ETO_GRAYED - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- ETO_OPAQUE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- EUCLIDEAN - Static variable in class com.actelion.research.util.datamodel.ByteVec
- EUCLIDEAN - Static variable in class com.actelion.research.util.DoubleVec
- EUCLIDEAN_FAST - Static variable in class com.actelion.research.util.datamodel.ByteVec
- EUCLIDEAN_FAST - Static variable in class com.actelion.research.util.DoubleVec
- euclideanDist(PointDouble, PointDouble) - Static method in class com.actelion.research.util.datamodel.PointDouble
- euclideanDistance(double[], double[]) - Static method in class com.actelion.research.util.DoubleVec
- euclideanDistance(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
-
Euclidean distance
- euclideanDistance(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
-
Euclidean distance
- EuclideanDistanceFast(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
-
Euclidean distance without sqrt
- EUROPEAN - com.actelion.research.util.Formatter.LocaleFormat
- Evaluable - Interface in com.actelion.research.chem.optimization
- EvaluableFlexibleOverlap - Class in com.actelion.research.chem.phesaflex
- EvaluableFlexibleOverlap(PheSAAlignment, StereoMolecule, StereoMolecule, double, boolean[], double[], Map<String, Object>) - Constructor for class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- EvaluableFlexibleOverlap(EvaluableFlexibleOverlap) - Constructor for class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- EvaluableOverlap - Class in com.actelion.research.chem.phesa
- EvaluableOverlap(EvaluableOverlap) - Constructor for class com.actelion.research.chem.phesa.EvaluableOverlap
- EvaluableOverlap(PheSAAlignment, double[]) - Constructor for class com.actelion.research.chem.phesa.EvaluableOverlap
- EvaluableOverlap(PheSAAlignment, double[], double) - Constructor for class com.actelion.research.chem.phesa.EvaluableOverlap
- evaluateNativePose() - Method in class com.actelion.research.chem.docking.DockingEngine
- eventDispatched(AWTEvent) - Method in class com.actelion.research.gui.dock.JDockingPanel
- exactly(int, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
-
Checks if this OutOfPlane term is exactly equal to a given set of four atoms.
- ExceptionConformationGenerationFailed - Exception in com.actelion.research.chem.descriptor.flexophore
- ExceptionConformationGenerationFailed(String) - Constructor for exception com.actelion.research.chem.descriptor.flexophore.ExceptionConformationGenerationFailed
- EXCLUSION - Static variable in class com.actelion.research.chem.phesa.VolumeGaussian
- execute(String[]) - Static method in class com.actelion.research.util.Platform
-
Start an executable with parameters.
- execute(String, String...) - Static method in class com.actelion.research.util.Platform
-
Start an executable with parameters.
- ExhaustiveFragmentGeneratorAtoms - Class in com.actelion.research.chem.mcs
- ExhaustiveFragmentGeneratorAtoms() - Constructor for class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
- ExhaustiveFragmentGeneratorBonds - Class in com.actelion.research.chem.mcs
- ExhaustiveFragmentGeneratorBonds(int, int) - Constructor for class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- ExhaustiveFragmentGeneratorParallizer - Class in com.actelion.research.chem.mcs
- ExhaustiveFragmentGeneratorParallizer(int) - Constructor for class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorParallizer
- ExhaustiveFragmentsStatistics - Class in com.actelion.research.chem.properties.complexity
- ExhaustiveFragmentsStatistics(int) - Constructor for class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- ExhaustiveFragmentsStatistics(int, int) - Constructor for class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- ExhaustiveFragmentsStatistics(int, int, int) - Constructor for class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- ExhaustiveMCSGeneratorParallel - Class in com.actelion.research.chem.mcs
- ExhaustiveMCSGeneratorParallel(int) - Constructor for class com.actelion.research.chem.mcs.ExhaustiveMCSGeneratorParallel
- EXIT_VECTOR - com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint.Functionality
- EXIT_VECTOR_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- ExitVectorPoint - Class in com.actelion.research.chem.phesa.pharmacophore
- ExitVectorPoint(ExitVectorPoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
- ExitVectorPoint(StereoMolecule, int, int) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
- EXTENDED - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- EXTENDED_ATOM_FLAG_COUNT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomFlagCount
- ExtendedDepictor - Class in com.actelion.research.chem
- ExtendedDepictor(Reaction, DrawingObjectList, boolean, boolean) - Constructor for class com.actelion.research.chem.ExtendedDepictor
- ExtendedDepictor(StereoMolecule[], int, DrawingObjectList, boolean) - Constructor for class com.actelion.research.chem.ExtendedDepictor
-
Use this constructor for markush structures.
- ExtendedDepictor(StereoMolecule[], DrawingObjectList, boolean) - Constructor for class com.actelion.research.chem.ExtendedDepictor
- ExtendedDepictor(StereoMolecule, DrawingObjectList, boolean) - Constructor for class com.actelion.research.chem.ExtendedDepictor
- ExtendedMolecule - Class in com.actelion.research.chem
-
While the Molecule class covers all primary molecule information as atom and bond properties, the atom connectivity and coordinates, its derived class ExtendedMolecule handles secondary, i.e.
- ExtendedMolecule() - Constructor for class com.actelion.research.chem.ExtendedMolecule
- ExtendedMolecule(int, int) - Constructor for class com.actelion.research.chem.ExtendedMolecule
- ExtendedMolecule(Molecule) - Constructor for class com.actelion.research.chem.ExtendedMolecule
- ExtendedMoleculeFunctions - Class in com.actelion.research.chem
-
ExtendedMoleculeFunctions
- ExtendedMoleculeFunctions() - Constructor for class com.actelion.research.chem.ExtendedMoleculeFunctions
- extendedToOriginalAtom(int) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- EXTENSION_MATCH_NODE_NR_LIMIT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- EXTENSION_MATCHES - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- extract(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphExtractor
-
Delivers a list of indices that describes sub structures of the given molecule.
- extract(String, String) - Static method in class com.actelion.research.util.StringFunctions
- extractAliphaticRingsAndEndStandingAliphaticGroups(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphExtractor
- extractAromaticRing(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- extractCol(double[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- extractFieldName(String) - Method in class com.actelion.research.chem.io.SDFileParser
- extractForGivenResolution(IntVec, int, int) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Converts the IntVec into an array.
- extractFragment(Molecule3D, T, int[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Extract the Ligand from mol and copy it into res
- extractFragment(Molecule3D, T, List<Integer>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- extractFragments(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Return all connex components with more than 5 atoms
- extractInverse(String, String) - Static method in class com.actelion.research.util.StringFunctions
- extractLigand(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Extract the Ligand from mol and copy it into res
- extractLigands(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Return all ligands with more than 5 atoms
- extractMols() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- extractValue(String) - Static method in class com.actelion.research.chem.io.ODEFileParser
- extractX(List<ScorePoint>) - Static method in class com.actelion.research.util.datamodel.ScorePoint
F
- FACTOR_CAPACITY - Static variable in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- FactorySolution - Class in com.actelion.research.util.graph.complete
-
FactorySolution
- FactorySolution() - Constructor for class com.actelion.research.util.graph.complete.FactorySolution
- FAILED_BYTES - Static variable in interface com.actelion.research.chem.descriptor.DescriptorHandler
- FAILED_OBJECT - Static variable in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
- FAILED_OBJECT - Static variable in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
- FAILED_OBJECT - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- FAILED_OBJECT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- FAILED_OBJECT - Static variable in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- FAILED_STRING - Static variable in interface com.actelion.research.chem.descriptor.DescriptorHandler
- FAKE_ATOM_NO - Static variable in class com.actelion.research.gui.JDrawArea
- FAKE_ATOM_NO - Static variable in class com.actelion.research.share.gui.editor.Model
- FALSE - com.actelion.research.chem.forcefield.mmff.RingBoolean
- FastSpline - Class in com.actelion.research.util
-
Represents a polynomial spline function.
- FastSpline(double[], FastSpline.Polynome[]) - Constructor for class com.actelion.research.util.FastSpline
-
Construct a polynomial spline function with the given segment delimiters and interpolating polynomials.
- FastSpline.Polynome - Class in com.actelion.research.util
- FeatureCalculator - Class in com.actelion.research.chem.descriptor.pharmacophoretree
-
calculates features for all atoms in a molecule: H-bond acceptors/donors, negatively/positively ionizable, aromatic, lipophilic
- FeatureCalculator(StereoMolecule) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.FeatureCalculator
- FeatureMatch(int[][]) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
- FF_DECORATIVE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FF_DONTCARE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FF_MODERN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FF_ROMAN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FF_SCRIPT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FF_SWISS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- fget(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.HerschbachLaurie
-
Gets a floating point value from a given row and column.
- fieldIndex - Variable in class com.actelion.research.chem.io.DWARFileParser.SpecialField
- FILE_SUPPORT_NONE - Static variable in class com.actelion.research.gui.CompoundCollectionPane
- FILE_SUPPORT_OPEN_AND_SAVE_FILES - Static variable in class com.actelion.research.gui.CompoundCollectionPane
- FILE_SUPPORT_OPEN_FILES - Static variable in class com.actelion.research.gui.CompoundCollectionPane
- FILE_SUPPORT_SAVE_FILES - Static variable in class com.actelion.research.gui.CompoundCollectionPane
- fileExists(File) - Static method in class com.actelion.research.gui.FileHelper
-
java.io.File.exists() and java.nio.file.Files.exists() may cause minutes of delay, if a file is/was on a network share which is currently unmounted.
- fileExists(File, long) - Static method in class com.actelion.research.gui.FileHelper
-
java.io.File.exists() and java.nio.file.Files.exists() may cause minutes of delay, if a file is/was on a network share which is currently unmounted.
- FileHelper - Class in com.actelion.research.gui
- FileHelper(Component) - Constructor for class com.actelion.research.gui.FileHelper
- fill(Shape) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- fillArc(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- fillArc(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- fillCircle(double, double, double) - Method in class com.actelion.research.chem.AbstractDepictor
- fillCircle(double, double, double) - Method in class com.actelion.research.chem.Depictor
- fillCircle(double, double, double) - Method in class com.actelion.research.chem.Depictor2D
- fillCircle(double, double, double) - Method in class com.actelion.research.chem.SVGDepictor
- fillCircle(double, double, double) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- fillElipse(double, double, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- fillElipse(double, double, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- fillOval(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- fillOval(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- fillPolygon(double[], double[], int) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- fillPolygon(double[], double[], int) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- fillPolygon(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- fillPolygon(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- fillRect(double, double, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- fillRect(double, double, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- fillRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- fillRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- fillRoundRect(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- fillRoundRect(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- fillText(String, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- fillText(String, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- filter(byte[]) - Method in class com.actelion.research.calc.filter.SlidingWindow
- filter(byte[], double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- filter(double[]) - Method in class com.actelion.research.calc.filter.SlidingWindow
- filter(int[]) - Method in class com.actelion.research.calc.filter.SlidingWindow
- filter(int[], double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- FILTER - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
- FILTER07_ - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
-
Filter for sliding window to blurr distance histograms 07.04.2020
- finalize() - Method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- finalize() - Method in class com.actelion.research.chem.properties.complexity.MolecularComplexityCalculator
- finalize() - Method in class com.actelion.research.io.StringReadChannel
- finalizeMolecule(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
Remove all atoms without connections.
- finalizeProcessMolecules() - Method in class com.actelion.research.chem.AtomTypeList
- finalizeThreads() - Method in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule
- findAlignment(double[][]) - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- findAlignment(double[][], boolean) - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- findAlleneCenterAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
If atom is one of the two ends of an allene then returns allene center atom.
- findAlleneEndAtom(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Crawls along a chain of sp-hybridized atoms starting from atom2 (which may not be sp-hybridized) away from its sp-hybridized neighbour atom1.
- findAtom(double, double) - Method in class com.actelion.research.chem.Molecule
- findAtom(StereoMolecule, Point2D) - Method in class com.actelion.research.share.gui.editor.actions.AtomHighlightAction
- findBINAPChiralityBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Checks whether atom is one of the two atoms of an axial chirality bond of BINAP type.
- findBond(double, double) - Method in class com.actelion.research.chem.Molecule
- findFragmentInMolecule() - Method in class com.actelion.research.chem.mcs.SubStructSearchBondIndex
- findFragmentInMolecule() - Method in class com.actelion.research.chem.mcs.SubStructSearchExhaustiveTreeWalker
- findFragmentInMolecule() - Method in class com.actelion.research.chem.SSSearcher
-
Locates all matches of the fragment in the molecule that result in distinguishable sets of molecule atoms.
- findFragmentInMolecule() - Method in class com.actelion.research.chem.SSSearcherWithIndex
- findFragmentInMolecule(int, int) - Method in class com.actelion.research.chem.SSSearcher
-
Locates all matches of the fragment in the molecule that result in distinguishable sets of molecule atoms.
- findFragmentInMolecule(int, int) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- findFragmentInMolecule(int, int, boolean[]) - Method in class com.actelion.research.chem.SSSearcher
-
Locates all matches of the fragment in the molecule that result in distinguishable sets of molecule atoms that are not flagged to be excluded from matching.
- findFragmentInMolecule(int, int, boolean[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- findFragmentInMoleculeWithoutIndex(int) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- findIdentical(int[], int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- findIn(MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
- findIn(Tables, MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.AngleBend
-
Helper function that builds a list of AngleBends for a molecule.
- findIn(Tables, MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.BondStretch
-
Finds all bond stretch energy terms in the current molecule.
- findIn(Tables, MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
-
Finds all out of plane angles in the current molecule.
- findIn(Tables, MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.StretchBend
-
Helper function that builds a list of StretchBends for a molecule.
- findIn(Tables, MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
-
Helper function that builds a list of TorsionAngles for a molecule.
- findIn(Tables, MMFFMolecule, Separation) - Static method in class com.actelion.research.chem.forcefield.mmff.Electrostatic
-
Overloaded wrapper function for 'findIn' which sets default values for the nonbonded cutoff, dielectric model and dielectric constant.
- findIn(Tables, MMFFMolecule, Separation, double) - Static method in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
-
Finds all van der Waals energy terms in the current molecule.
- findIn(Tables, MMFFMolecule, Separation, double, boolean, double) - Static method in class com.actelion.research.chem.forcefield.mmff.Electrostatic
-
Finds all Electrostatic energy terms in the current molecule.
- findInitialSplits() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- findLargest(double[][]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- findMostCentralRingSystem(StereoMolecule) - Static method in class com.actelion.research.chem.ScaffoldHelper
-
This method flags all atoms that are a member of that ring system in mol, which is most central within this molecule graph.
- findMurckoScaffold(StereoMolecule) - Static method in class com.actelion.research.chem.ScaffoldHelper
-
This method flags all atoms that are a member of the Murcko fragment of mol.
- findPrimeInRow(int[][], int) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- findRearAtoms(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
If the atom sequence contains a straight chain of sp-hybridized atoms, then the atom array contain the first two and last two atoms of a sequence of 2n+4 atoms (n: number of conjugated triple bonds).
- findRingSystem(int, boolean, boolean[], boolean[]) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Starting from startAtom this method locates a system of annelated or bridged ring systems with all members bonds being a ring bond.
- findRotatableBonds(StereoMolecule) - Static method in class com.actelion.research.chem.conf.TorsionDescriptorHelper
-
Calculates an array of all rotatable bonds that can be used multiple times as parameter to calculateDescriptor().
- findRotatableBonds(StereoMolecule, boolean, boolean[]) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Locates all relevant rotatable bonds, i.e.
- findSmallest(double[][], int[], int[], double) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- findStarInCol(int[][], int) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- findUncoveredZero(int[], double[][], int[], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- FingerPrintGenerator - Class in com.actelion.research.chem.descriptor
-
Generator of a path-based Fingerprint Not thread safe!
- FingerPrintGenerator() - Constructor for class com.actelion.research.chem.descriptor.FingerPrintGenerator
- FingerPrintGeneratorPharmGraph - Class in com.actelion.research.chem.descriptor
-
Generator of a path-based Fingerprint Not thread safe!
- FingerPrintGeneratorPharmGraph() - Constructor for class com.actelion.research.chem.descriptor.FingerPrintGeneratorPharmGraph
- fireDockableSelected(Dockable) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
Sends ActionEvent to listeners when the user interactively selected another dockable
- FISCHER_PROJECTION_LIMIT - Static variable in class com.actelion.research.chem.ExtendedMolecule
-
To interpret a stereo center as fisher projection, all non stereo bonds must be vertical and all stereo bonds must be horizontal.
- FIXED_PITCH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FLAG_CENTER_ATOM - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophore
- FLAG1 - Static variable in class com.actelion.research.chem.Molecule3D
- flagBackbone(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Return a List of int[] representing all the atom-atom pairs having an intermolecular interactions (distance close to sum of VDW)
- FLD_CMNT - Static variable in class com.actelion.research.chem.StructureInfo
- FLD_DENSITY - Static variable in class com.actelion.research.chem.StructureInfo
- FLD_ID - Static variable in class com.actelion.research.chem.StructureInfo
- FLD_NAME - Static variable in class com.actelion.research.chem.StructureInfo
- FLD_PURITY - Static variable in class com.actelion.research.chem.StructureInfo
- flexible - Variable in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- FlexibleShapeAlignment - Class in com.actelion.research.chem.phesaflex
-
Performs flexible Alignment of two Molecules that are prealigned.
- FlexibleShapeAlignment(StereoMolecule, StereoMolecule) - Constructor for class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
- FlexibleShapeAlignment(StereoMolecule, StereoMolecule, double) - Constructor for class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
- FlexibleShapeAlignment(StereoMolecule, StereoMolecule, MolecularVolume, MolecularVolume, double) - Constructor for class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
- FlexophoreCreateFunctions - Class in com.actelion.research.chem.descriptor.flexophore.generator
-
FlexophoreCreateFunctions
- FlexophoreCreateFunctions() - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.FlexophoreCreateFunctions
- FlexophorePoint - Class in com.actelion.research.chem.descriptor.flexophore.entity
-
FlexophorePoint
- FlexophorePoint(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- flip(boolean) - Method in class com.actelion.research.share.gui.editor.Model
- flip(double, double, double) - Method in class com.actelion.research.chem.coords.InventorFragment
- flipOneSide(int) - Method in class com.actelion.research.chem.coords.InventorFragment
- floatValue() - Method in class com.actelion.research.util.concurrent.AtomicFloat
- Fluorine - Static variable in class com.actelion.research.chem.PeriodicTable
- flush() - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- ForceField - Interface in com.actelion.research.chem.forcefield
- forceFieldAllowsOpenValences() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentProvider
-
For using a different forcefield you may override all three forceField...
- ForceFieldChangeListener - Interface in com.actelion.research.chem.forcefield
- forceFieldInitialize() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentProvider
-
For using a different forcefield you may override all three forceField...
- forceFieldMinimize(StereoMolecule) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentProvider
-
For using a different forcefield you may override all three forceField...
- ForceFieldMMFF94 - Class in com.actelion.research.chem.forcefield.mmff
- ForceFieldMMFF94(StereoMolecule, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
-
Forcefield constructor.
- ForceFieldMMFF94(StereoMolecule, String, Map<String, Object>) - Constructor for class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
-
Forcefield constructor.
- format(double, DecimalFormat, int) - Static method in class com.actelion.research.calc.Matrix
- format(int) - Static method in class com.actelion.research.calc.Matrix
- format(Object) - Static method in class com.actelion.research.util.Formatter
- format(String) - Static method in class com.actelion.research.util.StringFunctions
-
Keeps the minus.
- format(String, char) - Static method in class com.actelion.research.util.StringFunctions
-
Keeps the minus.
- format0(Double) - Static method in class com.actelion.research.util.Formatter
- format1(Double) - Static method in class com.actelion.research.util.Formatter
- format2(Double) - Static method in class com.actelion.research.util.Formatter
- format2DefinedLengthLeading(String, int) - Static method in class com.actelion.research.util.StringFunctions
- format2DefinedLengthTrailing(String, int) - Static method in class com.actelion.research.util.StringFunctions
- format3(Double) - Static method in class com.actelion.research.util.Formatter
- format4(Double) - Static method in class com.actelion.research.util.Formatter
- format8(Double) - Static method in class com.actelion.research.util.Formatter
- formatDate(Date) - Static method in class com.actelion.research.util.Formatter
- formatDateTime(Date) - Static method in class com.actelion.research.util.Formatter
- formatDateTimeShort(Date) - Static method in class com.actelion.research.util.Formatter
- formatDescription(String) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- formatE(Double) - Static method in class com.actelion.research.util.Formatter
- formatMax2(Double) - Static method in class com.actelion.research.util.Formatter
- formatMax3(Double) - Static method in class com.actelion.research.util.Formatter
- Formatter - Class in com.actelion.research.util
- Formatter() - Constructor for class com.actelion.research.util.Formatter
- Formatter.LocaleFormat - Enum in com.actelion.research.util
- formatTime(Date) - Static method in class com.actelion.research.util.Formatter
- formatToCharactersAndDigits(String) - Static method in class com.actelion.research.util.StringFunctions
- formatToPrintableCharactersOnly(String) - Static method in class com.actelion.research.util.StringFunctions
-
This function was implemented because in AxoSOMSampleView was a new line in SMILES molConvert from ChemAxon that is not detected by replaceAll("\n", "");
- formatYYYYMMDD() - Static method in class com.actelion.research.util.Formatter
- FormulaParser - Class in com.actelion.research.chem.io.pdb.parser
-
FormulaParser
- FormulaParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.FormulaParser
- FractalDimensionMolecule - Class in com.actelion.research.chem.properties.fractaldimension
-
FractalDimensionMolecule
- FractalDimensionMolecule(int, boolean) - Constructor for class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule
- FractalDimensionMoleculeMain - Class in com.actelion.research.chem.properties.fractaldimension
-
FractalDimensionMoleculeMain
- FractalDimensionMoleculeMain() - Constructor for class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMoleculeMain
- Fragment - Class in com.actelion.research.chem.shredder
-
Fragment Jan 18, 2013 MvK Start implementation
- Fragment(String) - Constructor for class com.actelion.research.chem.shredder.Fragment
- Fragment(String, String) - Constructor for class com.actelion.research.chem.shredder.Fragment
- Fragment3D - Class in com.actelion.research.chem.shredder
- Fragment3D(String, String, TorsionDescriptor, int[]) - Constructor for class com.actelion.research.chem.shredder.Fragment3D
- FragmentAssociation - Class in com.actelion.research.chem.coords
-
Created by thomas on 9/23/16.
- FragmentAssociation(InventorFragment, InventorFragment) - Constructor for class com.actelion.research.chem.coords.FragmentAssociation
-
Uses center of gravity of the fragments as anchor points
- FragmentAssociation(InventorFragment, InventorFragment, int, int) - Constructor for class com.actelion.research.chem.coords.FragmentAssociation
- FragmentDefinedByBondsHasher - Class in com.actelion.research.chem.properties.complexity
- FragmentDefinedByBondsHasher() - Constructor for class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsHasher
- FragmentDefinedByBondsIdCode - Class in com.actelion.research.chem.properties.complexity
- FragmentDefinedByBondsIdCode() - Constructor for class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- FragmentDefinedByBondsIdCode(FragmentDefinedByBondsIdCode) - Constructor for class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- FragmentDefinedByBondsIdCode(IBitArray) - Constructor for class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- Fragmenter3D - Class in com.actelion.research.chem.shredder
- Fragmenter3D(int, int, int, int, int) - Constructor for class com.actelion.research.chem.shredder.Fragmenter3D
- fromString(String) - Static method in class com.actelion.research.chem.phesa.AtomicGaussian
- fromString(String) - Static method in class com.actelion.research.chem.phesa.VolumeGaussian
- fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
- fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
- fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
- fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
- fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PharmacophorePointFactory
- fromString(String, StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
- FULL_HOSE_CODE - Static variable in class com.actelion.research.chem.contrib.HoseCodeCreator
- FUNC_GROUP_FLAG_COUNT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomFlagCount
- FUNCTIONAL_GROUP - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- FUNCTIONAL_GROUP_SHIFT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyShift
- FunctionalGroupClassifier - Class in com.actelion.research.chem.reaction
- FunctionalGroupClassifier(StereoMolecule) - Constructor for class com.actelion.research.chem.reaction.FunctionalGroupClassifier
- FUNCTIONALITY_WEIGHTS - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- FUNCTOL - Static variable in class com.actelion.research.chem.forcefield.AbstractForceField
- fusion(Molecule3D) - Method in class com.actelion.research.chem.Molecule3D
-
This method will append a Molecule3D to the end.
- FW_BLACK - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FW_BOLD - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FW_DONTCARE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FW_NORMAL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- FW_THIN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
G
- g_i(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
-
Returns 'G-i' from the table.
- Gaussian3D - Class in com.actelion.research.chem.phesa
- Gaussian3D() - Constructor for class com.actelion.research.chem.phesa.Gaussian3D
- Gaussian3D(int, int, Coordinates, double) - Constructor for class com.actelion.research.chem.phesa.Gaussian3D
- Gaussian3D(Gaussian3D) - Constructor for class com.actelion.research.chem.phesa.Gaussian3D
- GDIPolyPolygon(Polygon[]) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- generate() - Method in class com.actelion.research.chem.phesa.PheSABindingHypothesis
- generate(StereoMolecule) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
- generate(StereoMolecule, Map<Integer, List<Integer>>, List<Set<Integer>>) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
-
the parameter rings can be used for fragments/building blocks to submit atoms that will belong to a ring after they react
- generateConformerAndSetCoordinates(ConformerGenerator, int, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
-
08.03.2017 Method set to public for debugging purposes.
- generateConformerFromTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Computes a conformer from a TorsionSet object.
- generateConformerSet(StereoMolecule) - Method in class com.actelion.research.chem.conf.ConformerSetGenerator
- generateDescriptor(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.pharmacophoregraph.PharmGraphGenerator
- generateFragments() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
- generateFragments() - Method in class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
- generateFragmentsAllBonds() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- generateFragmentsForSingleBond(int) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- generateMutationList(StereoMolecule, int, boolean) - Method in class com.actelion.research.chem.Mutator
-
Creates a list of possible mutations and their probabilities
- generateOneConformer(long) - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
-
Generates the coordinates for one conformer in the calling thread.
- generateOneConformerInPlace(long) - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
-
This convenience method returns the StereoMolecule that has been passed to the constructor after modifying its atom coordinates to reflect the conformer internally created by generateOneConformer().
- generateRandomArray(double[][], String) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- generateSmiles(ExtendedMolecule) - Method in class com.actelion.research.chem.SmilesCreator
-
public String generateSmiles (Molecule inMol) Effect on instance variable: -> increment this.mVisitedMolAtoms -> increment this.mDisconnections, if inMol consists of several isolated molecules (or atoms).
- generateSubPharmacophores(MolDistHist, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- generateSubPharmacophores(MolDistHistViz, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
-
Generates a list of sub-fragments.
- generateSubPharmacophores(MolDistHistViz, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- generateSubPharmacophores(List<MolDistHistViz>, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- generateSubPharmacophoresCheckedRange(MolDistHist, int) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- GeometryCalculator - Class in com.actelion.research.chem.descriptor.flexophore.calculator
-
Utility class to perform 3D geometry calculations on molecules
- GeometryCalculator - Class in com.actelion.research.chem.io.pdb.converter
-
Utility class to perform 3D geometry calculations on molecules
- GeometryCalculator() - Constructor for class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
- GeometryCalculator() - Constructor for class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
- geomFactory - Variable in class com.actelion.research.share.gui.editor.Model
- GeomFactory - Class in com.actelion.research.share.gui.editor.geom
-
Project: User: rufenec Date: 11/24/2014 Time: 3:15 PM
- GeomFactory(DrawConfig) - Constructor for class com.actelion.research.share.gui.editor.geom.GeomFactory
- get() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- get() - Method in class com.actelion.research.chem.mcs.ContainerListWithIntVec
- get() - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- get() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- get() - Method in class com.actelion.research.util.concurrent.AtomicFloat
- get() - Method in class com.actelion.research.util.datamodel.ByteVec
- get() - Method in class com.actelion.research.util.datamodel.DoubleArray
- get() - Method in class com.actelion.research.util.datamodel.IntArray
- get() - Method in class com.actelion.research.util.datamodel.IntVec
- get() - Method in class com.actelion.research.util.DoubleVec
- get() - Method in class com.actelion.research.util.graph.complete.ContainerMemory
- get(double, double) - Static method in class com.actelion.research.calc.Logarithm
- get(int) - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
- get(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Torsion
- get(int) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
-
Returns a bit list.
- get(int) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- get(int) - Method in class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
-
Returns list with indices for fragments with
size
atoms. - get(int) - Method in interface com.actelion.research.share.gui.editor.geom.IPolygon
- get(int) - Method in class com.actelion.research.share.gui.Polygon
- get(int) - Method in class com.actelion.research.util.datamodel.ByteVec
- get(int) - Method in class com.actelion.research.util.datamodel.DoubleArray
- get(int) - Method in class com.actelion.research.util.datamodel.IntArray
- get(int) - Method in class com.actelion.research.util.datamodel.IntVec
- get(int) - Method in class com.actelion.research.util.DoubleVec
- get(int) - Method in class com.actelion.research.util.IntQueue
- get(int) - Method in class com.actelion.research.util.SortedList
-
Returns object at given index, or null if index==-1
- get(int) - Method in class com.actelion.research.util.UniqueList
- get(int, int) - Method in class com.actelion.research.calc.Matrix
- get(int, int) - Method in interface com.actelion.research.chem.forcefield.mmff.Searchable
-
This should get an integer value given a column and row.
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.Separation
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bndk
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bond
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.CovRad
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Dfsb
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.HerschbachLaurie
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.OutOfPlane
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Stbn
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Torsion
- get(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
- get(int, int) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- get(SortedPair) - Method in class com.actelion.research.chem.forcefield.mmff.Separation
-
Returns the relation of a given pair of atoms.
- get(Object) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- get(String) - Method in enum com.actelion.research.chem.io.pdb.converter.AminoAcidsLabeledContainer
- get(String) - Method in class com.actelion.research.util.CommandLineParser
- get_bci_f(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
- get_bci_len() - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
- get_bci_n(int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
- getAbs() - Method in class com.actelion.research.calc.Matrix
- getAbsoluteAtomParity(int) - Method in class com.actelion.research.chem.StereoMolecule
-
This returns the absolute(!) atom parity from the canonization procedure.
- getAbsoluteBondParity(int) - Method in class com.actelion.research.chem.StereoMolecule
-
This returns the absolute(!) bond parity from the canonization procedure.
- getAbsoluteBounds(Component) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
Calculates bounds of the dockable relative to this JDockingPanel
- getAbsoluteMass(int, int) - Static method in class com.actelion.research.chem.IsotopeHelper
- getAbsoluteWeight() - Method in class com.actelion.research.chem.MolecularFormula
- getAcceptedFormats(Clipboard) - Static method in class com.actelion.research.jfx.gui.misc.ClipboardHelper
- getAcceptorCount() - Method in class com.actelion.research.chem.PropertyCalculator
- getAcceptorID() - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
- getAdded() - Method in class com.actelion.research.util.Pipeline
- getAdjacencyList(int, List<int[]>) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeUtils
- getAdjacencyListWithBondOrders(int, List<PharmacophoreTree.BiGramInt>) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeUtils
- getAlignment() - Method in class com.actelion.research.chem.phesa.EvaluableOverlap
- getAlignment() - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- getAlkyneAtomCount() - Method in class com.actelion.research.chem.conf.TorsionDetail
- getAllAtoms() - Method in class com.actelion.research.chem.Molecule
- getAllBonds() - Method in class com.actelion.research.chem.Molecule
- getAllCommonSubstructures() - Method in class com.actelion.research.chem.mcs.MCS
-
All molecules which are sub structures of an other molecule in the list are removed.
- getAllCommonSubstructures() - Method in class com.actelion.research.chem.mcs.MCSFast
-
All molecules which are sub structures of an other molecule in the list are removed.
- getAllConnAtoms(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
The neighbours (connected atoms) of any atom are sorted by their relevance:
1. - getAllConnAtomsPlusMetalBonds(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
The neighbours (connected atoms) of any atom are sorted by their relevance:
1. - getAllHydrogens(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- getAllOutOf(int, int) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
-
Get all possible index combinations, order independent.
- getAllSubStrings(String, int) - Static method in class com.actelion.research.util.StringFunctions
- getAllSubtrees() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getAndSet(float) - Method in class com.actelion.research.util.concurrent.AtomicFloat
- getAngle(double, double, double, double) - Static method in class com.actelion.research.chem.coords.InventorAngle
- getAngle(double, double, double, double) - Static method in class com.actelion.research.chem.Molecule
- getAngle(int, int, int) - Method in class com.actelion.research.chem.conf.BondAngleSet
-
Returns the preferred angle between to three atoms in a row as positive value <= pi.
- getAngle(Coordinates) - Method in class com.actelion.research.chem.Coordinates
-
Gets the angle formed between the 2 vectors ([0,PI])
- getAngle(Coordinates, Coordinates, Coordinates) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
- getAngle(Coordinates, Coordinates, Coordinates) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
- getAngle(Molecule3D, int, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
-
Gets the Angle between 3 atoms
- getAngle(Molecule, int, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
- getAngle(StereoMolecule, int, int, int) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
-
Gets the Angle between 3 atoms
- getAngleDif(double, double) - Static method in class com.actelion.research.chem.Molecule
- getAngleXY(Coordinates) - Method in class com.actelion.research.chem.Coordinates
-
Calculates the angle of the line from this location to c projected into the x/y plane.
- getAnisou() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getAppendedSorted(String, String) - Static method in class com.actelion.research.util.StringFunctions
- getArea() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- getArea(double, double, double) - Static method in class com.actelion.research.calc.geometry.Triangle
- getAreaRightTriangle(double, double) - Static method in class com.actelion.research.calc.geometry.Triangle
- getAromaticRingCount() - Method in class com.actelion.research.chem.ExtendedMolecule
- getArray() - Method in class com.actelion.research.calc.Matrix
- getArrayAsInt() - Method in class com.actelion.research.calc.Matrix
- getArrayCopy() - Method in class com.actelion.research.calc.Matrix
- getArrIndexFrag() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.MultCoordFragIndex
- getArrIndexParentNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
- getArrNode() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- getArrowBoundingRect(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
- getAsBoolean(String) - Method in class com.actelion.research.util.CommandLineParser
-
Use contains(...) if only the flag is used.
- getAsDir(String) - Method in class com.actelion.research.util.CommandLineParser
- getAsDouble(String) - Method in class com.actelion.research.util.CommandLineParser
- getAsFile(String) - Method in class com.actelion.research.util.CommandLineParser
- getAsInt(String) - Method in class com.actelion.research.util.CommandLineParser
- getAtom() - Method in class com.actelion.research.chem.CanonizerBaseValue
- getAtomAbnormalValence(int) - Method in class com.actelion.research.chem.Molecule
-
Get an atom's defined maximum valance if different from the default one.
- getAtomAmino(int) - Method in class com.actelion.research.chem.Molecule3D
- getAtomAndBondCounts(byte[], int, int[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Determines atom and bond counts of the given idcode
- getAtomAndBondCounts(String, int[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Determines atom and bond counts of the given idcode
- getAtomBfactor(int) - Method in class com.actelion.research.chem.Molecule3D
- getAtomChainId(int) - Method in class com.actelion.research.chem.Molecule3D
- getAtomCharge(int) - Method in class com.actelion.research.chem.Molecule
- getAtomCIPParity(int) - Method in class com.actelion.research.chem.Molecule
-
The atom Cahn-Ingold-Prelog parity is a calculated property available above/equal helper level cHelperCIP.
- getAtomColor(int) - Method in class com.actelion.research.chem.Molecule
- getAtomCoordinates() - Method in class com.actelion.research.chem.Molecule
- getAtomCount(byte[], int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- getAtomCount(String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- getAtomCustomLabel(int) - Method in class com.actelion.research.chem.Molecule
-
If a custom atom label is set, a molecule depiction displays the custom label instead of the original one.
- getAtomCustomLabelBytes(int) - Method in class com.actelion.research.chem.Molecule
-
This method is more efficient than getAtomCustomLabel(), because internally atom custom labels are stored as a byte[].
- getAtomDescription(int) - Method in class com.actelion.research.chem.Molecule3D
- getAtomESRGroup(int) - Method in class com.actelion.research.chem.Molecule
-
This is MDL's enhanced stereo representation (ESR).
- getAtomESRType(int) - Method in class com.actelion.research.chem.Molecule
-
This is MDL's enhanced stereo representation (ESR).
- getAtomFlags(int) - Method in class com.actelion.research.chem.Molecule3D
- getAtomFunctionalities() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.FeatureCalculator
- getAtomHashkey(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Return a long representing the atom and its neighbours
- getAtomicGaussians() - Method in class com.actelion.research.chem.phesa.MolecularVolume
- getAtomicNo() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getAtomicNo() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getAtomicNo(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- getAtomicNo(int) - Method in class com.actelion.research.chem.Molecule
-
In addition to the natural atomic numbers, we support additional pseudo atomic numbers.
- getAtomicNoCodeString(int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- getAtomicNoFromInteractionType(int) - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- getAtomicNoFromLabel(String) - Static method in class com.actelion.research.chem.Molecule
- getAtomicNoRGroup(int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
-
Starts with 1 and goes until 16
- getAtomicNumber(int) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- getAtomId() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getAtomIds(StereoMolecule) - Static method in class com.actelion.research.chem.contrib.DiastereotopicAtomID
- getAtomIndex(int, int) - Method in class com.actelion.research.chem.RingCollection
- getAtomIndexConnectionFlexophorePoint() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
- getAtomIndexFirstLinkerAtom() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
- getAtomIndexLinkerId() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- getAtomIndices() - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- getAtomKeySet() - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- getAtomKeyStrokeValidity(String) - Method in class com.actelion.research.share.gui.editor.Model
- getAtomLabel(int) - Method in class com.actelion.research.chem.Molecule
- getAtomList() - Method in class org.openmolecules.chem.conf.so.ConformationRule
- getAtomList(int) - Method in class com.actelion.research.chem.Molecule
-
The list of atoms that are allowed at this position during sub-structure search.
- getAtomListString(int) - Method in class com.actelion.research.chem.Molecule
- getAtomMapNo(int) - Method in class com.actelion.research.chem.Molecule
-
Returns an atom mapping number within the context of a reaction.
- getAtomMass(int) - Method in class com.actelion.research.chem.Molecule
- getAtomName() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getAtomName(int) - Method in class com.actelion.research.chem.Molecule3D
- getAtomPairsBondsTable(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MDHIndexTables
- getAtomParity(int) - Method in class com.actelion.research.chem.Molecule
-
The atom parity is a calculated property available above/equal helper level cHelperParities.
- getAtomPi(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
This is different from the Hendrickson pi-value, which considers pi-bonds to carbons only.
- getAtomPi(StereoMolecule, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
-
Returns an atom's pi electron count for the purpose of classifying a connected bond to determine its length.
- getAtomPreferredStereoBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Locates that single bond which is the preferred one to be converted into up/down bond in order to define the atom chirality.
- getAtomQueryFeatures(int) - Method in class com.actelion.research.chem.Molecule
-
Returns all set query features for this atom.
- getAtomRadical(int) - Method in class com.actelion.research.chem.Molecule
-
Gets an atom's radical state as singulet,dublet,triplet or none
- getAtomRegionNumbers(int[]) - Method in class com.actelion.research.chem.TautomerHelper
-
Identifies connected tautomeric regions and assign region numbers to all atoms.
- getAtomRingBondCount(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- getAtomRingCount(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Calculates the number of independent rings of which 'atom' is a member.
- getAtomRingSize(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- getAtomRingSize(int) - Method in class com.actelion.research.chem.RingCollection
-
An atom's ring size is the size of the smallest ring the atom is a member of.
- getAtoms() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- getAtoms() - Method in class com.actelion.research.chem.ExtendedMolecule
-
A validated molecule (after helper array creation) contains a sorted list of all atoms with the plain (neglegible) hydrogen atoms at the end of the list.
- getAtoms() - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- getAtomSequence(int) - Method in class com.actelion.research.chem.Molecule3D
- getAtomsMolecule() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getAtomsOnPath(Molecule3D, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Finds on all atoms going on a path from a1 to a2.
- getAtomStrain(int) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- getAtomToGroups(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getAtomToGroups(Molecule3D, List<Integer>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
For each molecule in
mol
one group is created. - getAtomType(int) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.AtomTypeMap
- getAtomType(int) - Method in class com.actelion.research.chem.forcefield.mmff.MMFFMolecule
-
Get the MMFF atom type of an atom.
- getAtomType(InteractionAtomTypeCalculator.FunctionalGroup, int, boolean, int, boolean) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- getAtomType(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- getAtomType(StereoMolecule, int) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- getAtomType(StereoMolecule, int, int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- getAtomTypeList() - Method in class com.actelion.research.chem.AtomTypeList
- getAtomTypes() - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- getAtomVolumes(StereoMolecule) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
- getAtomX(int) - Method in class com.actelion.research.chem.coords.InventorFragment
- getAtomX(int) - Method in class com.actelion.research.chem.Molecule
- getAtomY(int) - Method in class com.actelion.research.chem.coords.InventorFragment
- getAtomY(int) - Method in class com.actelion.research.chem.Molecule
- getAtomZ(int) - Method in class com.actelion.research.chem.Molecule
- getAttachedHydrogenCount(int) - Method in class com.actelion.research.chem.Molecule3D
- getAuthor() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getAuxiliaryInfo(String) - Method in class com.actelion.research.chem.Molecule3D
- getAuxiliaryInfos() - Method in class com.actelion.research.chem.Molecule3D
- getAvailable() - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- getAvailable() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getAverageBondLength() - Method in class com.actelion.research.chem.Molecule
-
Calculates and returns the mean bond length.
- getAverageBondLength() - Method in class com.actelion.research.chem.reaction.Reaction
- getAverageBondLength(boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Calculates and returns the mean bond length of all bonds including or not including hydrogen bonds.
- getAverageBondLength(int, int) - Method in class com.actelion.research.chem.Molecule
-
Calculates and returns the mean bond length of all bonds 0...bonds.
- getAverageBondLength(int, int, double) - Method in class com.actelion.research.chem.Molecule
-
Calculates and returns the mean bond length of all bonds 0...bonds.
- getAverageBondLength(int, int, double, Coordinates[]) - Method in class com.actelion.research.chem.Molecule
-
Calculates and returns the mean bond length of all bonds 0...bonds.
- getAverageBondLength(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
- getAverageTopologicalAtomDistance() - Method in class com.actelion.research.chem.ExtendedMolecule
-
Calculates for every non-H atom the mean value of all shortest routes (bonds in between) to any other atom of the same fragment.
- getBackbone(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getBackboneCode(int, boolean) - Method in interface com.actelion.research.chem.StructureSearchDataSource
-
Returns a hash code representing the structure or its largest fragment without stereo information and with all unsaturated bonds converted to single bonds.
- getBackboneHash(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.CanonizerUtil
- getBackbones(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getBackbones(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Gets the backbone
- getBackground() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- getBackground() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getBackgroundColor() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- getBackgroundColor() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- getBackgroundColor() - Method in class com.actelion.research.share.gui.DrawConfig
- getBackgroundColor() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getBackSpaceKey() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getBar() - Static method in class com.actelion.research.gui.JMessageBar
- getBase() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getBase() - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- getBaseName(File) - Static method in class com.actelion.research.util.IO
- getBaseName(String) - Static method in class com.actelion.research.util.IO
- getBegin() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
- getBegin() - Method in class com.actelion.research.util.IntQueue
- getBestCollidingTorsionIndexes() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
-
If no collision free torsion set can be constructed, this method is called to get the torsion set with the least atom collision strain.
- getBestMatch(MolDistHistViz, MolDistHistViz) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- getBestMatch(MolDistHistViz, MolDistHistViz) - Method in interface com.actelion.research.chem.descriptor.flexophore.IDescriptorHandlerFlexophore
- getBestMatchingSolution() - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- getBiasFactor(StereoMolecule) - Method in interface com.actelion.research.chem.MutationBiasProvider
- getBiggestFragment(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getBiggestFragmentIDCode(String) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getBin(int) - Method in class com.actelion.research.calc.histogram.Histogram
- getBindingSiteAtoms(StereoMolecule, Set<Integer>, MoleculeGrid, boolean) - Static method in class com.actelion.research.chem.docking.DockingEngine
- getBinIndex(double) - Method in class com.actelion.research.calc.histogram.Histogram
- getBinomialCoefficient(int, int) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
-
Calculate binomial coefficient or n choose k
- getBins() - Method in class com.actelion.research.calc.histogram.Histogram
- getBinWidth() - Method in class com.actelion.research.calc.histogram.Histogram
- getBitArray() - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- getBitSetBits(BitSet) - Static method in class com.actelion.research.chem.descriptor.FingerPrintGenerator
- getBitsSet() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- getBitsSet() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- getBitsSet() - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- getBitsSet() - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- getBitsSet() - Method in class com.actelion.research.util.datamodel.ByteVec
- getBitsSet() - Method in class com.actelion.research.util.datamodel.IntVec
- getBitsSet(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getBitWise() - Method in class com.actelion.research.util.datamodel.IntVec
- getBond() - Method in class org.openmolecules.chem.conf.gen.RotatableBond
- getBond(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
- getBond(int, int) - Method in class com.actelion.research.chem.Molecule3D
- getBondAndFragmentCollisionIntensities(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
-
Calculates for every rotatable bond and for every rigid fragment a collision intensity sum for the given torsion/conformer state from the collision rules already known.
- getBondAngle(int, int) - Method in class com.actelion.research.chem.Molecule
- getBondAtom(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getBondAtom(int, int) - Method in class com.actelion.research.chem.Molecule
- getBondBridgeMaxSize(int) - Method in class com.actelion.research.chem.Molecule
- getBondBridgeMinSize(int) - Method in class com.actelion.research.chem.Molecule
- getBondCIPParity(int) - Method in class com.actelion.research.chem.Molecule
-
The bond Cahn-Ingold-Prelog parity is a calculated property available above/equal helper level cHelperCIP.
- getBondCount(int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
- getBondESRGroup(int) - Method in class com.actelion.research.chem.Molecule
-
This is MDL's enhanced stereo representation (ESR).
- getBondESRType(int) - Method in class com.actelion.research.chem.Molecule
-
This is MDL's enhanced stereo representation (ESR).
- getBondID(StereoMolecule, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
-
Constructs a bond classification index from a specific bond in a molecule.
- getBondIDString(int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
- getBondIndex(int, boolean, boolean, int, int, int, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
-
Constructs a bond classification ID from individual parameters and returns the ID's index in the sorted list of bond length information.
- getBondIndex(int, int) - Method in class com.actelion.research.chem.RingCollection
- getBondIndex(StereoMolecule, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
-
Constructs a bond classification ID from a specific bond in a molecule and returns the ID's index in the sorted list of bond length information.
- getBondLength(int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
-
Returns an estimate of the bond length based on atom and bond characteristics.
- getBondLength(int) - Method in class com.actelion.research.chem.Molecule
- getBondLengthFromCovalentRadii(StereoMolecule, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
-
Returns an estimate of the bond length based on atom and bond characteristics.
- getBondNo(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getBondOrder(int) - Method in class com.actelion.research.chem.Molecule
-
Returns the formal bond order.
- getBondOrder(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getBondParity(int) - Method in class com.actelion.research.chem.Molecule
-
Returns the pre-calculated bond parity, e.g.
- getBondParity(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getBondPreferredStereoBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Locates that single bond which is the preferred one to be converted into up/down bond in order to define the bond chirality.
- getBondQueryFeatures(int) - Method in class com.actelion.research.chem.Molecule
- getBondRingSize(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- getBondRingSize(int) - Method in class com.actelion.research.chem.RingCollection
-
A bond's ring size is the size of the smallest ring the bond is a member of.
- getBonds() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getBonds() - Method in class com.actelion.research.chem.ExtendedMolecule
-
The bond list is preprocessed such that all bonds leading to a plain hydrogen atom (natural abundance, no custom labels) are at the end of the list.
- getBonds() - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- getBondsAtMaxFrag() - Method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- getBondsBetweenFragments(int, int) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- getBondsFragment() - Method in class com.actelion.research.chem.mcs.ModelSampleFragments
- getBondsMolecule() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getBondsMolecule() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getBondStdDev(int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
-
Returns an the standard deviation of bond lengths from bonds with similar characteristics from crystallographic data.
- getBondTorsion(int) - Method in class com.actelion.research.chem.conf.Conformer
-
Returns the current bond torsion angle in degrees, it is was set before.
- getBondType() - Method in class com.actelion.research.share.gui.editor.actions.BondBaseAction
- getBondType() - Method in class com.actelion.research.share.gui.editor.actions.DownBondAction
- getBondType() - Method in class com.actelion.research.share.gui.editor.actions.NewBondAction
- getBondType() - Method in class com.actelion.research.share.gui.editor.actions.UpBondAction
- getBondType(int) - Method in class com.actelion.research.chem.Molecule
-
Returns bond type combining bond order and stereo orientation.
- getBondType(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getBondTypeSimple(int) - Method in class com.actelion.research.chem.Molecule
-
This is the bond type without stereo information.
- getBorderColor() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- getBorderInsets(Component) - Method in class com.actelion.research.gui.dock.ShadowBorder
- getBordersMostFreqOccBin(Matrix, int) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
-
Gets the upper and lower limit of the most occupied bin.
- getBoundingBox() - Method in class com.actelion.research.share.gui.Polygon
- getBoundingRect() - Method in class com.actelion.research.chem.AbstractDepictor
- getBoundingRect() - Method in class com.actelion.research.chem.AbstractDrawingObject
- getBoundingRect() - Method in class com.actelion.research.chem.reaction.ReactionArrow
- getBoundingRect() - Method in class com.actelion.research.chem.TextDrawingObject
- getBoundingRect() - Method in class com.actelion.research.share.gui.Arrow
- getBoundingRect() - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
- getBoundingRect() - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
- getBoundingRect(ExtendedMolecule) - Static method in class com.actelion.research.chem.ChemistryHelper
- getBoundingRect(ExtendedMolecule[]) - Static method in class com.actelion.research.chem.ChemistryHelper
- getBoundingRect(Reaction, boolean) - Static method in class com.actelion.research.chem.ChemistryHelper
- getBoundingRect(StereoMolecule) - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getBounds() - Method in class com.actelion.research.gui.dock.TreeLeaf
- getBounds() - Method in class com.actelion.research.share.gui.editor.actions.PasteAction
- getBounds(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
-
Gets the Bounds of a molecule
- getBounds(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getBounds(StereoMolecule) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
-
Gets the Bounds of a molecule
- getBounds(Rectangle2D.Double) - Method in class com.actelion.research.chem.Molecule
- getBounds(String) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- getBounds(String) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- getBrushFillStyle() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- getBufferedReader(String) - Static method in class com.actelion.research.util.IO
-
Do not forget to close BufferedReader
- getBuffWrite(String, boolean) - Static method in class com.actelion.research.util.IO
- getBumpTerm() - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- getButtonImage(boolean) - Method in class com.actelion.research.share.gui.editor.ImageProvider
- getByte(int) - Method in class com.actelion.research.util.datamodel.IntVec
- getByte(int[], int) - Static method in class com.actelion.research.util.datamodel.IntVec
- getByteVec() - Method in class com.actelion.research.util.datamodel.IntVec
- getByteVec(int) - Static method in class com.actelion.research.util.datamodel.IntVec
- getByteVec(int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
- getByteWise() - Method in class com.actelion.research.util.datamodel.IntVec
- getCandidatePose() - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- getCanMolecule() - Method in class com.actelion.research.chem.Canonizer
- getCanMolecule(boolean) - Method in class com.actelion.research.chem.Canonizer
- getCanonizer() - Method in class com.actelion.research.chem.StereoMolecule
-
This is a convenience method returning the StereoMolecule's Canonizer object after calling internally ensureHelperArrays(cHelperParities) and, thus, effectively running the canonicalization and validating the Canonizer itself.
- getCapacity() - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- getCapacity() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getCapacityLimitBreakes() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
-
Is increased by one if more than the the allowed number of fragments was generated.
- getCartCoordinates(int[]) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- getCartesianTorsionGradient(int[], Conformer, double[], double, Coordinates[], int[][]) - Static method in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionTerm
- getCatalyst(int) - Method in class com.actelion.research.chem.reaction.Reaction
- getCatalysts() - Method in class com.actelion.research.chem.reaction.Reaction
- getcAtomColor2String(int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getCaveat() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getCcMissedMinRange() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator.ViolatedConditionsCount
- getCcViolatedMaxRange() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator.ViolatedConditionsCount
- getCcViolatedMinDiffInteractionTypes() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator.ViolatedConditionsCount
- getCenter() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getCenter() - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
- getCenter() - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
- getCenter() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- getCenter() - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
- getCenter() - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
- getCenter() - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
- getCenter(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getCentered(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getCenteredMatrix() - Method in class com.actelion.research.calc.Matrix
- getCenteredMatrix(Matrix) - Method in class com.actelion.research.calc.Matrix
- getCenterGravity(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMolecule
- getCenterGravity(ExtendedMolecule, int[]) - Static method in class com.actelion.research.chem.ExtendedMolecule
- getCenterGravity(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
-
Gets the center of Gravity of a molecule
- getCenterGravity(StereoMolecule) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
-
Gets the center of Gravity of a molecule
- getCenterID() - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
- getCenterID() - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
- getCenterID() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- getCenterID() - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
- getCenterID() - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
- getCenterID() - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
- getCentralAtom(int) - Method in class com.actelion.research.chem.conf.TorsionDetail
-
Returns one of the atoms of the torsion fragment's central rotatable bond.
- getCEntries() - Method in class com.actelion.research.chem.reaction.ClassificationData
- getChainID() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getChainID() - Method in class com.actelion.research.chem.io.pdb.parser.Residue
- getChainLength() - Method in class com.actelion.research.chem.coords.InventorChain
- getCharge() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- getChargeAtom() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- getCharges(Tables, MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Charge
-
Computes the partial MMFF charges.
- getChargeType(int) - Static method in class com.actelion.research.chem.io.Mol2FileParser
- getCheckerArray() - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- getChemDrawBuffer(Reaction) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- getChemDrawBuffer(StereoMolecule) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- getChemistryBounds() - Method in class com.actelion.research.gui.JChemistryView
- getChemistryType() - Method in class com.actelion.research.gui.JChemistryView
- getChild() - Method in class com.actelion.research.gui.dock.TreeRoot
- getChildFieldIndex(String, String) - Method in class com.actelion.research.chem.io.DWARFileParser
- getChirality() - Method in class com.actelion.research.chem.Molecule
-
Gets the overall chirality of the molecule, which is a calculated information considering: Recognition of stereo centers and stereo bonds, defined ESR features, meso detection.
- getChiralText() - Method in class com.actelion.research.chem.ExtendedMolecule
- getChiralText() - Method in class com.actelion.research.chem.StereoMolecule
- getCisPep() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getClassification() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getClip() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- getClip() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getClipboardData(String) - Static method in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- getClipboardHandler() - Method in class com.actelion.research.gui.CompoundCollectionPane
- getClipboardHandler() - Method in class com.actelion.research.gui.JStructureView
- getClipBounds() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- getClipBounds() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getCLogPIncrements(StereoMolecule, float[]) - Method in class com.actelion.research.chem.prediction.CLogPPredictor
-
Normalizes ambiguous bonds and assigns cLogP increments to every atom based on its enhanced atom type.
- getClosestNeighbour(Coordinates, double) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
-
Returns the closest neighbour.
- getClusterCenter(int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
-
Calculates for nodes cluster the node with the minimum rmsd to the cluster center.
- getClusterMember() - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
- getCode() - Method in interface com.actelion.research.share.gui.editor.io.IKeyEvent
- getCoefficients() - Method in class com.actelion.research.util.FastSpline.Polynome
- getCoefficientVariation() - Method in class com.actelion.research.calc.Matrix
-
Coefficient of variation (CV) is a normalized measure of dispersion of a probability distribution.
- getCol(int) - Method in class com.actelion.research.calc.Matrix
- getColAsDouble(int) - Method in class com.actelion.research.calc.Matrix
- getColAsFloat(int) - Method in class com.actelion.research.calc.Matrix
- getColAsList(int) - Method in class com.actelion.research.calc.Matrix
- getColDim() - Method in class com.actelion.research.calc.Matrix
- getColIndexContainingMaxVal(int) - Method in class com.actelion.research.calc.Matrix
- getColIndexContainingMaxVal(int, int) - Method in class com.actelion.research.calc.Matrix
- getCollisionIntensity() - Method in class org.openmolecules.chem.conf.gen.TorsionSetEliminationRule
- getCollisionIntensityMatrix() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- getCollisionIntensitySum() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- getCollisionList() - Method in class com.actelion.research.chem.coords.InventorFragment
- getCollisionPanalty() - Method in class com.actelion.research.chem.coords.InventorFragment
- getColName(int) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- getColor() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- getColor() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getColorRecord(Molecule, Collection<Integer>, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getColorVal2String(Molecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getColorVectorSubstructure(StereoMolecule, StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
-
Returns the colors vector for the substructure in mol.
- getCols() - Method in class com.actelion.research.util.datamodel.table.TableModelString
- getColumnProperties(String) - Method in class com.actelion.research.chem.io.DWARFileParser
-
Returns the original column properties of any source column by column name.
- getColumns(List<Integer>) - Method in class com.actelion.research.calc.Matrix
- getColumns(Vector<Integer>) - Method in class com.actelion.research.calc.Matrix
-
Deprecated.use getColumns(List
vecIndices) instead - getCOM() - Method in class com.actelion.research.chem.phesa.MolecularVolume
- getCOM(Conformer) - Static method in class com.actelion.research.chem.docking.DockingUtils
- getCOM(StereoMolecule) - Static method in class com.actelion.research.chem.docking.DockingUtils
- getCombinations(List<int[]>) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
- getComment() - Method in class com.actelion.research.chem.StructureInfo
- getCompactCopy() - Method in class com.actelion.research.chem.ExtendedMolecule
- getCompactCopy() - Method in class com.actelion.research.chem.StereoMolecule
- getCompactMolecule(byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Creates and returns a molecule from the idcode with its atom and bond arrays being just as large as needed to hold the molecule.
- getCompactMolecule(byte[], byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Creates and returns a molecule from the idcode with its atom and bond arrays being just as large as needed to hold the molecule.
- getCompactMolecule(byte[], byte[], int, int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- getCompactMolecule(byte[], int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- getCompactMolecule(BufferedReader) - Method in class com.actelion.research.chem.MolfileParser
- getCompactMolecule(File) - Method in class com.actelion.research.chem.MolfileParser
- getCompactMolecule(String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Creates and returns a molecule from the idcode with its atom and bond arrays being just as large as needed to hold the molecule.
- getCompactMolecule(String) - Method in class com.actelion.research.chem.MolfileParser
- getCompactMolecule(String, String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Creates and returns a molecule from the idcode with its atom and bond arrays being just as large as needed to hold the molecule.
- getComparatorArea() - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- getComparatorAtomsBonds() - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getComparatorBonds() - Static method in class com.actelion.research.chem.mcs.ModelSampleFragments
- getComparatorCoverage() - Static method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- getComparatorDouble() - Static method in class com.actelion.research.util.datamodel.IntegerDouble
- getComparatorId() - Static method in class com.actelion.research.util.datamodel.IdentifiedObject
- getComparatorInt() - Static method in class com.actelion.research.util.datamodel.IntegerDouble
- getComparatorLength() - Static method in class com.actelion.research.util.StringFunctions
- getComparatorNumBonds() - Static method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- getComparatorNumIndices() - Static method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- getComparatorOrderNumber() - Static method in class com.actelion.research.chem.Element
- getComparatorScore() - Static method in class com.actelion.research.util.datamodel.ScorePoint
- getComparatorX() - Static method in class com.actelion.research.util.datamodel.ScorePoint
- getComparatorX() - Static method in class com.actelion.research.util.PointUtils
- getComparatorY() - Static method in class com.actelion.research.util.datamodel.ScorePoint
- getCompatibleFileList(File, int) - Static method in class com.actelion.research.gui.FileHelper
- getComplexityScore() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getComponent() - Method in class com.actelion.research.gui.dock.TreeElement
- getComposite() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getCompound() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getCompound(int) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- getCompound(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- getConformer(MolecularVolume) - Method in class com.actelion.research.chem.phesa.PheSAMolecule
-
Returns the corresponding conformer of a molecular volume
- getConformerCount() - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
- getConformerCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- getConformerIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangleMatcher.AlignmentResult
- getConformerIndexes() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- getConformerLikelihood(int) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- getConnAngle(int, int, int) - Method in class com.actelion.research.chem.conf.BondAngleSet
-
Returns the preferred angle between to three atoms in a row as positive value <= pi.
- getConnAtom(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- getConnAtom(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getConnAtom(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
The neighbours (connected atoms) of any atom are sorted by their relevance:
1. - getConnAtoms(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
The neighbours (connected atoms) of any atom are sorted by their relevance:
1. - getConnBond(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getConnBond(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
The neighbours (connected atoms) of any atom are sorted by their relevance:
1. - getConnBondOrder(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
The neighbours (connected atoms) of any atom are sorted by their relevance:
1. - getConnectionPointCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- getConnectionTable(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MDHIndexTables
- getConnexComponents(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Returns a List of all Connex Components of the graph (List of List of Integer)
- getContainer() - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- getContent() - Method in class com.actelion.research.gui.dock.Dockable
-
Returns the content - null, if none has been set.
- getContent(MouseEvent) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- getContext() - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- getContrastColor(Color, Color) - Static method in class com.actelion.research.util.ColorHelper
-
Based on the differences of hue and perceived brightness of foreground color
fg
and background colorbg
, this method checks and possibly adjusts the given foreground colorfg
such that its hue stays unchanged, but its brightness is adapted to make it better perceivable on the background. - getContribution(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
-
With best current knowledge about colliding torsion combinations and based on the individual frequencies of currently active torsions this method returns the conformers's overall contribution to the total set of non colliding conformers.
- getConverted2CarbonSkeleton(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
-
Replaces all hetero-atoms, except hydrogen, with carbon.
- getCoord() - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
- getCoordinates() - Method in class com.actelion.research.chem.conf.Conformer
- getCoordinates() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.PPNodeRGroup
- getCoordinates() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.MultCoordFragIndex
- getCoordinates() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getCoordinates() - Method in class com.actelion.research.chem.io.CompoundFileParser
-
Either getIDCode and this method or getMolecule() must be overwritten!!!
- getCoordinates() - Method in class com.actelion.research.chem.io.DWARFileParser
-
This returns encoded atom coordinates according to the defined mode.
- getCoordinates() - Method in class com.actelion.research.chem.io.ODEFileParser
- getCoordinates() - Method in class com.actelion.research.chem.Molecule3D
- getCoordinates() - Method in class com.actelion.research.util.datamodel.IDCodeCoord
- getCoordinates(int) - Method in class com.actelion.research.chem.conf.Conformer
- getCoordinates(int) - Method in class com.actelion.research.chem.Molecule
- getCoordinates(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
-
Returns the encoded reaction coordinates.
- getCoordinates(Molecule, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
- getCoordinates(StereoMolecule, int) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
- getCoordinates2D() - Method in class com.actelion.research.chem.io.DWARFileParser
- getCoordinates3D() - Method in class com.actelion.research.chem.io.DWARFileParser
- getCoordinatesA() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- getCoordinatesB() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- getCoordinatesC() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- getCopy() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
-
node deep copy.
- getCopy() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getCoreCoordinates(int, int) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- getCoreCount() - Method in class com.actelion.research.chem.MarkushStructure
- getCoreSize() - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- getCoreStructure(int) - Method in class com.actelion.research.chem.MarkushStructure
- getCorrPearson(double[], double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getCorrPearson(Matrix, Matrix) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getCorrPearson(List<PointDouble>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getCorrPearsonStandardized(double[], double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getCosine(int[], int[]) - Static method in class com.actelion.research.calc.VectorSimilarity
- getCosine(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- getCosine(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
-
Vectors have to be normed!
- getCount() - Method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomFlagCount
- getCountFromType(long) - Method in class com.actelion.research.chem.AtomTypeList
- getCovalentRadius() - Method in class com.actelion.research.chem.Element
- getCovalentRadius(int) - Static method in interface com.actelion.research.chem.conf.VDWRadii
- getCovarianceCentered(double[], double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getCreatedSolutions() - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- getCRingClosureName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getCRingOpeningName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getCRxnDelta(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getCryst1() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getCurrentDirectory() - Static method in class com.actelion.research.chem.io.CompoundFileHelper
- getCurrentPositions() - Method in interface com.actelion.research.chem.forcefield.ForceField
- getCurrentPositions() - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
- getCursor() - Method in interface com.actelion.research.share.gui.editor.actions.Action
- getCursor() - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- getCursor() - Method in class com.actelion.research.share.gui.editor.actions.DeleteAction
- getCursor() - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- getCursor() - Method in class com.actelion.research.share.gui.editor.actions.NewChainAction
- getCursor() - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
- getCursor() - Method in class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
- getCursor(int) - Static method in class com.actelion.research.util.CursorHelper
- getCustomTemplateAtomMask() - Method in class com.actelion.research.chem.coords.CoordinateInventor
- getData() - Method in class com.actelion.research.util.datamodel.IdentifiedObject
- getData() - Method in interface com.actelion.research.util.datamodel.IIdentifiedObject
- getData() - Method in class org.openmolecules.chem.conf.gen.TorsionSetEliminationRule
- getData(String) - Method in class com.actelion.research.chem.StructureInfo
- getDateDeposition() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getDateFloat(String) - Method in class com.actelion.research.util.DateAnalysis
- getDateMillis(String) - Method in class com.actelion.research.util.DateAnalysis
- getDBRef() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getDBRef1DBRef2() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getDConstructionName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getDecimalFormat(int) - Static method in class com.actelion.research.util.StringFunctions
- getDefaultAverageBondLength() - Static method in class com.actelion.research.chem.Molecule
- getDefaultDescriptorHandler(String) - Method in interface com.actelion.research.chem.descriptor.DescriptorHandlerFactory
- getDefaultDescriptorHandler(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerStandard2DFactory
- getDefaultDescriptorHandler(String) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerStandardFactory
- getDefaultDescriptorHandler(String) - Method in interface com.actelion.research.chem.descriptor.ISimilarityHandlerFactory
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedPharmSphere
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerPharmPath
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- getDefaultInstance() - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- getDefaultInstance() - Static method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- getDefaultInstance() - Static method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- getDefaultMaxValenceUncharged(int) - Method in class com.actelion.research.chem.Molecule
-
This is the default maximum valence of the atom neglecting atom charge or radical influences, e.g.
- getDeleteAtomsBondMap(boolean[]) - Method in class com.actelion.research.chem.Molecule
- getDeleteAtomsBondMap(int[]) - Method in class com.actelion.research.chem.Molecule
- getDeleteColsZeroVar(List<Integer>) - Method in class com.actelion.research.calc.Matrix
-
Deletes columns with zero variance.
- getDeleteKey() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getDeltaNanoBaseBlur() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getDeltaNanoQueryBlur() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getDeltaNanoSimilarity() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getDensity() - Method in class com.actelion.research.chem.StructureInfo
- getDEntries() - Method in class com.actelion.research.chem.reaction.ClassificationData
- getDepictor() - Method in class com.actelion.research.gui.JStructureView
- getDescription() - Method in class com.actelion.research.chem.io.CompoundFileFilter
-
Returns the human readable description of this filter.
- getDescriptor() - Method in class com.actelion.research.chem.AbstractDrawingObject
- getDescriptor(int) - Method in class com.actelion.research.chem.StructureSearchSpecification
-
Depending on the mode isLargestFragmentOnly() the descriptor is expected to be represent the whole structure or the largest fragment.
- getDescriptor(int, int, boolean) - Method in interface com.actelion.research.chem.StructureSearchDataSource
- getDescriptor(String) - Method in class com.actelion.research.chem.io.CompoundFileParser
-
If the file source contains encoded descriptors, then overwrite this method to save the calculation time.
- getDescriptor(String) - Method in class com.actelion.research.chem.io.DWARFileParser
- getDescriptorColumn(String) - Method in interface com.actelion.research.chem.StructureSearchDataSource
-
Returns a number to be used in getDescriptor() to address the the descriptor with the given short name.
- getDescriptorDetail() - Method in class com.actelion.research.chem.AbstractDrawingObject
-
Creates a string encoding all properties specific to this drawing object.
- getDescriptorDetail() - Method in class com.actelion.research.chem.reaction.ReactionArrow
- getDescriptorDetail() - Method in class com.actelion.research.chem.TextDrawingObject
- getDescriptorHandlerFactory() - Method in class com.actelion.research.chem.io.CompoundFileParser
- getDescriptorInfo(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- getDescriptorShortName() - Method in class com.actelion.research.chem.StructureSearchSpecification
- getDescriptorType(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- getDetail() - Method in class com.actelion.research.chem.prediction.DruglikenessPredictor
-
If assessDruglikeness() was called multiple times in multiple threads, then getDetail() won't retrieve the expected detail.
- getDetail(StereoMolecule) - Method in class com.actelion.research.chem.prediction.CLogPPredictor
- getDetail(StereoMolecule) - Method in class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
- getDetail(StereoMolecule) - Method in class com.actelion.research.chem.prediction.SolubilityPredictor
- getDetail(StereoMolecule, int) - Method in class com.actelion.research.chem.prediction.ToxicityPredictor
- getDetails() - Method in class com.actelion.research.chem.io.DWARFileParser
-
Provided that the mode contains MODE_EXTRACT_DETAILS, then this method returns a map of all embedded detail objects of the DWAR file.
- getDeviceConfiguration() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getDFragmentationName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getDiagonal() - Method in class com.actelion.research.calc.Matrix
-
Matrix diagonal extraction.
- getDiffRect(Rectangle2D, Rectangle2D) - Static method in class com.actelion.research.chem.ChemistryHelper
- getDihedral(Coordinates, Coordinates, Coordinates) - Method in class com.actelion.research.chem.Coordinates
- getDihedral(Coordinates, Coordinates, Coordinates, Coordinates) - Static method in class com.actelion.research.chem.Coordinates
-
Calculates a signed torsion as an exterior spherical angle from a valid sequence of 4 points in space.
- getDihedral(Molecule3D, int, int, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
-
Gets the Dihedral Angle between 4 atoms
- getDihedral(StereoMolecule, int, int, int, int) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
-
Gets the Dihedral Angle between 4 atoms
- getDirectionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
- getDirectionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
- getDirectionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- getDirectionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
- getDirectionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
- getDirectionality() - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
- getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
- getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
- getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
- getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
- getDirectionalityDerivativeCartesian(double[], double[], Coordinates, double) - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
- getDirectSim(PharmacophoreTree) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getDiscreteValue(double) - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
- getDisplayMode() - Method in class com.actelion.research.gui.JDrawArea
- getDisplayMode() - Method in class com.actelion.research.share.gui.editor.Model
- getDisplayMolecule() - Method in class com.actelion.research.gui.JStructureView
- getDisplaySize() - Method in class com.actelion.research.share.gui.editor.Model
- getDissimilarity(int, int) - Method in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable
-
D(LigandType_1, LigandType_2) = Sum( d( F(ProteinType_i, LigandType_1), F(ProteinType_i, LigandType_2)), i)
- getDissimilarity(TorsionDescriptor, float[]) - Method in class com.actelion.research.chem.conf.TorsionDescriptor
-
Calculates a similarity value between td and this considering individual torsion values, the importance of the rotatable bond, and the ratio of rotatable/non-rotatable bonds.
- getDistance(int, int) - Method in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable
- getDistanceArray(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getDistanceHistogram() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- getDistanceMatrix(Molecule3D, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getDistanceTables() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getDistHist(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getDistHist(int, int, byte[]) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getDistHist(int, int, byte[]) - Method in interface com.actelion.research.chem.descriptor.flexophore.IMolDistHist
- getDistHist(MultCoordFragIndex, MultCoordFragIndex) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.MultCoordFragIndex
- getDistHists() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getDividerLocation() - Method in class com.actelion.research.gui.dock.TreeFork
- getDockable() - Method in class com.actelion.research.gui.dock.DockableHeader
- getDockable(int) - Method in class com.actelion.research.gui.dock.TreeLeaf
- getDockable(Component) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
Returns the Dockable that contains the given content.
- getDockable(String) - Method in class com.actelion.research.gui.dock.JDockingPanel
- getDockableCount() - Method in class com.actelion.research.gui.dock.JDockingPanel
- getDockableCount() - Method in class com.actelion.research.gui.dock.TreeLeaf
- getDockables() - Method in class com.actelion.research.gui.dock.JDockingPanel
- getDockableTitles() - Method in class com.actelion.research.gui.dock.JDockingPanel
- getDockInfoSequence() - Method in class com.actelion.research.gui.dock.JDockingPanel
-
returns the persistence information necessary to recreate the current docking state.
- getDonorCount() - Method in class com.actelion.research.chem.PropertyCalculator
- getDouble() - Method in class com.actelion.research.util.datamodel.IntegerDouble
- getDoublePivot() - Method in class com.actelion.research.calc.LUDecomposition
-
Return pivot permutation vector as a one-dimensional double array
- getDragable(Point) - Method in class com.actelion.research.gui.dock.TreeLeaf
- getDragHandle() - Method in class com.actelion.research.gui.dock.Dockable
- getDrawArea() - Method in class com.actelion.research.gui.JDrawDialog
- getDrawArea() - Method in class com.actelion.research.gui.JDrawPanel
- getDrawConfig() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getDrawingObjects() - Method in class com.actelion.research.chem.reaction.Reaction
- getDrawingObjects() - Method in class com.actelion.research.gui.JDrawArea
- getDrawingObjects() - Method in class com.actelion.research.share.gui.editor.Model
- getDruglikenessString(StereoMolecule) - Method in class com.actelion.research.chem.prediction.DruglikenessPredictor
- getDRxnDelta(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getDummy() - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- getEdgeLengths() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangle
- getEdges() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getEEntries() - Method in class com.actelion.research.chem.reaction.ClassificationData
- getEFGName(int, int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getEigenvector(Matrix, int, Matrix, Matrix) - Static method in class com.actelion.research.calc.Matrix
-
Householder reduction according num rec 11.2.
- getElectronegativity() - Method in class com.actelion.research.chem.Element
- getElectronValenceCorrection(int, int) - Method in class com.actelion.research.chem.Molecule
-
This is the maximum valence correction caused by atom charge or radical status, e.g.
- getElement(int) - Static method in class com.actelion.research.chem.PeriodicTable
- getEliminationRuleList() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- getEncodedCoordinates() - Method in class com.actelion.research.chem.Canonizer
-
Encodes the molecule's atom coordinates into a compact String.
- getEncodedCoordinates() - Method in class com.actelion.research.chem.SimpleCanonizer
- getEncodedCoordinates(boolean) - Method in class com.actelion.research.chem.Canonizer
-
Encodes the molecule's atom coordinates into a compact String.
- getEncodedCoordinates(boolean, Coordinates[]) - Method in class com.actelion.research.chem.Canonizer
-
Encodes the molecule's atom coordinates into a compact String.
- getEncodedMapping() - Method in class com.actelion.research.chem.Canonizer
- getEncodedQuery(int) - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
-
Returns the (or one of the) query structures encodes as idcode.
- getEnd() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
- getEnd() - Method in class com.actelion.research.util.IntQueue
- getEnergy() - Method in class com.actelion.research.chem.conf.Conformer
- getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.AngleBend
-
Calculates the angle energy.
- getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.BondStretch
-
Calculates the bond stretch energy.
- getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.Electrostatic
-
Calculates the electrostatic energy.
- getEnergy(double[]) - Method in interface com.actelion.research.chem.forcefield.mmff.EnergyTerm
- getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
-
Calculates the out of plane energy.
- getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.PositionConstraint
- getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.StretchBend
-
Calculates the stretch bend energy.
- getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
-
Calculates the torsional energy.
- getEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
-
Calculates the van der Waals energy.
- getEnterKey() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getEquivalentTypes(int, double) - Method in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable
-
Compare similarity values of 2 types (across all lines)
- getERearrangementName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getERegNo() - Method in class com.actelion.research.chem.io.RDFileParser
- getErrorCount() - Method in class com.actelion.research.chem.io.CompoundFileHelper
- getErrors() - Method in class com.actelion.research.chem.io.AbstractParser
- getERSGroupMemberCounts() - Method in class com.actelion.research.chem.StereoMolecule
- getERxnDelta(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getEscapeKey() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getESRImage(boolean) - Method in class com.actelion.research.share.gui.editor.ImageProvider
- getESRImageRows() - Method in class com.actelion.research.share.gui.editor.ImageProvider
- getESRType() - Method in class com.actelion.research.share.gui.editor.Model
- getEuclidDist(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Euclidean distance
- getEuclidDistBitWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- getEuclidDistFast(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Euclidean distance without sqrt
- getEuclideanDistanceFast(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
-
Euclidean distance without sqrt
- getEuclideanDistanceFastRows(int, int) - Method in class com.actelion.research.calc.Matrix
-
Skipping the sqrt.
- getEuclideanDistanceFastRows(int, Matrix, int) - Method in class com.actelion.research.calc.Matrix
-
Skipping the sqrt.
- getExactHash(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
-
Returns a hash code representing the exact reaction.
- getExcludedNeighbourCount(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
This method returns the count of atom neighbours which are marked as being an exclude group.
- getExhaustiveStatistics() - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- getExitAtoms() - Method in class com.actelion.research.chem.shredder.Fragment3D
- getExitVectorGaussians() - Method in class com.actelion.research.chem.phesa.MolecularVolume
- getExpdata() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getExplicitHydrogens(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- getExplicitHydrogens(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getExtendedAtomSequence(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
If the atom sequence contains a straight chain of sp-hybridized atoms, then the atom array contain the first two and last two atoms of a sequence of 2n+4 atoms (n: number of conjugated triple bonds).
- getExtendedCoordinates(int, int) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- getExtendedSize() - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- getExtension(int) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
- getExtension(File) - Method in class com.actelion.research.chem.io.CompoundFileFilter
-
Return the extension portion of the file's name .
- getExtension(File) - Static method in class com.actelion.research.util.IO
- getExtensionCuts(List<Integer>, List<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
-
get a list of int[] arrays that define an extension cut: Given a subtree with a designated head-node, an extension cut separates an extension match from the remaining subtrees.
- getExtensionList(int) - Method in class com.actelion.research.chem.io.CompoundFileHelper
- getEZParity(int) - Method in class com.actelion.research.chem.Canonizer
-
Returns the absolute bond parity, which is based on priority ranks.
- getFactorial(int) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
- getFactorIsomorphSymmetric() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- getFactory() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerStandard2DFactory
- getFactory() - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerStandardFactory
- getFailureCount() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- getFcadj(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
-
Returns the formal charge adjustment for a given atom type.
- getFFP() - Method in class com.actelion.research.chem.coords.InventorTemplate
- getFGValue(double) - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
- getFGValue(double[]) - Method in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionTerm
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.LigandPose
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.ChemPLP
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.chemscore.HBTerm
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.chemscore.MetalTerm
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.chemscore.SimpleMetalTerm
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.IdoScore
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.idoscore.InteractionTerm
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.plp.PLPTerm
- getFGValue(double[]) - Method in class com.actelion.research.chem.docking.scoring.plp.REPTerm
- getFGValue(double[]) - Method in interface com.actelion.research.chem.optimization.Evaluable
- getFGValue(double[]) - Method in class com.actelion.research.chem.phesa.EvaluableOverlap
- getFGValue(double[]) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- getFGValue(double[]) - Method in class com.actelion.research.chem.potentialenergy.AngleConstraint
- getFGValue(double[]) - Method in class com.actelion.research.chem.potentialenergy.BondConstraint
- getFGValue(double[]) - Method in class com.actelion.research.chem.potentialenergy.EmpiricalLigandStrain
- getFGValue(double[]) - Method in interface com.actelion.research.chem.potentialenergy.PotentialEnergyTerm
- getFGValue(double[]) - Method in class com.actelion.research.chem.potentialenergy.TorsionConstraint
- getFGValuePP(double[]) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- getFGValueSelfPP(double[], MolecularVolume, boolean) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- getFGValueShape(double[]) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
-
calculates the gradient of the overlap function with respect to the cartesian coordinates of the atoms
- getFGValueShapeSelf(double[], MolecularVolume, boolean) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- getFieldData() - Method in class com.actelion.research.chem.io.RDFileParser
- getFieldData(int) - Method in class com.actelion.research.chem.io.CompoundFileParser
-
Returns the cell content of the current row.
- getFieldData(int) - Method in class com.actelion.research.chem.io.DWARFileParser
- getFieldData(int) - Method in class com.actelion.research.chem.io.ODEFileParser
- getFieldData(int) - Method in class com.actelion.research.chem.io.SDFileParser
- getFieldData(String) - Method in class com.actelion.research.chem.io.RDFileParser
- getFieldData(String) - Method in class com.actelion.research.chem.SDFileMolecule
- getFieldIndex(String) - Method in class com.actelion.research.chem.io.CompoundFileParser
- getFieldNames() - Method in class com.actelion.research.chem.io.CompoundFileParser
-
Compiles all column names that contain alpha-numerical information.
- getFieldNames() - Method in class com.actelion.research.chem.io.DWARFileParser
- getFieldNames() - Method in class com.actelion.research.chem.io.ODEFileParser
- getFieldNames() - Method in class com.actelion.research.chem.io.RDFileParser
-
Returns a list of field names.
- getFieldNames() - Method in class com.actelion.research.chem.io.SDFileParser
-
Returns a list of field names.
- getFieldNames(int) - Method in class com.actelion.research.chem.io.SDFileParser
-
Returns a list of field names.
- getFields() - Method in class com.actelion.research.chem.SDFileMolecule
- getFile() - Method in class com.actelion.research.gui.JFileChooserOverwrite
- getFile(Component, String, int) - Static method in class com.actelion.research.gui.FileHelper
-
For compatibility reasons...
- getFileType(String) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
- getFinalRank() - Method in class com.actelion.research.chem.Canonizer
- getFingerprint(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.FingerPrintGenerator
-
Generates a fingerprint of the default size for the given ExtendedMolecule
- getFingerprint(StereoMolecule) - Method in class com.actelion.research.chem.descriptor.FingerPrintGeneratorPharmGraph
-
Generates a fingerprint of the default size for the given ExtendedMolecule
- getFingerprint(StereoMolecule, int) - Method in class com.actelion.research.chem.descriptor.FingerPrintGenerator
-
Generates the fingerprint of a molecule
- getFingerprint(StereoMolecule, int) - Method in class com.actelion.research.chem.descriptor.FingerPrintGeneratorPharmGraph
-
Generates the fingerprint of a molecule
- getFirstHittingLongIndexBlockNo() - Method in class com.actelion.research.chem.SSSearcherWithIndex
- getFisherProjectionParity(int, int[], double[], int[]) - Method in class com.actelion.research.chem.ExtendedMolecule
-
If the atom is a stereo center in fisher projection, then its tetrahedral parity is returned.
- getFitMol() - Method in class com.actelion.research.chem.phesa.PheSAAlignment.PheSAResult
- getFlatness() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getFlavors() - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- getFlavors() - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- getFlavors() - Method in class com.actelion.research.gui.dnd.SDFileMoleculeDropAdapter
- getFlipped() - Method in class com.actelion.research.calc.Matrix
-
Opposite direction to transpose.
- getFont() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- getFont() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getFont() - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- getFont() - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- getFont(AttributeSet) - Method in class com.actelion.research.gui.hidpi.ScaledStyleSheet
- getFontMetrics(Font) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- getFontMetrics(Font) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getFontRenderContext() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getFontScaleFactor() - Static method in class com.actelion.research.gui.hidpi.ScaledEditorKit
- getForceConstants(MMFFMolecule, int, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Torsion
-
Gets the force constants associated with a torsion angle.
- getForegroundColor() - Method in class com.actelion.research.share.gui.DrawConfig
- getForegroundColor() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getFormalCharges(MMFFMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Charge
-
Computes the MMFF formal charges for a molecules atoms.
- getFormula() - Method in class com.actelion.research.chem.MolecularFormula
- getFormula(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getFormulaIDs() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getFractalDimension() - Method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- getFractionCarbonInteractions() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- getFragment() - Method in class com.actelion.research.chem.conf.TorsionDetail
-
Returns the direct surrounding of the previously classified rotatable bond.
- getFragment() - Method in class com.actelion.research.chem.coords.InventorTemplate
- getFragment(int) - Method in class com.actelion.research.chem.coords.FragmentAssociation
- getFragment(int) - Method in class com.actelion.research.chem.prediction.IncrementTable
- getFragment(int) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
- getFragment(IBitArray) - Method in class com.actelion.research.chem.mcs.BondVector2IdCode
- getFragment(IBitArray, boolean) - Method in class com.actelion.research.chem.mcs.BondVector2IdCode
- getFragmentAt(Point2D, boolean) - Method in class com.actelion.research.share.gui.editor.Model
- getFragmentAtoms(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Returns an array of all atoms for which a path of bonds leads to rootAtom not considering metal ligand bonds.
- getFragmentAtoms(int, boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Returns an array of all atoms for which a path of bonds leads to rootAtom.
- getFragmentIdCode(IBitArray) - Method in class com.actelion.research.chem.mcs.BondVector2IdCode
- getFragmentIdCodeCarbonSkeleton(IBitArray) - Method in class com.actelion.research.chem.mcs.BondVector2IdCode
- getFragmentList() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorParallizer
- getFragmentMatches(Molecule3D, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Find all fragment occurences in mol (only the movable atoms are considered).
- getFragmentNo(int) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
- getFragmentNumbers(int[], boolean[], boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Locates all disconnected fragments in the molecule and assigns fragment numbers (starting from 0) to all atoms.
- getFragmentNumbers(int[], boolean, boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Locates all unconnected fragments in the Molecule and assigns fragment indexes for every atom starting with 0.
- getFragments() - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- getFragments() - Method in class com.actelion.research.chem.StereoMolecule
-
Separates all disconnected fragments of this Molecule into individual Molecule objects.
- getFragments() - Method in class com.actelion.research.gui.JDrawArea
- getFragments() - Method in class com.actelion.research.share.gui.editor.Model
- getFragments(int) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
-
Returns list with indices for fragments with
size
bonds. - getFragments(int[], int) - Method in class com.actelion.research.chem.StereoMolecule
-
Separates all disconnected fragments of this Molecule into individual molecule objects.
- getFragments(StereoMolecule) - Method in class com.actelion.research.chem.shredder.Fragmenter3D
-
Applying the constraints passed to the Fragmenter3D constructor, this method shredders the given 3D-molecule and returns all generated 3D-fragments as an ArrayList.
- getFragmentsForSingleAtom(int) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
- getFreeValence(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
The free valence is the number of potential additional single bonded neighbours to reach the atom's maximum valence.
- getFrequencies() - Method in class com.actelion.research.calc.histogram.Histogram
- getFrequency() - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- getFrequency() - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- getFrequency(int) - Method in class com.actelion.research.calc.histogram.Histogram
- getFrequencyOnePerMol() - Method in class com.actelion.research.chem.shredder.Fragment
- getFrequencySumAll() - Method in class com.actelion.research.chem.shredder.Fragment
- getFromQuadraticMatrix(Matrix, double, double, int) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getFullyMappedReactions() - Method in class com.actelion.research.chem.reaction.Reactor
-
After instantiating the Reactor with MODE_FULLY_MAP_REACTIONS and after supplying real reactants, this method may be used to construct the fully mapped reaction.
- getFunction(int, int) - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- getFunction(long) - Method in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
- getFunction(long) - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- getFunction(String) - Method in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
- getFunctionalGroupEquivalenceLevel(int, int) - Static method in class com.actelion.research.chem.reaction.FunctionalGroupClassifier
-
Determines the similarity of two functional groups based on their location in the binary functional group similarity tree.
- getFunctionalities() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- getFunctionality() - Method in class com.actelion.research.chem.phesa.pharmacophore.SimplePPGaussian
- getFunctionalityIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
- getFunctionalityIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
- getFunctionalityIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- getFunctionalityIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
- getFunctionalityIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
- getFunctionalityIndex() - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
- getFunctionGroupCountMap() - Method in class com.actelion.research.chem.reaction.FunctionalGroupClassifier
-
Applying a predefined dictionary of logically arranged 1024 functional groups this method determines all functional groups present in the molecule, counts how often they occurr in the molecule.
- getGenericAcceptor() - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- getGenericDonor() - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- getGenericNegCharge() - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- getGenericPosCharge() - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- getGeomFactory() - Method in class com.actelion.research.share.gui.editor.Model
- getGlobalAtom(int) - Method in class com.actelion.research.chem.coords.InventorFragment
- getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.AngleBend
-
Calculates the gradient and adds it to the gradients array.
- getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.BondStretch
-
Calculates the gradient and adds it to the gradients array.
- getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.Electrostatic
-
Calculates the gradient and adds it to the gradients array.
- getGradient(double[], double[]) - Method in interface com.actelion.research.chem.forcefield.mmff.EnergyTerm
- getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
-
Calculates the gradient and adds it to the gradients array.
- getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.PositionConstraint
- getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.StretchBend
-
Calculates the gradient and adds it to the gradients array.
- getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
-
Calculates the gradient and adds it to the gradients array.
- getGradient(double[], double[]) - Method in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
-
Calculates the gradient and adds it to the gradients array.
- getGradientContribution(Gaussian3D, Gaussian3D, double[], boolean) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- getGraphAtoms() - Method in class com.actelion.research.chem.Canonizer
- getGraphIndexes() - Method in class com.actelion.research.chem.Canonizer
- getGridCoordinates(Coordinates) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- getGridSize() - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- getGyrationRadius() - Method in class com.actelion.research.chem.docking.LigandPose
- getHalignment() - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Gets the Halignment attribute of the VerticalFlowLayout object
- getHandleHydrogenAtomMap(boolean[]) - Method in class com.actelion.research.chem.ExtendedMolecule
-
If ensureHelperArrays() (and with it handleHydrogens()) was not called yet on a fresh molecule and if the molecule contains simple hydrogen atoms within non-hydrogens atoms, then this function returns a map from current atom indexes to those new atom indexes that would result from a call to handleHydrogens.
- getHandleHydrogenBondMap() - Method in class com.actelion.research.chem.ExtendedMolecule
-
If ensureHelperArrays() (and with it handleHydrogens()) was not called yet on a fresh molecule and if the molecule contains simple hydrogen atoms within non-hydrogens atoms, then this function returns a map from current bond indexes to those new bond indexes that would result from a call to handleHydrogens.
- getHandleHydrogenMap() - Method in class com.actelion.research.chem.ExtendedMolecule
-
If ensureHelperArrays() (and with it handleHydrogens()) was not called yet on a fresh molecule and if the molecule contains simple hydrogen atoms within non-hydrogens atoms, then this function returns a map from current atom indexes to those new atom indexes that would result from a call to handleHydrogens.
- getHandleHydrogenMap() - Method in class com.actelion.research.chem.MolfileParser
-
If this MoflileParser was instantiated with MODE_KEEP_HYDROGEN_MAP
- getHash() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangle
- getHash(StereoMolecule, CanonizerUtil.IDCODE_TYPE, boolean) - Static method in class com.actelion.research.chem.CanonizerUtil
- getHashCode(byte[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
- getHashMap(List<IdentifiedObject<T>>) - Static method in class com.actelion.research.util.datamodel.IdentifiedObject
- getHashSetIndexInevitablePPPoints() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getHConstructionName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getHDonorsAcceptors(ExtendedMolecule) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Returns a array of 2 elements [number of donors, number of acceptors]
- getHeaderPaint(boolean, int) - Static method in class com.actelion.research.gui.HeaderPaintHelper
- getHeaderString(int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- getHeaderTags() - Static method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getHeadOrTail() - Method in class com.actelion.research.chem.io.DWARFileParser
-
Provided that the mode contains MODE_BUFFER_HEAD_AND_TAIL, then this method returns a list of all header/footer rows of the DWAR file.
- getHeight() - Method in class com.actelion.research.chem.coords.InventorFragment
- getHeight() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getHeight() - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
- getHelix() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getHelperArrayStatus() - Method in class com.actelion.research.chem.ExtendedMolecule
- getHEntries() - Method in class com.actelion.research.chem.reaction.ClassificationData
- getHet() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getHetAtomRecords() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getHeteroOnlyNode(PPNode) - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- getHeteroPosition(int) - Method in class com.actelion.research.chem.RingCollection
-
Returns the position of the electron pair providing hetero atom or carbenium atom in case of 5-membered, respective 7-membered aromatic ring.
- getHexStringFromIndex(int[]) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getHFragmentationName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getHgap() - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Gets the Hgap attribute of the VerticalFlowLayout object
- getHighestAtomStrain() - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- getHighestMapNo() - Method in class com.actelion.research.chem.reaction.Reaction
- getHighLightColor() - Method in class com.actelion.research.share.gui.DrawConfig
- getHighLightColor() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getHiliteAtom() - Method in class com.actelion.research.gui.JDrawArea
- getHiliteBond() - Method in class com.actelion.research.gui.JDrawArea
- getHistogram() - Method in class com.actelion.research.calc.histogram.Histogram
- getHistogram(double[], Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getHistogram(float[][], int, Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getHistogram(float[], Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getHistogram(Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getHistogram(Matrix, int) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getHistogram(Matrix, Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getHistogramBins(double, double, int) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getHitCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- getHitQuote() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- getHMId_Formula() - Method in class com.actelion.research.chem.io.pdb.parser.FormulaParser
- getHmId_Name() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getHMId_Name() - Method in class com.actelion.research.chem.io.pdb.parser.HetNameParser
- getHMId_Site() - Method in class com.actelion.research.chem.io.pdb.parser.SiteParser
- getHMId_Synonyms() - Method in class com.actelion.research.chem.io.pdb.parser.HetSynonymParser
- getHmNo_Remark() - Method in class com.actelion.research.chem.io.pdb.parser.RemarkParser
- getHorizontalFill() - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Gets the Hfill attribute of the VerticalFlowLayout object
- getHoseCodes(StereoMolecule, int, int) - Static method in class com.actelion.research.chem.contrib.HoseCodeCreator
-
This descriptor requires proper up/down bonds, because it encodes stereo parities.
- getHoseCodesFromDiaID(String, int, int) - Static method in class com.actelion.research.chem.contrib.HoseCodeCreator
- getHRxnDelta(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getHRxnGroupDef(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getHydrogenMap() - Method in class com.actelion.research.chem.forcefield.mmff.MMFFMolecule
- getHydrogens() - Method in class com.actelion.research.chem.phesa.MolecularVolume
- getIconScaleFactor() - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
- getId() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- getId() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- getId() - Method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- getId() - Method in class com.actelion.research.chem.io.pdb.parser.ListInteger
- getId() - Method in class com.actelion.research.chem.StructureInfo
- getId() - Method in class com.actelion.research.chem.SVGDepictor
- getId() - Method in class com.actelion.research.util.datamodel.IdentifiedObject
- getId() - Method in interface com.actelion.research.util.datamodel.IIdentifiedObject
- getID() - Method in class com.actelion.research.calc.Matrix
- getID() - Method in class com.actelion.research.chem.conf.TorsionDetail
-
Returns the torsion identifier that resulted from the most previous classification.
- getID() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getIdcode() - Method in class com.actelion.research.util.datamodel.IDCodeCoord
- getIdCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- getIdCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- getIdCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.PPNodeRGroup
- getIdCode() - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- getIdCode() - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- getIDCode() - Method in class com.actelion.research.chem.Canonizer
- getIDCode() - Method in class com.actelion.research.chem.io.CompoundFileParser
-
Either this method and getCoordinates() or getMolecule() must be overwritten!!!
- getIDCode() - Method in class com.actelion.research.chem.io.DWARFileParser
- getIDCode() - Method in class com.actelion.research.chem.io.ODEFileParser
- getIDCode() - Method in class com.actelion.research.chem.shredder.Fragment3D
- getIDCode() - Method in class com.actelion.research.chem.SimpleCanonizer
- getIDCode() - Method in class com.actelion.research.chem.StereoMolecule
-
This is a convenience method that creates the molecule's idcode without explicitly creating a Canonizer object for this purpose.
- getIDCode() - Method in class com.actelion.research.share.gui.editor.Model
- getIDCode(int) - Method in class com.actelion.research.chem.StructureSearchSpecification
-
Returns the (or one of the) query structures encodes as idcode.
- getIDCode(int, boolean) - Method in interface com.actelion.research.chem.StructureSearchDataSource
-
Returns the idcode of the structure or largest fragment.
- getIDCode(StereoMolecule, CanonizerUtil.IDCODE_TYPE, boolean) - Static method in class com.actelion.research.chem.CanonizerUtil
-
Generates an IDCODE for a defined and simplified state of a given molecule.
- getIdCodeFromFragment(StereoMolecule, ListWithIntVec) - Static method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
- getIDCodeVersion(byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- getIDCodeVersion(String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- getIDCoordinates() - Method in class com.actelion.research.chem.shredder.Fragment3D
- getIDCoordinates() - Method in class com.actelion.research.chem.StereoMolecule
-
This is a convenience method that creates the molecule's id-coordinates matching the idcode available with getIDCode().
- getIdentifier() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getIdFlexophorePoint1() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- getIdFlexophorePoint2() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- getImage() - Static method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Deprecated.Use ImageClipboardHandler.pasteImage for consistency reasons
- getImageProvider() - Method in class com.actelion.research.share.gui.editor.Model
- getImplicitHigherValence(int, boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
-
If the explicitly attached neighbors cause an atom valence to exceed the lowest allowed valence for this atomic no, then this method returns the next higher allowed valence, e.g.
- getImplicitHydrogens(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Calculates and return the number of implicit hydrogens at atom.
- getImplicitHydrogens(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Return the number of implicit hydrogens, ie.
- getIncrement(int) - Method in class com.actelion.research.chem.prediction.IncrementTable
- getIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
- getIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getIndex() - Method in class com.actelion.research.chem.io.DWARFileParser
- getIndex() - Method in class com.actelion.research.chem.io.ODEFileParser
- getIndex() - Method in enum com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint.Functionality
- getIndex() - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- getIndex() - Method in class com.actelion.research.chem.properties.complexity.IndexHash
- getIndex() - Method in class com.actelion.research.util.datamodel.IDCodeCoord
- getIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.AtomTypeMap
- getIndex(int, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getIndex(T) - Method in class com.actelion.research.util.SortedList
-
Returns the position index of object in the sorted list.
- getIndex(T) - Method in class com.actelion.research.util.UniqueList
-
When objects were added after the last getIndex() call, then the original-index-map needs to be re-created.
- getIndexAboveEqual(T) - Method in class com.actelion.research.util.SortedList
-
If object is not member of this list, returns potential insert index.
- getIndexBaseFromHeap(int) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- getIndexBelowEqual(T) - Method in class com.actelion.research.util.SortedList
-
If object is not member of this list, returns potential insert index.
- getIndexCenter() - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
- getIndexCorrespondingBaseNode(int) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- getIndexFromCoord(double, double, double) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getIndexFromHexString(byte[]) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getIndexFromHexString(String) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getIndexLine() - Method in class com.actelion.research.chem.io.pdb.parser.FormulaParser
- getIndexLine() - Method in class com.actelion.research.chem.io.pdb.parser.HetNameParser
- getIndexLine() - Method in class com.actelion.research.chem.io.pdb.parser.HetSynonymParser
- getIndexLine() - Method in class com.actelion.research.chem.io.pdb.parser.ModelParser
- getIndexLine() - Method in class com.actelion.research.chem.io.pdb.parser.RemarkParser
- getIndexLine() - Method in class com.actelion.research.chem.io.pdb.parser.SiteParser
- getIndexMaxNumUniqueFrags(List<Point>) - Static method in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule
- getIndexOriginalAtom() - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
- getIndexOrInsertIndex(T) - Method in class com.actelion.research.util.SortedList
-
Returns the position index of object in the sorted list.
- getIndexPosStartForDistHist(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getIndexQueryFromHeap(int) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- getIndexSphereVisualization() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getIndicesBitsSet() - Method in class com.actelion.research.util.datamodel.IntVec
- getInevitablePharmacophorePoints() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getInfo() - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedPharmSphere
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPharmPath
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- getInfo() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- getInfo() - Method in interface com.actelion.research.chem.descriptor.ISimilarityCalculator
- getInfo() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- getInfo() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- getInfo(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getInitialRot() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangle
- getInitialTranslate() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangle
- getInsertionCode() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getInsertionCode() - Method in class com.actelion.research.chem.io.pdb.parser.Residue
- getInstance() - Static method in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
- getInstance() - Static method in class com.actelion.research.chem.descriptor.flexophore.DistHistEncoder
- getInstance() - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.AtomTypeMap
- getInstance() - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- getInstance() - Static method in class com.actelion.research.chem.descriptor.flexophore.MDHIndexTables
- getInstance() - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistEncoder
- getInstance() - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizEncoder
- getInstance() - Static method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- getInstance() - Static method in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable
- getInstance() - Static method in class com.actelion.research.chem.name.StructureNameResolver
- getInstance() - Static method in class com.actelion.research.chem.phesa.QuickMathCalculator
- getInstance() - Static method in class com.actelion.research.chem.reaction.ClassificationData
- getInstance(int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
-
Use this as constructor for serial mode.
- getInt() - Method in class com.actelion.research.util.datamodel.IntegerDouble
- getInt(byte[]) - Static method in class com.actelion.research.util.datamodel.IntVec
- getIntegratedAreaWeighted(int[], double[], int) - Static method in class com.actelion.research.chem.properties.complexity.SummaryFragments
-
Takes the natural logarithm for each area fraction.
- getInteractionAtomType(int) - Method in class com.actelion.research.chem.Molecule3D
- getInteractionClass() - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
- getInteractionClass() - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
- getInteractionClasses() - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- getInteractionSimilarity(PPGaussian) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
- getInteractionType(int) - Method in interface com.actelion.research.chem.descriptor.flexophore.IPPNode
- getInteractionType(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- getInteractionTypeCount() - Method in interface com.actelion.research.chem.descriptor.flexophore.IPPNode
- getInteractionTypeCount() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
-
realize() may be called first.
- getInteractionTypeFromByteArray(byte, byte, byte) - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- getInteractionTypes() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- getIntercept() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getInterMolecularInteractions(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Return a List of int[] representing all the atom-atom pairs having an intermolecular interactions (distance close to sum of VDW)
- getInverseTransformation() - Method in class com.actelion.research.chem.DepictorTransformation
- getIonizableGroups() - Method in class com.actelion.research.chem.phesa.pharmacophore.IonizableGroupDetector
- getIRegNo() - Method in class com.actelion.research.chem.io.RDFileParser
- getIsotopeList(int) - Static method in class com.actelion.research.chem.IsotopeHelper
- getJrnl() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getKey(int) - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- getKeyFragment(int) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getKeyStrokeBuffer() - Method in class com.actelion.research.share.gui.editor.Model
- getKeywords() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getKoop() - Method in class com.actelion.research.chem.forcefield.mmff.OutOfPlane
- getKoop(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.OutOfPlane
- getKoop(MMFFMolecule, int, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.OutOfPlane
-
Returns the Koop parameters from the OutOfPlane table.
- getL() - Method in class com.actelion.research.calc.LUDecomposition
-
Return lower triangular factor
- getL1() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- getL2() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- getLambda() - Method in class com.actelion.research.util.SmoothingSplineInterpolator
- getLeftChild() - Method in class com.actelion.research.gui.dock.TreeFork
- getLength() - Method in class com.actelion.research.chem.Coordinates
- getLength() - Method in class com.actelion.research.chem.reaction.ReactionArrow
- getLength() - Method in interface com.actelion.research.share.gui.editor.chem.IArrow
- getLength(int) - Method in class com.actelion.research.chem.conf.BondLengthSet
- getLengthIntVec() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- getLi() - Method in class com.actelion.research.chem.io.pdb.parser.ListInteger
- getLiConnect() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getLigandBounds(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getLigandCenter(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getLigandRMSD(Molecule3D, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Gets the root mean square deviation between 2 positions.
- getLigConf() - Method in class com.actelion.research.chem.docking.LigandPose
- getLikelihood() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- getLikelyhood() - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
-
Tries to estimate the relative likelyhood of this conformer from atom strains considering an unstrained conformer to have a likelyhood of 1.0.
- getLikelyRandomConformerIndex(double, double) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
-
Calculates a random conformer index giving conformers with lower strains a higher chance to be selected.
- getLikelyRandomTorsionIndex(double, double) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
-
Calculates a random torsion index giving torsions with higher likelyhoods (i.e.
- getLiLiIdCode() - Method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- getLinedCol() - Method in class com.actelion.research.calc.Matrix
- getLineWidth() - Method in class com.actelion.research.chem.AbstractDepictor
- getLineWidth() - Method in class com.actelion.research.chem.Depictor
- getLineWidth() - Method in class com.actelion.research.chem.Depictor2D
- getLineWidth() - Method in class com.actelion.research.chem.SVGDepictor
- getLineWidth() - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- getLink() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getLinkerId() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
- getLinkNodes() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getLiNonOverLappingIsomorphSubstruct() - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- getList() - Method in class com.actelion.research.calc.Matrix
- getList(int) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getListIndex(String) - Method in class com.actelion.research.chem.SortedStringList
- getListIndex(String) - Method in class com.actelion.research.chem.UniqueStringList
- getListIndexOriginalAtoms() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getLocalAtom(int) - Method in class com.actelion.research.chem.coords.InventorFragment
- getLocaleDateFormat() - Method in enum com.actelion.research.util.Formatter.LocaleFormat
- getLocaleFormat() - Method in class com.actelion.research.util.Formatter
- getLocaleTimeFormat() - Method in enum com.actelion.research.util.Formatter.LocaleFormat
- getLogP() - Method in class com.actelion.research.chem.PropertyCalculator
- getLogPDetail() - Method in class com.actelion.research.chem.PropertyCalculator
- getLogS() - Method in class com.actelion.research.chem.PropertyCalculator
- getLogSDetail() - Method in class com.actelion.research.chem.PropertyCalculator
- getLongestChain(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Return the longest molecular chain starting at atm
- getLongIndexFromHexString(byte[]) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getLongIndexFromHexString(String) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getLowestFreeValence(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
The lowest free valence is the number of potential additional single bonded neighbours to reach the atom's lowest valence above or equal its current occupied valence.
- getManhattanBlockDistance(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
- getMapping(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
-
Returns the encoded reaction mapping.
- getMappingIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getMapToolColor() - Method in class com.actelion.research.share.gui.DrawConfig
- getMapToolColor() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getMarkushCount() - Method in class com.actelion.research.share.gui.editor.Model
- getMarkushStructure() - Method in class com.actelion.research.gui.JDrawArea
- getMarkushStructure() - Method in class com.actelion.research.share.gui.editor.Model
- getMask() - Method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- getMask() - Method in class org.openmolecules.chem.conf.gen.TorsionSetEliminationRule
- getMaster() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getMatch() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
- getMatches() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
- getMatches() - Method in class com.actelion.research.chem.mcs.SubStructSearchExhaustiveTreeWalker
- getMatchingTransform(PPTriangle, double[][]) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangle
- getMatchingTransforms(Map<Integer, ArrayList<PPTriangle>>, Map<Integer, ArrayList<PPTriangle>>, int, int) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangleMatcher
- getMatchList() - Method in class com.actelion.research.chem.SSSearcher
-
If the match count mode is one of cCountModeFirstMatch, cCountModeOverlapping, cCountModeRigorous then this method returns an arraylist of all counted matches, i.e.
- getMatchList() - Method in class com.actelion.research.chem.SSSearcherWithIndex
-
If the match count mode is one of cCountModeFirstMatch, cCountModeOverlapping, cCountModeRigorous then this method returns an arraylist of all counted matches, i.e.
- getMatrix(int[], int[]) - Method in class com.actelion.research.calc.Matrix
-
Get a submatrix.
- getMatrix(int[], int, int) - Method in class com.actelion.research.calc.Matrix
-
Get a submatrix.
- getMatrix(int, int, int[]) - Method in class com.actelion.research.calc.Matrix
-
Get a submatrix.
- getMatrix(int, int, int, int) - Method in class com.actelion.research.calc.Matrix
- getMatrixFromString(String, String) - Static method in class com.actelion.research.util.StringFunctions
- getMax() - Method in class com.actelion.research.calc.Matrix
- getMax(int) - Method in class com.actelion.research.calc.Matrix
-
get max value for that col.
- getMaxAtoms() - Method in class com.actelion.research.chem.Molecule
-
The currently defined maximum of atoms, which increases automatically when using high level construction methods and new atoms exceed the current maximum.
- getMaxBonds() - Method in class com.actelion.research.chem.Molecule
-
The currently defined maximum of bonds, which increases automatically when using high level construction methods and new bonds exceed the current maximum.
- getMaxDistInHist(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getMaxFreeValence(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getMaximumCapacityBondsInFragment() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- getMaximumCapacityBondsInFragment() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getMaximumCommonSubstructure(List<StereoMolecule>) - Method in class com.actelion.research.chem.mcs.MCSFunctions
- getMaximumDistanceInPPPoint(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getMaximumIonCharge(Molecule3D, int) - Static method in class com.actelion.research.chem.io.pdb.converter.BondsCalculator
- getMaximumNumberBondsInMolecule() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- getMaximumNumberBondsInMolecule() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getMaximumNumberBondsInMolecule() - Method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- getMaximumOverlap(List<String>, int) - Static method in class com.actelion.research.util.StringFunctions
-
Finds the maximum common String in all Strings.
- getMaximumSlope() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getMaximumValue() - Method in class com.actelion.research.calc.Matrix
- getMaximumX() - Method in class com.actelion.research.calc.histogram.Histogram
- getMaximumY() - Method in class com.actelion.research.calc.histogram.Histogram
- getMaxIndex() - Method in class com.actelion.research.calc.Matrix
- getMaxIndexNotZero(byte[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.DistHistHelper
- getMaxMin() - Method in class com.actelion.research.calc.Matrix
-
max and min vals for all cols
- getMaxNumUniqueFrags() - Method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- getMaxNumUniqueFrags(List<Point>) - Static method in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule
- getMaxOccBin(Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getMaxRow(int) - Method in class com.actelion.research.calc.Matrix
- getMaxRowIndex(int) - Method in class com.actelion.research.calc.Matrix
- getMaxRowIndexRND(int) - Method in class com.actelion.research.calc.Matrix
-
Shuffles the indices before searching the minimum.
- getMaxValence(int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getMaxValence(int) - Method in class com.actelion.research.chem.Molecule
-
This is the defined maximum valence (or set abnormal valence) corrected by atom charge or radical influences, e.g.
- getMaxValenceUncharged(int) - Method in class com.actelion.research.chem.Molecule
-
This is the defined maximum valence (or set abnormal valence) neglecting atom charge or radical influences, e.g.
- getMaxX() - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
- getMaxY() - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
- getMCS() - Method in class com.actelion.research.chem.mcs.MCS
- getMCS() - Method in class com.actelion.research.chem.mcs.MCSFast
- getMCS(Reaction, boolean[], SSSearcher) - Static method in class com.actelion.research.chem.reaction.CommonSubGraphHelper
- getMCSBondArray(boolean[], boolean[]) - Method in class com.actelion.research.chem.mcs.MCS
-
Calculates the bond arrays for molecule and fragment for their maximum common substructure.
- getMdltyp() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getMean() - Method in class com.actelion.research.calc.Matrix
- getMean() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getMean(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getMeanAngle(InventorAngle[], int) - Static method in class com.actelion.research.chem.coords.CoordinateInventor
- getMeanCol(int) - Method in class com.actelion.research.calc.Matrix
- getMeanCol(int, int[]) - Method in class com.actelion.research.calc.Matrix
- getMeanCols() - Method in class com.actelion.research.calc.Matrix
- getMeanCols(int[]) - Method in class com.actelion.research.calc.Matrix
- getMeanRow(int) - Method in class com.actelion.research.calc.Matrix
- getMeanRows() - Method in class com.actelion.research.calc.Matrix
- getMedian() - Method in class com.actelion.research.calc.Matrix
- getMedian(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getMedian(int) - Method in class com.actelion.research.calc.Matrix
- getMedian(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getMedianBin(byte[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.DistHistHelper
- getMedianCols() - Method in class com.actelion.research.calc.Matrix
- getMedianForDouble(List<Double>) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getMedianForInteger(List<Integer>) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getMedianForLong(List<Long>) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getMergedCopy() - Method in class com.actelion.research.chem.reaction.Reaction
-
Merges all reactants into one molecule and all products into another ad creates a new Reaction object from those.
- getMergeRows(Matrix) - Method in class com.actelion.research.calc.Matrix
- getMessage() - Method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- getMetalBondedConnAtoms(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- getMin() - Method in class com.actelion.research.calc.Matrix
- getMin(int) - Method in class com.actelion.research.calc.Matrix
- getMinColIndex(int) - Method in class com.actelion.research.calc.Matrix
- getMinDist(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getMinimumX() - Method in class com.actelion.research.calc.histogram.Histogram
- getMinMaxSimilarity(int[], int[]) - Static method in class com.actelion.research.calc.VectorSimilarity
- getMinOccBin(Matrix) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- getMinPos() - Method in class com.actelion.research.calc.Matrix
- getMinRow(int) - Method in class com.actelion.research.calc.Matrix
- getMinRowIndex(int) - Method in class com.actelion.research.calc.Matrix
- getMinRowIndexRND(int) - Method in class com.actelion.research.calc.Matrix
-
03.10.04 MvK Shuffles the indices before searching the minimum.
- getMinRows() - Method in class com.actelion.research.calc.Matrix
- getMinRowsPosCol() - Method in class com.actelion.research.calc.Matrix
- getMinX() - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
- getMinY() - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
- getMirror(Coordinates, Coordinates, Coordinates, Coordinates) - Static method in class com.actelion.research.chem.Coordinates
-
Get the mirror image of p through the plane defined by c1, c2, c3
- getMMFFMolecule() - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
- getMode() - Method in class com.actelion.research.gui.JDrawArea
- getMode() - Method in class com.actelion.research.share.gui.editor.Model
- getModeFlexophore() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- getModeFlexophore() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- getModel() - Method in class com.actelion.research.gui.CompoundCollectionPane
- getModRes() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getMol() - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- getMol() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getMol() - Method in class com.actelion.research.chem.shredder.Fragment
- getMolDistHist() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getMolecularPathCount(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Returns the number of paths of the given length (gives an idea of the number of branches)
- getMolecule() - Method in class com.actelion.research.chem.conf.Conformer
- getMolecule() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
The atoms of the ff molecule contain the corresponding PPNode indices in the first field of the PPP vector.
- getMolecule() - Method in class com.actelion.research.chem.io.CompoundFileParser
-
Either this method or getIDCode() and getCoordinates() must be overwritten!!!
- getMolecule() - Method in class com.actelion.research.chem.io.pdb.parser.Residue
- getMolecule() - Method in class com.actelion.research.chem.io.SDFileParser
- getMolecule() - Method in class com.actelion.research.chem.phesa.PheSAMolecule
- getMolecule() - Method in class com.actelion.research.chem.SSSearcherWithIndex
-
Returns the most recently defined molecule.
- getMolecule() - Method in class com.actelion.research.chem.StructureTransferData
- getMolecule() - Method in class com.actelion.research.gui.JDrawArea
- getMolecule() - Method in class com.actelion.research.gui.JStructureView
- getMolecule() - Method in class com.actelion.research.share.gui.editor.Model
- getMolecule() - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- getMolecule(int) - Method in class com.actelion.research.chem.ExtendedDepictor
- getMolecule(int) - Method in class com.actelion.research.chem.reaction.Reaction
- getMolecule(int) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- getMolecule(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- getMolecule(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCode
- getMolecule(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCodeWithName
- getMolecule(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.Molecule
- getMolecule(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.Native
- getMolecule(int) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- getMoleculeAt(Point2D, boolean) - Method in class com.actelion.research.share.gui.editor.Model
- getMoleculeBounds(int) - Method in class com.actelion.research.gui.JChemistryView
-
Returns the bounding rectangle of the indicated molecule, if multiple molecules are shown, e.g.
- getMoleculeColor() - Method in class com.actelion.research.chem.Molecule
-
cMoleculeColorDefault: atom coloring depends on atomic number.
- getMoleculeCount() - Method in class com.actelion.research.chem.ExtendedDepictor
- getMoleculeCount() - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- getMoleculeDepictor(int) - Method in class com.actelion.research.chem.ExtendedDepictor
- getMoleculeDepictor(int) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- getMoleculeForDisplay(int) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- getMoleculeForDisplay(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- getMoleculeName() - Method in class com.actelion.research.chem.io.CompoundFileParser
- getMoleculeName() - Method in class com.actelion.research.chem.io.DWARFileParser
- getMoleculeName() - Method in class com.actelion.research.chem.io.ODEFileParser
- getMoleculeName() - Method in class com.actelion.research.chem.io.SDFileParser
- getMoleculeRemovedUnrelatedAtoms() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getMolecules() - Method in class com.actelion.research.chem.reaction.Reaction
- getMoleculeTransferable() - Method in class com.actelion.research.gui.JChemistryView
- getMoleculeTransferable(Point) - Method in class com.actelion.research.gui.JStructureView
- getMolfile() - Method in class com.actelion.research.chem.MolfileCreator
-
If a pre-filled StringBuilder was passed to the constructor, then this returns the original content with the appended molfile.
- getMolfile() - Method in class com.actelion.research.chem.MolfileV3Creator
-
If a pre-filled StringBuilder was passed to the constructor, then this returns the original content with the appended molfile.
- getMolFile(boolean) - Method in class com.actelion.research.share.gui.editor.Model
- getMolGauss() - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- getMolweight() - Method in class com.actelion.research.chem.ExtendedMolecule
-
Calculates a rounded mass of the molecule
- getMostCentralRingSystem(StereoMolecule) - Static method in class com.actelion.research.chem.ScaffoldHelper
-
Creates most central ring system as new StereoMolecule from mol without touching mol.
- getMST() - Method in class com.actelion.research.calc.graph.MinimumSpanningTree
- getmTransformation() - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- getMtrix1() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getMtrix2() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getMtrix3() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getMurckoScaffold(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.ScaffoldHelper
-
Creates Murcko scaffold as new StereoMolecule from mol without touching mol.
- getMutatedSet(StereoMolecule, int, boolean, int) - Method in class com.actelion.research.chem.Mutator
- getName() - Method in class com.actelion.research.chem.conf.Conformer
- getName() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getName() - Method in class com.actelion.research.chem.Element
- getName() - Method in class com.actelion.research.chem.Molecule
-
Allows to set a molecule name or identifier, that is, for instance, written to or read from molfiles.
- getName() - Method in class com.actelion.research.chem.Molecule3D
- getName() - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- getName() - Method in class com.actelion.research.chem.reaction.Reaction
- getName() - Method in class com.actelion.research.chem.StructureInfo
- getName(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getNameIDs() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getNative() - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- getNative() - Method in class com.actelion.research.share.gui.Delegator
- getNative() - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- getNative() - Method in interface com.actelion.research.share.gui.editor.geom.StrokeLineCap
- getNaturalPercentage(int, int) - Static method in class com.actelion.research.chem.IsotopeHelper
- getNeededBits(int) - Static method in class com.actelion.research.chem.Canonizer
- getNeededNumberOfBondsInFragment(StereoMolecule) - Static method in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
- getNegativeNeighbourCount(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- getNegIonizableAtoms() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.IonizableGroupDetector2D
- getNeighbours() - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- getNeighbours(Coordinates[], double) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
-
Gets a Set of all neigbouring atoms.
- getNeighbours(Coordinates, double) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
-
Gets a Set of all neigbouring atoms.
- getNeighbours(Coordinates, double, boolean) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- getNeighbours(Coordinates, double, boolean, int) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
-
Gets a Set of all neigbouring atoms.
- getNeighbours(Molecule, int, double) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- getNeighbours(Molecule, int, double, boolean) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- getNew(int) - Method in class com.actelion.research.chem.properties.complexity.BitArray128Factory
- getNew(int) - Method in interface com.actelion.research.chem.properties.complexity.IBitArrayFactory
- getNewCompleteGraphMatcher() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- getNext4NeighboursTorus(int, int) - Method in class com.actelion.research.calc.Matrix
- getNext8NeighboursTorus(int, int) - Method in class com.actelion.research.calc.Matrix
- getNextColor() - Static method in class com.actelion.research.chem.reaction.MCSReactionMapper
- getNextConformer() - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
- getNextConformer() - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
-
Picks a new conformer from the conformer pool created by initializeConformers().
- getNextConformer(TorsionSet[]) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Creates the next random, likely or systematic new(!) conformer of the molecule that was passed when calling initializeConformers().
- getNextConformerAsMolecule(StereoMolecule) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Creates the next random, likely or systematic new(!) conformer of the molecule that was passed when calling initializeConformers().
- getNextEnumeration() - Method in class com.actelion.research.chem.MarkushStructure
-
After calling validate() this method may be called until null is returned to construct one by one a new representation of the Markush structure.
- getNextFieldData() - Method in class com.actelion.research.chem.io.SDFileParser
-
Returns the field data of the current record as one big String as it was read from the input file.
- getNextFileName(String) - Static method in class com.actelion.research.util.IO
-
Has to be the total path of the file or there will be errors.
- getNextMapNo() - Method in class com.actelion.research.share.gui.editor.Model
-
*********************************************************************************************************
- getNextMolecule() - Method in class com.actelion.research.chem.io.RDFileParser
-
RD-files may contains lists of molecules or lists of reactions.
- getNextMolFile() - Method in class com.actelion.research.chem.io.SDFileParser
-
Returns the molfile of the current record as one big String as it was read from the input file.
- getNextReaction() - Method in class com.actelion.research.chem.io.RDFileParser
-
RD-files may contains lists of molecules or lists of reactions.
- getNextTautomer(StereoMolecule) - Method in class com.actelion.research.chem.TautomerHelper
- getNextTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
-
Creates the next set of torsion indexes to be tried by the ConformerGenerator.
- getNMovables() - Method in class com.actelion.research.chem.Molecule3D
- getNode() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- getNode(int) - Method in interface com.actelion.research.chem.descriptor.flexophore.IMolDistHist
- getNode(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
-
!Slow method, it has to iterate through a loop to find the node in the array!
- getNode(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getNodeA() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- getNodeB() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- getNodeC() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- getNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getNodes() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getNodes(Collection<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getNodesFromEdges(List<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getNodesQuery() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- getNonCachableCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- getNonHydrogenNeighbourCount(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
This method returns the non-hydrogen neighbour count of atom.
- getNoOfKeys() - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getNorm() - Method in class com.actelion.research.util.datamodel.ByteVec
- getNorm() - Method in class com.actelion.research.util.datamodel.IntVec
- getNorm() - Method in class com.actelion.research.util.DoubleVec
- getNorm(double[]) - Static method in class com.actelion.research.chem.optimization.OptimizerLBFGS
- getNormalized(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getNormalizedAtomX(int) - Method in class com.actelion.research.chem.coords.InventorTemplate
- getNormalizedAtomY(int) - Method in class com.actelion.research.chem.coords.InventorTemplate
- getNormalizedMatrix() - Method in class com.actelion.research.calc.Matrix
- getNormalizedMatrix(Matrix) - Method in class com.actelion.research.calc.Matrix
- getNormalizedTorsionIndex(String, double) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Normalizes a torsion angle considering the fragments symmetry type by returning the lowest symmetrically equivalent torsion that is >= 0.
- getNormSq(double[]) - Static method in class com.actelion.research.chem.optimization.OptimizerLBFGS
- getNoStereoCode(int, boolean) - Method in interface com.actelion.research.chem.StructureSearchDataSource
-
Returns a hash code representing the structure or its largest fragment without any stereo information.
- getNoStereoHash(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
-
Returns a hash code representing the reaction without any stereo information.
- getNoStereoHash(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.CanonizerUtil
- getNoStereoTautomerCode(int, boolean) - Method in interface com.actelion.research.chem.StructureSearchDataSource
-
Returns a hash code representing the generic tautomer of the structure or its largest fragment with the stereo information removed before creating the generic tautomer.
- getNoStereoTautomerHash(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.CanonizerUtil
- getNumAcidicOxygen(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumAlcoholicOxygen(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumAliphaticRingAtoms(ExtendedMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumAmide(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumArguments() - Method in class com.actelion.research.util.CommandLineParser
- getNumAromaticAtoms(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumArylAmine(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumBasicNitrogen(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumberAbove(int[], int) - Static method in class com.actelion.research.util.datamodel.IntVec
- getNumberOfAtomsBetweenBonds(Molecule3D, int, int[][]) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Computes a matrix of distances between all the bonds in the graph.
- getNumberOfBondsBetweenAtoms(Molecule3D, int, int[][]) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Computes a matrix of distances between all the atoms in the graph.
- getNumberOfBondsBetweenAtoms(StereoMolecule, int, int[][]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
-
From Joel Freyss developed for the FFMolecule Computes a matrix of distances between all the atoms in the graph.
- getNumberOfHydrogens(StereoMolecule) - Static method in class com.actelion.research.chem.contrib.HydrogenHandler
- getNumBins() - Method in class com.actelion.research.calc.histogram.Histogram
- getNumBondsAtMaximumFrequency() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getNumBondsAtMaxSlope() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getNumBondsInFragment() - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- getNumBytesEntry() - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- getNumBytesEntry() - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- getNumCarbonAtoms(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumCarboxy(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumCExclusiveNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getNumCyanoGroups(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
-
Counts cyano and iso-cyano
- getNumElements() - Method in class com.actelion.research.calc.Matrix
- getNumElementsEqual(double) - Method in class com.actelion.research.calc.Matrix
- getNumElementsLarger(double) - Method in class com.actelion.research.calc.Matrix
- getNumHeavyAtoms(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumHeteroAromaticAtoms(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumHeteroAtoms(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumHeteroNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getNumIndices() - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- getNumInevitablePharmacophorePoints() - Method in interface com.actelion.research.chem.descriptor.flexophore.IMolDistHist
- getNumInevitablePharmacophorePoints() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
-
Only for interface compliance needed.
- getNumInevitablePharmacophorePoints() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- getNumIsopropyl(ExtendedMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNummdl() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getNumNitroGroupN(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumOverlappingIndices(SubGraphIndices) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- getNumPPNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getNumPPNodes() - Method in interface com.actelion.research.util.graph.complete.ICompleteGraph
- getNumQueryAtoms(ExtendedMolecule, int[]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumRegressionPoints() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- getNumSubstructure(StereoMolecule, String) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumSulfOxyGroups(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumThioEther(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getNumWildcards(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getObjectiveCompleteGraph() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- getObjectiveCompleteGraph() - Method in interface com.actelion.research.chem.descriptor.flexophore.IDescriptorHandlerFlexophore
- getObjectiveCompleteGraph() - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- getObsolete() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getOccupiedValence(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
The sum of bond orders of explicitly connected neighbour atoms including explicit hydrogen.
- getOccupiedValence(int) - Method in class com.actelion.research.chem.Molecule
-
The sum of bond orders of explicitly connected neighbour atoms.
- getOccupiedValence(int) - Method in class com.actelion.research.chem.Molecule3D
- getOccurencesArray() - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
- getOffsetX() - Method in class com.actelion.research.chem.DepictorTransformation
- getOffsetY() - Method in class com.actelion.research.chem.DepictorTransformation
- getOneConformer(StereoMolecule) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Fills all free valences of mol with explicit hydrogens and tries to create a reasonable conformer by starting with the most likely torsion set.
- getOneConformerAsMolecule(StereoMolecule) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Fills all free valences of mol with explicit hydrogens and tries to create a reasonable conformer by starting with the most likely torsion set.
- getOrderNumber() - Method in class com.actelion.research.chem.Element
- getOrganicFunctionalGroupCounts() - Method in class com.actelion.research.chem.reaction.FunctionalGroupClassifier
- getOriginalAtomIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- getOriginalAtomIndex() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- getOrigX1() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getOrigX2() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getOrigX3() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getOverlap(int[], int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getOverlap(Molecule3D, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getOverlap(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- getPaint() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getPairPotentials() - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- getParent() - Method in class com.actelion.research.gui.dock.TreeElement
- getParsed(Vector<String>) - Static method in class com.actelion.research.calc.Matrix
-
Parses an vector with Strings and converts it to a Matrix.
- getPartial(int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
-
Gets the partial charge of a bond type and its two atom types.
- getPartialCharge(int) - Method in class com.actelion.research.chem.Molecule3D
- getPath(int[], int, int, int, boolean[]) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Locates and returns the shortest path between atoms atom1 and atom2
- getPathBonds(int[], int[], int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Finds bonds of a path that is defined by an atom sequence.
- getPathLength(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Calculates the length of the shortest path between atoms atom1 and atom2
- getPathLength(int, int, int, boolean[]) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Calculates the length of the shortest path between atoms atom1 and atom2, which is not larger than maxLength and avoids atoms indicated by neglectAtom.
- getPathsFromHeadNode(int, List<Set<Integer>>, Set<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getPbci(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Charge
- getPenStyle() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- getPercentageOverlap(DistHist, int, int, DistHist, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.HistogramMatchCalculator
- getPercentileFromSorted(double[], double) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getPercentileFromSorted(double[], double) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getPercentileFromSorted(double[], double, int, int) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getPercentileFromSorted(float[], double) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getPercentileFromSorted(float[], double, int, int) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getPercentileFromSorted(int[], double) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getPercentileFromSorted(List<Double>, double) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getPercentileFromSortedInt(List<Integer>, double) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getPercentileFromSortedLong(List<Long>, double) - Static method in class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- getPeripherySimilarity() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- getPeripherySimilarity(long[], long[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- getPermutationCount() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- getPermutations(int[], int) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
- getPharmacophorePoint() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
- getPharmacophorePoints(StereoMolecule) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- getPivot() - Method in class com.actelion.research.calc.LUDecomposition
-
Return pivot permutation vector
- getPlainHydrogens(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- getPointsBetween(Point, Point) - Static method in class com.actelion.research.util.PointUtils
- getPolarAtomTypeCount() - Static method in class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
- getPolarAtomTypeCounts(StereoMolecule) - Method in class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
- getPolarSurfaceArea() - Method in class com.actelion.research.chem.PropertyCalculator
- getPolarSurfaceAreaDetail() - Method in class com.actelion.research.chem.PropertyCalculator
- getPolled() - Method in class com.actelion.research.util.Pipeline
- getPopupProvider() - Method in class com.actelion.research.gui.dock.Dockable
- getPopupProvider() - Method in class com.actelion.research.gui.dock.DockableHeader
- getPopupProvider() - Method in class com.actelion.research.gui.dock.HeaderMouseAdapter
- getPose() - Method in class com.actelion.research.chem.docking.DockingEngine.DockingResult
- getPosIonizableAtoms() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.IonizableGroupDetector2D
- getPositionInContainer() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- getPositionInContainer() - Method in class com.actelion.research.util.graph.complete.AMemorizedObject
- getPositions(String) - Static method in class com.actelion.research.chem.forcefield.mmff.Sdf
-
Parses a SDF file to extract the positions of each atom.
- getPotentialConformerCount() - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Calculates the potential count of conformers by multiplying degrees of freedom (torsions per rotatable bond & rigid fragment multiplicities).
- getPPGaussians() - Method in class com.actelion.research.chem.phesa.MolecularVolume
- getPPP(int) - Method in class com.actelion.research.chem.Molecule3D
- getPPPoints(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- getPpWeight() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- getPrefactor(int, int) - Method in class com.actelion.research.chem.phesa.QuickMathCalculator
- getPreviousAlignment() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- getPreviousConformerContribution() - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
With best current knowledge about colliding torsion combinations and based on the individual frequencies of currently active torsions this method returns the conformers's overall contribution to the total set of non colliding conformers.
- getPreviousPheSAResult() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
-
additional output: element 0: total similarity (identical to getSimilarity(...)) element 1: pharmacophore similarity element 2: contribution to similarity that originates from additional volumes (incl/excl)
- getPriority() - Method in class com.actelion.research.chem.coords.FragmentAssociation
- getProbabilityFromType(long) - Method in class com.actelion.research.chem.AtomTypeList
- getProduct(int) - Method in class com.actelion.research.chem.reaction.Reaction
- getProductDescriptor(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
- getProductDescriptor(int) - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- getProductIDCodes() - Method in class com.actelion.research.chem.reaction.Reactor
- getProducts() - Method in class com.actelion.research.chem.reaction.Reaction
- getProducts() - Method in class com.actelion.research.chem.reaction.Reactor
- getProducts(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
- getProductsBoundingRect(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
- getProtAtomRecords() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getPseudoEZGroup(int) - Method in class com.actelion.research.chem.Canonizer
-
If mMode includes CREATE_PSEUDO_STEREO_GROUPS, then this method returns this bond's relative stereo feature group number provided this bond is a pseudo stereo bond, i.e.
- getPseudoStereoGroupCount() - Method in class com.actelion.research.chem.Canonizer
-
If mMode includes CREATE_PSEUDO_STEREO_GROUPS, then this method returns the number of independent relative stereo feature groups.
- getPseudoTHGroup(int) - Method in class com.actelion.research.chem.Canonizer
-
If mMode includes CREATE_PSEUDO_STEREO_GROUPS, then this method returns this atom's relative stereo feature group number provided this atom is a pseudo stereo center, i.e.
- getPurity() - Method in class com.actelion.research.chem.StructureInfo
- getPythag(double, double) - Static method in class com.actelion.research.calc.Matrix
-
pythag computes sqrt(a^2 + b^2) without destructive underflow or overflow.
- getPythag2(double, double) - Static method in class com.actelion.research.calc.Matrix
- getQ0() - Method in class com.actelion.research.chem.phesa.Quaternion
- getQ1() - Method in class com.actelion.research.chem.phesa.Quaternion
- getQ2() - Method in class com.actelion.research.chem.phesa.Quaternion
- getQ3() - Method in class com.actelion.research.chem.phesa.Quaternion
- getQuery() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getQuery() - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- getRandom() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategyRandom
- getRandom(int, int) - Static method in class com.actelion.research.util.StringFunctions
- getRandomRotation() - Static method in class com.actelion.research.chem.phesa.Quaternion
-
get a random quaternion, from: https://stackoverflow.com/questions/31600717/how-to-generate-a-random-quaternion-quickly
- getRangeStatistics(MolDistHist) - Static method in class com.actelion.research.chem.descriptor.flexophore.DistHistHelper
- getRatioCoveredBonds() - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- getRatioNonSymmetricAtoms() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getRatioSymmetricAtoms(StereoMolecule) - Static method in class com.actelion.research.chem.properties.complexity.SymmetryCalculator
- getRatioUsedBondsUpToMaxFreq() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getReactant(int) - Method in class com.actelion.research.chem.reaction.Reaction
- getReactantCount() - Method in class com.actelion.research.share.gui.editor.Model
- getReactantDescriptor(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
- getReactantDescriptor(int) - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- getReactants() - Method in class com.actelion.research.chem.reaction.Reaction
- getReactants(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
- getReactantsBoundingRect(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
- getReaction() - Method in class com.actelion.research.chem.ExtendedDepictor
- getReaction() - Method in class com.actelion.research.gui.JDrawArea
- getReaction() - Method in class com.actelion.research.gui.JDrawDialog
- getReaction() - Method in class com.actelion.research.gui.JEditableChemistryView
- getReaction() - Method in class com.actelion.research.share.gui.editor.Model
- getReaction(File) - Method in class com.actelion.research.chem.io.RXNFileParser
- getReaction(File, boolean) - Method in class com.actelion.research.chem.io.RXNFileParser
- getReaction(String) - Method in class com.actelion.research.chem.io.RXNFileParser
- getReaction(String, boolean) - Method in class com.actelion.research.chem.io.RXNFileParser
- getReactionAndDrawings() - Method in class com.actelion.research.gui.JDrawArea
- getReactionAndDrawings() - Method in class com.actelion.research.gui.JDrawDialog
- getReactionCenterAtoms(int, boolean[], boolean[], int[]) - Method in class com.actelion.research.chem.reaction.Reaction
-
Fills an array mapping on the atoms for the given molecule of this reaction.
- getReactionCenterMapNos() - Method in class com.actelion.research.chem.reaction.Reaction
-
This method determines the largest mapping number in use (maxMapNo), creates a boolean array[maxMapNo+1], and within this array flags every mapping number that refers to atoms, which change bonds in the course of the reaction.
- getReactionCenterSimilarity() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- getReactionCenterSimilarity(long[], long[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- getReactionCode(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
-
Returns the reaction idcode.
- getReactionCount() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
-
Returns the search type as integer including mode flags.
- getReactionDescriptor(int) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
- getReactionDescriptor(int) - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- getReactionTransferable() - Method in class com.actelion.research.gui.JChemistryView
- getReactionType(Reaction) - Static method in class com.actelion.research.chem.ChemistryHelper
- getRearAtom(int) - Method in class com.actelion.research.chem.conf.TorsionDetail
-
Returns that neighbor atom of a central atom that lies in the rotatable bond axis.
- getRearAtoms() - Method in class com.actelion.research.chem.conf.BondRotationHelper
- getRecentException() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- getReceptorAtomTypes(StereoMolecule) - Static method in class com.actelion.research.chem.docking.DockingEngine
- getRecordCount() - Method in class com.actelion.research.chem.io.CompoundFileHelper
- getRefConformerIndex() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangleMatcher.AlignmentResult
- getReferenceAtom(int) - Method in class com.actelion.research.chem.conf.TorsionDetail
-
Returns the reference atom of one part of the torsion fragment.
- getReferenceVector() - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- getRefMol() - Method in class com.actelion.research.chem.phesa.PheSAAlignment.PheSAResult
- getRefMolGauss() - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- getRelativeWeight() - Method in class com.actelion.research.chem.MolecularFormula
- getRelevance() - Method in class org.openmolecules.chem.conf.gen.RotatableBond
-
The relevance of a rotatable bond and its torsion angle for creating substantially different conformers depends on how close the bond is to the center of the molecule.
- getRelevance(StereoMolecule, boolean[]) - Static method in class com.actelion.research.chem.conf.TorsionRelevanceHelper
-
The relevance of a rotatable bond and its torsion angle for creating substantially different conformers depends on how close the bond is to the center of the molecule.
- getRelevance(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.conf.TorsionRelevanceHelper
-
The relevance of a rotatable bond and its torsion angle for creating substantially different conformers depends on how close the bond is to the center of the molecule.
- getRelMaxDistInHist() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
-
To get the distance in Angstrom the relative distance has to be multiplied with the histogram range
CGMult.RANGE_HISTOGRAM
. - getRelMaxDistInHist(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
-
To get the distance in Angstrom the relative distance has to be multiplied with the histogram range
CGMult.RANGE_HISTOGRAM
. - getRelMaxDistInHist(int, int) - Method in interface com.actelion.research.chem.descriptor.flexophore.IMolDistHist
- getRemainingStructure(StereoMolecule, StereoMolecule) - Method in class com.actelion.research.chem.mcs.MCSFunctions
- getRemark(int) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getRemark0() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getRemark1() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getRemark2() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getRemark3() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getRemarks() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getRenderingHint(RenderingHints.Key) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getRenderingHints() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getREntries() - Method in class com.actelion.research.chem.reaction.ClassificationData
- getRequestCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- getResiduals() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getResiduals() - Method in class com.actelion.research.util.SmoothingSplineInterpolator
- getResname() - Method in class com.actelion.research.chem.io.pdb.parser.Residue
- getResName() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getResnum() - Method in class com.actelion.research.chem.io.pdb.parser.Residue
- getResNum() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getResolution() - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
- getResSequence(int) - Method in class com.actelion.research.chem.Molecule3D
- getRetinaScaleFactor() - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
-
Macintosh retina display support for Java 7 and newer.
- getRetronDescriptor(int) - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- getRevdat() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getRGroup(int) - Method in class com.actelion.research.chem.MarkushStructure
- getRGroupCount() - Method in class com.actelion.research.chem.MarkushStructure
- getRightChild() - Method in class com.actelion.research.gui.dock.TreeFork
- getRingAtoms() - Method in class com.actelion.research.chem.coords.InventorChain
- getRingAtoms(int) - Method in class com.actelion.research.chem.RingCollection
- getRingBonds() - Method in class com.actelion.research.chem.coords.InventorChain
- getRingBonds(int) - Method in class com.actelion.research.chem.RingCollection
- getRings(Molecule3D, List<int[]>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getRingsAccurate(Molecule3D, List<int[]>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Find the smallest covering set of rings for the Molecule.
- getRingSet() - Method in class com.actelion.research.chem.ExtendedMolecule
- getRingSetSimple() - Method in class com.actelion.research.chem.ExtendedMolecule
- getRingsFast(Molecule3D, List<int[]>) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Find the list of rings for the Molecule.
- getRingSize(int) - Method in class com.actelion.research.chem.RingCollection
- getRingSizeAdjust(int) - Method in class com.actelion.research.chem.AtomTypeList
- getRMS(double[]) - Static method in class com.actelion.research.chem.optimization.OptimizerLBFGS
- getRmsd(Coordinates[], Coordinates[]) - Static method in class com.actelion.research.chem.Coordinates
- getRmsd(Coordinates[], Coordinates[], int) - Static method in class com.actelion.research.chem.Coordinates
- getRMSD() - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
- getRMSD(ClusterNode, DistHist) - Static method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
- getRND(int) - Static method in class com.actelion.research.util.datamodel.IntVec
- getRND(int, int) - Static method in class com.actelion.research.calc.Matrix
- getRole() - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- getRotatableBondCount() - Method in class com.actelion.research.chem.ExtendedMolecule
-
Simple method to calculate rotatable bonds.
- getRotatableBondCount() - Method in class com.actelion.research.chem.PropertyCalculator
- getRotatableBondCount() - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
After calling initializeConformers() this method returns the number of rotatable bonds, which are used to separate the molecule into rigid fragments.
- getRotatableBonds() - Method in class com.actelion.research.chem.conf.BondRotationHelper
- getRotatableBondWeights(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.conf.TorsionDescriptor
-
The relevance of a rotatable bond and its torsion angle for creating substantially different conformers depends on how close the bond is to the center of the molecule.
- getRotatedCenter(double[][], double, double[]) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getRotatedDirectionality(double[][], double) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
- getRotationCenters() - Method in class com.actelion.research.chem.conf.BondRotationHelper
- getRotationMatrix(double, Coordinates, double[][]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- getRotMatrix() - Method in class com.actelion.research.chem.phesa.Quaternion
- getRotMatrix(Coordinates, double, double[][]) - Static method in class com.actelion.research.chem.phesaflex.MathHelper
- getRotMatrixDerivative(Coordinates, double, Coordinates[][]) - Static method in class com.actelion.research.chem.phesaflex.MathHelper
- getRow() - Method in class com.actelion.research.chem.io.DWARFileParser
-
Returns the entire line containing all row data
- getRow(int) - Method in class com.actelion.research.calc.Matrix
-
Flat copy.
- getRowAsFloat(int) - Method in class com.actelion.research.calc.Matrix
- getRowAsList(int) - Method in class com.actelion.research.calc.Matrix
- getRowCopy(int) - Method in class com.actelion.research.calc.Matrix
- getRowCount() - Method in class com.actelion.research.chem.io.CompoundFileParser
-
Depending on data source returns the total row count or -1 if unknown
- getRowCount() - Method in class com.actelion.research.chem.io.DWARFileParser
- getRowCount() - Method in class com.actelion.research.chem.io.ODEFileParser
- getRowCount() - Method in class com.actelion.research.chem.io.RDFileParser
-
Only accurate if getFieldNames() or getFieldNames(int) was called earlier and if the number of records of the SD-file is smaller than the number of records that were examined within the the getFieldNames() method.
- getRowCount() - Method in class com.actelion.research.chem.io.SDFileParser
-
Only accurate if getFieldNames() or getFieldNames(int) was called earlier and if the number of records of the SD-file is smaller than the number of records that were examined within the the getFieldNames() method.
- getRowCount() - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
-
This is the total number of records, whether they qualify for a structure search or not.
- getRowCount() - Method in interface com.actelion.research.chem.StructureSearchDataSource
-
This is the total number of records, whether they qualify for a structure search or not.
- getRowDim() - Method in class com.actelion.research.calc.Matrix
- getRowName(int) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- getRows() - Method in class com.actelion.research.util.datamodel.table.TableModelString
- getRRefuncName(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getRRxnDef(int, int, int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getRRxnDelta(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getRRxnFGroups(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getRRxnMasks(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getRRxnSymmetric(int) - Method in class com.actelion.research.chem.reaction.ClassificationData
- getRuleList() - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- getRuleStrain(int) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- getRuleType() - Method in class org.openmolecules.chem.conf.so.AxialStereoRule
- getRuleType() - Method in class org.openmolecules.chem.conf.so.ConformationRule
- getRuleType() - Method in class org.openmolecules.chem.conf.so.DistanceRule
- getRuleType() - Method in class org.openmolecules.chem.conf.so.PlaneRule
- getRuleType() - Method in class org.openmolecules.chem.conf.so.StraightLineRule
- getRuleType() - Method in class org.openmolecules.chem.conf.so.TetrahedralStereoRule
- getRuleType() - Method in class org.openmolecules.chem.conf.so.TorsionRule
- getRXNfile() - Method in class com.actelion.research.chem.io.RXNFileCreator
- getRXNfile() - Method in class com.actelion.research.chem.io.RXNFileV3Creator
- getScale1() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getScale2() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getScale3() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getScaleFactor() - Static method in class com.actelion.research.gui.hidpi.HiDPIUtil
- getScaleFactor(Graphics2D) - Static method in class com.actelion.research.gui.hidpi.HiDPIUtil
- getScaling() - Method in class com.actelion.research.chem.DepictorTransformation
- getScalingFactor() - Method in class com.actelion.research.chem.MolfileV3Creator
- getScore() - Method in class com.actelion.research.chem.docking.DockingEngine.DockingResult
- getScore() - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- getScore() - Method in class com.actelion.research.chem.docking.scoring.ChemPLP
- getScore() - Method in class com.actelion.research.chem.docking.scoring.IdoScore
- getScore() - Method in class com.actelion.research.chem.mcs.MCS
-
Calculates the score by bonds_mcs/Max(bonds_mol, bonds_frag)
- getScore() - Method in class com.actelion.research.chem.mcs.MCSFast
- getScore() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- getScore() - Method in class com.actelion.research.util.datamodel.ScorePoint
- getScore(StereoMolecule, StereoMolecule) - Method in class com.actelion.research.chem.mcs.MCSFunctions
- getScoreFracBitsCommonQuery(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
(sum bits set common) / (sum bits set in query)
- getScoreFracBitsInCommonBitWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
(sum bits set common) / (sum bits set in both)
- getScoreQueryInBase(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- getScoreQueryInBaseBitWise(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
-
(sum bits set only in query) / (sum bits set in query)
- getScoreQueryInBaseBitWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- getScoreQueryInBaseByteWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- getSelectedAtom() - Method in class com.actelion.research.share.gui.editor.Model
- getSelectedBond() - Method in class com.actelion.research.share.gui.editor.Model
- getSelectedCopy(StereoMolecule) - Method in class com.actelion.research.share.gui.editor.Model
- getSelectedDockable() - Method in class com.actelion.research.gui.dock.JDockingPanel
-
Returns the currently active Dockable, i.e.
- getSelectedDrawingObject() - Method in class com.actelion.research.share.gui.editor.Model
- getSelectedReaction() - Method in class com.actelion.research.share.gui.editor.Model
- getSelectionColor() - Method in class com.actelion.research.share.gui.DrawConfig
- getSelectionColor() - Method in class com.actelion.research.share.gui.editor.geom.GeomFactory
- getSelfAtomOverlap(MolecularVolume) - Method in class com.actelion.research.chem.phesa.PheSAAlignment
-
calculate the self-overlap of the base molecule
- getSelfAtomOverlapFit() - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- getSelfAtomOverlapRef() - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- getSelfPPOverlap(MolecularVolume) - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- getSelfPPOverlapFit() - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- getSelfPPOverlapRef() - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- getSEQADV() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getSEQRES() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getSerialId() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getSharedRing(int, int) - Method in class com.actelion.research.chem.RingCollection
-
brute force method to check, whether and which ring is shared by two bonds
- getSheet() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getShift() - Method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyShift
- getShiftVector() - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- getShortName() - Method in class com.actelion.research.chem.Molecule3D
- getSigma() - Method in class com.actelion.research.util.SmoothingSplineInterpolator
- getSim() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
- getSim() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
- getSim() - Method in class com.actelion.research.chem.phesa.PheSAAlignment.PheSAResult
- getSimilarity() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangleMatcher.AlignmentResult
- getSimilarity() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- getSimilarity(byte[], byte[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- getSimilarity(int[][], int[][]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- getSimilarity(int[], int[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
- getSimilarity(int[], int[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
- getSimilarity(int[], int[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedPharmSphere
- getSimilarity(int[], int[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
- getSimilarity(int[], int[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPharmPath
- getSimilarity(long[], long[]) - Method in class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP
- getSimilarity(long[], long[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
- getSimilarity(long[], long[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
- getSimilarity(long[], long[]) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- getSimilarity(DistHist, int, int, DistHist, int, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.HistogramMatchCalculator
- getSimilarity(IPPNode, IPPNode) - Method in interface com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.IPPNodeSimilarity
- getSimilarity(IPPNode, IPPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- getSimilarity(PharmacophoreTree, PharmacophoreTree) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- getSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
- getSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
- getSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- getSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
- getSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
- getSimilarity(IPharmacophorePoint) - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
- getSimilarity(PPGaussian) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
- getSimilarity(PPGaussian, Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
- getSimilarity(PheSAMolecule, PheSAMolecule) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
-
calculates the Shape- and/or Pharmacophore similarity of a query molecule with a base molecule
- getSimilarity(StereoMolecule, StereoMolecule, DescriptorHandler) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getSimilarity(SolutionCompleteGraph) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getSimilarity(SolutionCompleteGraph) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- getSimilarity(Object, Object) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- getSimilarity(Collection<PharmacophoreNode>, Collection<PharmacophoreNode>) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- getSimilarity(Collection<Integer>, Collection<Integer>, List<PharmacophoreNode>, List<PharmacophoreNode>) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- getSimilarity(T, T) - Method in interface com.actelion.research.chem.descriptor.ISimilarityCalculator
- getSimilarityAngleCosine(int[], int[]) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getSimilarityBytewiseOverlap(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
- getSimilarityExtraCarbonConsideration(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- getSimilarityHardMatchAverage(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- getSimilarityHardMatchMultiplicative(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- getSimilarityHardMatchOptimistic(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- getSimilarityHistogram(int, int, int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getSimilarityHistogram(int, int, int, int) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- getSimilarityList(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- getSimilarityMappingNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getSimilarityNode(int) - Method in class com.actelion.research.chem.descriptor.flexophore.ModelSolutionSimilarity
- getSimilarityNodes(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getSimilarityNodes(IPPNode, IPPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- getSimilarityNodes(IPPNode, IPPNode) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- getSimilaritySimple(PPNode, PPNode) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- getSimilarityTanimoto(int[], int[]) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getSimilarityTanimoto(long[], long[]) - Static method in class com.actelion.research.chem.SSSearcherWithIndex
- getSimilarityTanimoto(long[], long[], int, int) - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- getSimilarityThreshold() - Method in class com.actelion.research.chem.StructureSearchSpecification
- getSimilars(int) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.InteractionTypeMap
- getSimpleAtomicNoCodeString(int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- getSingularValues() - Method in class com.actelion.research.calc.SingularValueDecomposition
-
Return the one-dimensional array of singular values
- getSite(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getSiteIDs() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getSize() - Method in class com.actelion.research.chem.conf.Conformer
- getSize() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
- getSize() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- getSize() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getSize() - Method in class com.actelion.research.chem.prediction.IncrementTable
- getSize() - Method in class com.actelion.research.chem.prediction.ParameterizedStringList
- getSize() - Method in class com.actelion.research.chem.RingCollection
- getSize() - Method in class com.actelion.research.chem.shredder.Fragment
- getSize() - Method in class com.actelion.research.chem.SortedStringList
- getSize() - Method in class com.actelion.research.chem.TextDrawingObject
- getSize() - Method in interface com.actelion.research.gui.CompoundCollectionModel
- getSize() - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- getSize() - Method in class com.actelion.research.util.ErrorHashMap
- getSize() - Method in class com.actelion.research.util.IntQueue
- getSize1() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
- getSize2() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
- getSizeAfterLastBitSet() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- getSizeAfterLastBitSet() - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- getSizeArrayLIV() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- getSizeArrayLIV() - Static method in class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
- getSizeBinaryArray() - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- getSizeBinaryArray() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getSizeBytes() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getSizeBytes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- getSizeForBits(int) - Static method in class com.actelion.research.util.datamodel.IntVec
- getSizeHeap() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- getSizes() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
- getSkinnable() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- getSlope() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getSlope() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- getSlopeFragments() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- getSlopeR2() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- getSmallerSideAtomCount() - Method in class org.openmolecules.chem.conf.gen.RotatableBond
- getSmallerSideAtomLists() - Method in class com.actelion.research.chem.conf.BondRotationHelper
- getSmallestRingsOfAtom(RingCollection, int) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
- getSmiles() - Method in class com.actelion.research.chem.IsomericSmilesCreator
- getSmiles() - Method in class com.actelion.research.chem.properties.fractaldimension.InputObjectFracDimCalc
- getSmiles() - Method in class com.actelion.research.share.gui.editor.Model
- getSmoothing() - Method in class com.actelion.research.util.SmoothingSplineInterpolator
- getSolution() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
-
The index is the index of the node in the query molecule.
- getSorted() - Method in class com.actelion.research.calc.Matrix
-
Sorts the row of the matrix according the compareTo(...) function in DoubleVec
- getSorted(int) - Method in class com.actelion.research.util.UniqueList
- getSortedIndex(T) - Method in class com.actelion.research.util.UniqueList
- getSortedListIndex(String) - Method in class com.actelion.research.chem.UniqueStringList
- getSortedStringAt(int) - Method in class com.actelion.research.chem.UniqueStringList
- getSource() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getSpecialFieldData(int) - Method in class com.actelion.research.chem.io.DWARFileParser
- getSpecialFieldIndex(String) - Method in class com.actelion.research.chem.io.DWARFileParser
- getSpecialFieldMap() - Method in class com.actelion.research.chem.io.DWARFileParser
-
Returns a columnName->SpecialField map of all non-alphanumerical columns.
- getSpline() - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
- getSplit() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getSplittedOverlappingText(List<String>, int, int) - Static method in class com.actelion.research.util.StringFunctions
-
Generates a list with overlap
- getSpread(byte[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.DistHistHelper
- getSprsde() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getSQRT() - Method in class com.actelion.research.calc.Matrix
- getSSBond() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getStandardDeviation() - Method in class com.actelion.research.calc.Matrix
- getStandardDeviation(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getStandardDeviationCols() - Method in class com.actelion.research.calc.Matrix
- getStandardized() - Method in class com.actelion.research.calc.Matrix
-
Get the standard scores, also known as z-scores.
- getStandardized(String, String, int) - Static method in class com.actelion.research.chem.MoleculeStandardizer
-
Under normal circumstances, one should never need to standardize a molecule from an idcode, because molecules should be standardized before generating the canonical encoding.
- getState() - Method in class com.actelion.research.chem.docking.LigandPose
- getState() - Method in interface com.actelion.research.chem.optimization.Evaluable
- getState() - Method in class com.actelion.research.chem.phesa.EvaluableOverlap
- getState() - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- getState(double[]) - Method in class com.actelion.research.chem.docking.LigandPose
- getState(double[]) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
- getState(double[]) - Method in class com.actelion.research.chem.phesa.EvaluableOverlap
- getState(double[]) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- getStbnType(Tables, MMFFMolecule, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Angle
-
Given three atoms which form an angle, returns the MMFF stretch-bend type of the angle.
- getStdDev(int) - Method in class com.actelion.research.chem.conf.BondLengthSet
- getStdDevFromCovalentRadii(StereoMolecule, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
-
Returns an the standard deviation of bond lengths from bonds with similar characteristics from crystallographic data.
- getStereoBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Checks whether at least one of the connected bonds is a stereo bond.
- getStereoCenterCount() - Method in class com.actelion.research.chem.PropertyCalculator
- getStereoCenterCount() - Method in class com.actelion.research.chem.StereoMolecule
- getStereoProblem(int) - Method in class com.actelion.research.chem.Molecule
-
The stereo problem flag is set by the stereo recognition (available equal/above helper level cHelperParities) if an atom has over- or under-specified stereo bonds attached, i.e.
- getStrain(double[]) - Method in class com.actelion.research.chem.docking.scoring.IdoScore
- getString() - Method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- getString() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getString(int) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- getString(String, String, String) - Static method in class com.actelion.research.util.StringFunctions
- getString(String, String, String, int) - Static method in class com.actelion.research.util.StringFunctions
- getStringAt(int) - Method in class com.actelion.research.chem.prediction.ParameterizedStringList
- getStringAt(int) - Method in class com.actelion.research.chem.SortedStringList
- getStringAt(int) - Method in class com.actelion.research.chem.UniqueStringList
- getStringFromRegEx(String, String) - Static method in class com.actelion.research.util.StringFunctions
- getStringTypeAt(int) - Method in class com.actelion.research.chem.prediction.ParameterizedStringList
- getStringWidth(String) - Method in class com.actelion.research.chem.AbstractDepictor
- getStringWidth(String) - Method in class com.actelion.research.chem.Depictor
- getStringWidth(String) - Method in class com.actelion.research.chem.Depictor2D
- getStringWidth(String) - Method in class com.actelion.research.chem.SVGDepictor
- getStringWidth(String) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- getStroke() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getStructure() - Method in class com.actelion.research.gui.JDrawDialog
- getStructureCenter(Molecule3D, int[], int[][]) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getStructureCenter(Molecule3D, int, int[], int[][]) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
The Structure Center Atom is defined as the atom with the biggest no of rotatables bonds and the closest to the center
- getStructureCoordinates3DColumnName() - Method in class com.actelion.research.chem.io.DWARFileParser
- getStructureCount() - Method in class com.actelion.research.chem.StructureSearchSpecification
-
Returns the search type as integer including mode flags.
- getStructureInfo() - Method in class com.actelion.research.chem.StructureTransferData
- getStructures() - Method in class com.actelion.research.gui.JEditableChemistryView
-
If chemistryType is
- getStyle() - Method in class com.actelion.research.chem.TextDrawingObject
- getStyleSheet() - Method in class com.actelion.research.gui.hidpi.ScaledEditorKit
-
Overriden to return our own slimmed down style sheet.
- getSubFragment(MolDistHist, int[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- getSubFragment(MolDistHistViz, int[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- getSubFragmentCheckedRange(MolDistHist, int[]) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- getSubFragments(MolDistHistViz, List<int[]>) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
-
Inevitable pharmacophore points are considered (01.11.2012)
- getSubMatrix(int, int, int, int) - Method in class com.actelion.research.calc.Matrix
- getSubMatrix(List<Integer>) - Method in class com.actelion.research.calc.Matrix
- getSubset(int) - Method in class com.actelion.research.chem.conf.ConformerSet
- getSubstituent(int, int, boolean[], ExtendedMolecule, int[]) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Determines all atoms of the substituent attached to coreAtom and starting with firstAtom.
- getSubstituent(String) - Static method in class com.actelion.research.chem.NamedSubstituents
- getSubstituentIDCode(String) - Static method in class com.actelion.research.chem.NamedSubstituents
- getSubstituentSize(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Counts the number of atoms of the substituent connected to coreAtom defined by firstAtom and not including the coreAtom.
- getSubTreeSize(List<Integer>, int) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- getSum() - Method in class com.actelion.research.calc.Matrix
- getSumCol(int) - Method in class com.actelion.research.calc.Matrix
- getSumCols() - Method in class com.actelion.research.calc.Matrix
- getSumFragsUntilMaximumFrequency() - Method in class com.actelion.research.chem.properties.complexity.SummaryFragments
- getSumFromRange(double, double) - Method in class com.actelion.research.calc.histogram.Histogram
-
Parts of the range outside the bins are not considered.
- getSumRow(int) - Method in class com.actelion.research.calc.Matrix
- getSumRows() - Method in class com.actelion.research.calc.Matrix
- getSumSquared() - Method in class com.actelion.research.calc.Matrix
- getSumUniqueFrags() - Method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- getSumUniqueFrags(List<Point>) - Static method in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule
- getSumUpperTriangle() - Method in class com.actelion.research.calc.Matrix
-
Matrix has to be quadratic.
- getSumY() - Method in class com.actelion.research.calc.histogram.Histogram
- getSymbol() - Method in class com.actelion.research.chem.Element
- getSymmetryRank(int) - Method in class com.actelion.research.chem.Canonizer
-
Returned symmetry rank before tie breaking.
- getSymmetryRank(int) - Method in class com.actelion.research.chem.StereoMolecule
-
This returns atom symmetry numbers from within the molecule canonicalization procedure.
- getSymmetryType(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
A fragment's symmetry type defines whether one part of a full 360 degree matches symmetrically another range.
- getSynonymIDs() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getSynonyms(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getSystemProperty(String) - Static method in class com.actelion.research.gui.hidpi.HiDPIUtil
-
Tries to look up the System property for the given key.
- getTagDescriptorSimilarity(DescriptorInfo) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- getTagDescriptorSimilarity(ISimilarityCalculator<?>) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
-
Creates a header tag name from the descriptor short name.
- getTagDescriptorSimilarity(SimilarityCalculatorInfo) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- getTagDescriptorSimilarity(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- getTanimotoDist(byte[], byte[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
- getTanimotoDist(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
-
Calculates the Tanimoto coefficient
- getTanimotoDist(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Calculates the Inverse Tanimoto coefficient
- getTanimotoDistance(double[], double[]) - Static method in class com.actelion.research.util.DoubleVec
- getTanimotoDistance(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
-
Calculates the Inverse Tanimoto coefficient
- getTanimotoDistanceDotProd(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
- getTanimotoDistBitWise(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
- getTanimotoDistBitWise(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
-
Calculates the Tanimoto coefficient
- getTanimotoDistBitWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Calculates the Tanimoto coefficient
- getTanimotoDistInv(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
-
Byte wise inverse Tanimoto distance.
- getTanimotoDistInv(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- getTanimotoDistInvBitWise(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
- getTanimotoDistInvBitWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Calculates the Inverse Tanimoto coefficient
- getTanimotoDistInvByteWise(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
- getTanimotoDistInvByteWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- getTanimotoSimilarity(double[], double[]) - Static method in class com.actelion.research.calc.VectorSimilarity
- getTanimotoSimilarity(double[], double[]) - Static method in class com.actelion.research.util.DoubleVec
- getTanimotoSimilarity(float[], float[]) - Static method in class com.actelion.research.calc.VectorSimilarity
- getTanimotoSimilarity(int[], int[]) - Static method in class com.actelion.research.calc.VectorSimilarity
- getTanimotoSimilarity(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
-
Calculates the Tanimoto coefficient according broken link 22.01.2019 http://www.pnylab.com/pny/papers/nmet/nmet/
- getTautomerCode(int, boolean) - Method in interface com.actelion.research.chem.StructureSearchDataSource
-
Returns a hash code representing the generic tautomer of the structure or its largest fragment.
- getTautomerCount() - Method in class com.actelion.research.chem.TautomerHelper
- getTautomerHash(StereoMolecule, boolean) - Static method in class com.actelion.research.chem.CanonizerUtil
- getText() - Method in class com.actelion.research.chem.TextDrawingObject
- getText() - Method in interface com.actelion.research.share.gui.editor.io.IKeyEvent
- getTextSize() - Method in class com.actelion.research.chem.AbstractDepictor
- getTextSize() - Method in class com.actelion.research.chem.Depictor
- getTextSize() - Method in class com.actelion.research.chem.Depictor2D
- getTextSize() - Method in class com.actelion.research.chem.SVGDepictor
- getTextSize() - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- getThemeColor(int) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
- getTHParity(int) - Method in class com.actelion.research.chem.Canonizer
-
Returns the absolute tetrahedral parity, which is based on priority ranks.
- getThreadSafeCopy() - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedPharmSphere
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPharmPath
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- getThreadSafeCopy() - Method in interface com.actelion.research.chem.descriptor.ISimilarityCalculator
- getThreadSafeCopy() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- getThreadSafeCopy() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- getThreadSafeCopy() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShapeOneConf
- getTitle() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- getTitle() - Method in class com.actelion.research.gui.dock.Dockable
-
Returns the title of dockable header.
- getTitle() - Method in class com.actelion.research.gui.dock.DockableHeader
- getTitle(Dockable) - Method in class com.actelion.research.gui.dock.JDockingPanel
- getTokenized(String, String) - Static method in class com.actelion.research.util.StringFunctions
-
Returns the tokenized and trimmed values.
- getTokenizedBySeperatorRegex(String, String) - Static method in class com.actelion.research.util.StringFunctions
- getTokenizedQuoted(String) - Static method in class com.actelion.research.util.StringFunctions
-
Get a list from quoted and comma or otherwise separated phrases.
- getToleratedVDWRadius(int) - Static method in class org.openmolecules.chem.conf.gen.ConformerGenerator
- getTopologicalDistance(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getTopologicalDistanceMatrix(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- getTorsion(int) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
- getTorsionAtoms() - Method in class com.actelion.research.chem.conf.BondRotationHelper
- getTorsionBinCounts(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Returns the full circle histogram of torsion angles.
- getTorsionCount() - Method in class org.openmolecules.chem.conf.gen.RotatableBond
- getTorsionDescriptor() - Method in class com.actelion.research.chem.conf.TorsionDescriptorHelper
-
Creates a TorsionDescriptor from the coordinates of the molecule passed to the constructor using the default method to detect rotatable bonds.
- getTorsionDescriptor(Conformer) - Method in class com.actelion.research.chem.conf.TorsionDescriptorHelper
-
Creates a TorsionDescriptor from the coordinates of the passed conformer assuming that its underlying molecule is the same that waas passed to this TorsionDescriptorHelper's constructor.
- getTorsionFrequencies() - Method in class com.actelion.research.chem.conf.TorsionPrediction
- getTorsionFrequencies(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Returns an array of frequencies in rounded percent.
- getTorsionID(StereoMolecule, int, int[], TorsionDetail) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Determines uniquely an identifying name for the rotatable bond and its vicinity.
- getTorsionIDs() - Method in class com.actelion.research.chem.conf.BondRotationHelper
- getTorsionIndexes() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- getTorsionLikelyhood(int) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
- getTorsionRanges() - Method in class com.actelion.research.chem.conf.TorsionPrediction
- getTorsionRanges(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Returns an array containing left and right limits of the torsion curves, of which the maxima are returned by getTorsions().
- getTorsions() - Method in class com.actelion.research.chem.conf.TorsionPrediction
- getTorsions(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Returns an array of maxima of the smoothened torsion histogram as short values in the range: 0 <= v < 360.
- getTorsionSetCount() - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- getTorsionStrainClass(String, double) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Checks, whether the torsion angle lies within statistical limits.
- getTorus(int, int) - Method in class com.actelion.research.calc.Matrix
- getTotalAtomOverlap(double[]) - Method in class com.actelion.research.chem.phesa.PheSAAlignment
-
calculate the Overlap of the two molecular volumes as a function a transform vector that is applied to the query molecule overlap Volume of two molecular Volumes formulated as a summed overlap of atomic Gaussians taken from Grant, Gallardo, Pickup, Journal of Computational Chemistry, 17, 1653-1666, 1996 returns a double[2]: the first double is the total overlap, whereas the second value is the specific contribution of additional volume gaussians (inclusion, exclusion)
- getTotalEnergy() - Method in interface com.actelion.research.chem.forcefield.ForceField
- getTotalEnergy() - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
-
Gets the total energy of the molecule as the sum of the energy terms.
- getTotalEnergy(double[]) - Method in interface com.actelion.research.chem.forcefield.ForceField
- getTotalEnergy(double[]) - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
-
Gets the total energy of the molecule as the sum of the energy terms.Requires the atomic positions to be in the correct order.
- getTotalOccurences() - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
- getTotalPPOverlap(double[]) - Method in class com.actelion.research.chem.phesa.PheSAAlignment
- getTotalSizeResults() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getTotalStrain() - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- getTrace() - Method in class com.actelion.research.calc.Matrix
-
Matrix trace.
- getTransferable(Point) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- getTransferable(Point) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- getTransferData(DataFlavor) - Method in class com.actelion.research.gui.clipboard.ImageClipboardHandler.ImageSelection
- getTransferData(DataFlavor) - Method in class com.actelion.research.gui.dnd.MoleculeTransferable
- getTransferData(DataFlavor) - Method in class com.actelion.research.gui.dnd.ReactionTransferable
- getTransferData(DataFlavor) - Method in class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
- getTransferDataFlavors() - Method in class com.actelion.research.gui.clipboard.ImageClipboardHandler.ImageSelection
- getTransferDataFlavors() - Method in class com.actelion.research.gui.dnd.MoleculeTransferable
- getTransferDataFlavors() - Method in class com.actelion.research.gui.dnd.ReactionTransferable
- getTransferDataFlavors() - Method in class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
- getTransform() - Method in class com.actelion.research.chem.phesa.pharmacophore.PPTriangleMatcher.AlignmentResult
- getTransform() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- getTransformation() - Method in class com.actelion.research.chem.AbstractDepictor
- getTranspose() - Method in class com.actelion.research.calc.Matrix
- getType() - Method in class com.actelion.research.gui.DrawAreaEvent
- getType(MMFFMolecule, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
-
Returns the MMFF type of an atom in a molecule.
- getType(Tables, MMFFMolecule, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Bond
-
Returns the MMFF bond type of a bond on a molecule.
- getType(Tables, MMFFMolecule, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Bond
-
Returns the MMFF bond type of a bond on a molecule.
- getType(Tables, MMFFMolecule, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Angle
-
Gets the angle type of an angle bend.
- getType(Tables, MMFFMolecule, int, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Torsion
-
Returns the torsion type of a torsion angle.
- getTypeString() - Method in class com.actelion.research.chem.AbstractDrawingObject
- getTypeString() - Method in class com.actelion.research.chem.reaction.ReactionArrow
- getTypeString() - Method in class com.actelion.research.chem.TextDrawingObject
- getTypeString(long, int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- getU() - Method in class com.actelion.research.calc.LUDecomposition
-
Return upper triangular factor
- getU() - Method in class com.actelion.research.calc.SingularValueDecomposition
-
Return the left singular vectors
- getUIScaleFactor() - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
-
For Windows and Linux this method returns the user defined UI scaling factor.
- getUnique() - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- getUnique(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getUnique(int[], int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getUniqueDateDir(File) - Static method in class com.actelion.research.util.IO
- getUniqueDateDir(File, String) - Static method in class com.actelion.research.util.IO
- getUniqueDateDir(String) - Static method in class com.actelion.research.util.IO
- getUniqueDir(File, String) - Static method in class com.actelion.research.util.IO
- getUniqueFileName(File) - Static method in class com.actelion.research.util.IO
- getUniqueFileName(File, File) - Static method in class com.actelion.research.util.IO
- getUniqueFileName(File, File, DecimalFormat) - Static method in class com.actelion.research.util.IO
-
If the file does not exists the input file is returned.
- getUniqueFileName(String) - Static method in class com.actelion.research.util.IO
-
A number is added to the base name of the file
- getUniqueFileName(String, String) - Static method in class com.actelion.research.util.IO
- getUniqueFragments() - Method in class com.actelion.research.chem.mcs.ModelSampleFragments
- getUniqueFragmentsEstimated() - Method in class com.actelion.research.chem.mcs.ModelSampleFragments
- getUniqueUserDir() - Static method in class com.actelion.research.util.IO
- getUpperTriangle() - Method in class com.actelion.research.calc.Matrix
-
For a quadratic matrix only.
- getUserData() - Method in class com.actelion.research.chem.Molecule
- getV() - Method in class com.actelion.research.calc.SingularValueDecomposition
-
Return the right singular vectors
- getValence(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- getValidSolutions() - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- getValignment() - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Gets the Valignment attribute of the VerticalFlowLayout object
- getValue() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- getValue() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- getValue() - Method in class com.actelion.research.util.Angle
- getValueAt(int) - Method in interface com.actelion.research.calc.INumericalDataColumn
- getValueAt(int) - Method in class com.actelion.research.util.datamodel.DoubleArray
- getValueAtAbsolutePosition(int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- getValueCount() - Method in class com.actelion.research.calc.CorrelationCalculator
- getValueCount() - Method in interface com.actelion.research.calc.INumericalDataColumn
- getValueCount() - Method in class com.actelion.research.util.datamodel.DoubleArray
- getValueCountMatrix() - Method in class com.actelion.research.calc.CorrelationCalculator
- getValues() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getValues() - Method in class com.actelion.research.util.hash.HashSetInt
-
Deep copy.
- getValuesAsArray() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getValuesAsArrayX() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getValuesAsArrayY() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getVariance() - Method in class com.actelion.research.calc.Matrix
- getVariance(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- getVarianceCentered() - Method in class com.actelion.research.calc.Matrix
- getVarianceCol(int) - Method in class com.actelion.research.calc.Matrix
- getVarianceCols() - Method in class com.actelion.research.calc.Matrix
- getVDWRadius() - Method in class com.actelion.research.chem.Element
- getVDWRadius(int) - Static method in interface com.actelion.research.chem.conf.VDWRadii
- getVectorSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
- getVectorSimilarity(IPharmacophorePoint) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- getVectorSimilarity(IPharmacophorePoint) - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
- getVectorSimilarity(IPharmacophorePoint, Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
- getVectorSimilarity(IPharmacophorePoint, Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- getVectorSimilarity(IPharmacophorePoint, Coordinates) - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
- getVectorSimilarity(PPGaussian) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
- getVectorSimilarity(PPGaussian, Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
- getVersion() - Method in interface com.actelion.research.chem.descriptor.DescriptorHandler
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFunctionalGroups
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedCFp
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerHashedPharmSphere
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongCFP
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerLongPFP512
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPFP512
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerPharmPath
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- getVersion() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- getVersion() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.DescriptorHandlerPTree
- getVersion() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- getVgap() - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Gets the Vgap attribute of the VerticalFlowLayout object
- getViewFactory() - Method in class com.actelion.research.gui.hidpi.ScaledEditorKit
-
Returns the ViewFactory that is used to make sure the Views don't load in the background.
- getViolatedConditionsCount() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- getVolume() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getVolumeGaussians() - Method in class com.actelion.research.chem.phesa.MolecularVolume
- getVolumeOverlap(Gaussian3D) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getVolumeOverlap(Gaussian3D, double) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getVolumeOverlap(Gaussian3D, Coordinates, double) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getVolumes() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- getVolumes() - Method in class com.actelion.research.chem.phesa.PheSAMolecule
- getWeight() - Method in class com.actelion.research.chem.Element
- getWeight() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getWeight(int) - Static method in class com.actelion.research.chem.PeriodicTable
- getWeights() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- getWidth() - Method in class com.actelion.research.chem.coords.InventorFragment
- getWidth() - Method in class com.actelion.research.chem.phesa.Gaussian3D
- getWidth() - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
- getWithCopy(ListWithIntVec) - Method in class com.actelion.research.chem.mcs.ContainerListWithIntVec
- getWithCopy(BitArray128) - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- getWithCopy(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- getWithCopy(S) - Method in class com.actelion.research.util.graph.complete.ContainerMemory
- getWordsFormatted(String) - Static method in class com.actelion.research.util.StringFunctions
-
Removes all non characters and digits.
- getWordsFormattedUniqueLowerCase(String) - Static method in class com.actelion.research.util.StringFunctions
- getX() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getX() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getX() - Method in interface com.actelion.research.share.gui.editor.io.IMouseEvent
- getX(int) - Method in class com.actelion.research.chem.conf.Conformer
- getXMean() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getXMLElement(Document) - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- getXMLElement(Document) - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- getXMLElement(Document) - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- getY() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getY() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getY() - Method in interface com.actelion.research.share.gui.editor.io.IMouseEvent
- getY(double) - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getY(int) - Method in class com.actelion.research.chem.conf.Conformer
- getYMean() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- getZ() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- getZ() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- getZ(int) - Method in class com.actelion.research.chem.conf.Conformer
- getZNeighbour(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Provided that the bond parity of a double bond is available, this method determines, whether connAtom has a counterpart with Z- (cis) configuration at the other end of the double bond.
- gfxConfig - Variable in class com.actelion.research.share.gui.Arrow
- GhostPreview - Class in com.actelion.research.gui.dock
- GhostPreview() - Constructor for class com.actelion.research.gui.dock.GhostPreview
- Graph - Class in com.actelion.research.chem.descriptor.pharmacophoretree
- Graph(Map<Integer, List<Integer>>) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.Graph
- Graph.Edge - Class in com.actelion.research.chem.descriptor.pharmacophoretree
- GraphicsContextImpl - Class in com.actelion.research.jfx.gui
-
Project: User: rufenec Date: 11/24/2014 Time: 6:24 PM
- GraphicsContextImpl(GraphicsContext) - Constructor for class com.actelion.research.jfx.gui.GraphicsContextImpl
- GRAY - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
- GREEN - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
- grid - Variable in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- grid - Variable in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- GRID_DIMENSION - Static variable in class com.actelion.research.chem.docking.DockingEngine
- GRID_RESOLUTION - Static variable in class com.actelion.research.chem.docking.DockingEngine
- gridSize - Variable in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- gridWidth - Variable in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- GUANIDINE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
H
- HARD_MATCH_OPTIMISTIC_PERCENTILE - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- hasCIPParityDistinctionProblem() - Method in class com.actelion.research.chem.Canonizer
- hascode() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondType
- hasErrors() - Method in class com.actelion.research.util.ErrorHashMap
- hash - Variable in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- hash - Variable in class com.actelion.research.chem.properties.complexity.IndexHash
- hash(String) - Static method in class com.actelion.research.chem.CanonizerUtil.StrongHasher
- hashCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- hashCode() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- hashCode() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- hashCode() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- hashCode() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
- hashCode() - Method in class com.actelion.research.chem.forcefield.mmff.SortedPair
-
Returns the hash code of this sorted pair object.
- hashCode() - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Returns the hashcode of this vector.
- hashCode() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- hashCode() - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- hashCode() - Method in class com.actelion.research.chem.properties.complexity.IndexHash
- hashCode() - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- hashCode() - Method in class com.actelion.research.util.datamodel.ByteVec
-
The hash code has to be calculated before.
- hashCode() - Method in class com.actelion.research.util.datamodel.IDCodeCoord
-
Taken from idcode.
- hashCode() - Method in class com.actelion.research.util.datamodel.IntArray
- hashCode() - Method in class com.actelion.research.util.datamodel.IntegerDouble
- hashCode() - Method in class com.actelion.research.util.datamodel.IntVec
- hashCode() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- hasHeteroAtom() - Method in interface com.actelion.research.chem.descriptor.flexophore.IPPNode
- hasHeteroAtom() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- hashlittle(byte[], long) - Static method in class com.actelion.research.util.BurtleHasher
- hashlittle(byte[], long, int) - Static method in class com.actelion.research.util.BurtleHasher
- hashlittle(int[], long) - Static method in class com.actelion.research.util.BurtleHasher
-
MvK 10.02.2010
- hashlittle(int[], long, int) - Static method in class com.actelion.research.util.BurtleHasher
- hashlittle(String, long) - Static method in class com.actelion.research.util.BurtleHasher
- hashmask(int) - Static method in class com.actelion.research.util.BurtleHasher
- HashSetInt - Class in com.actelion.research.util.hash
-
HashSetInt
- HashSetInt() - Constructor for class com.actelion.research.util.hash.HashSetInt
- HashSetInt(int) - Constructor for class com.actelion.research.util.hash.HashSetInt
- HashSetInt(int[]) - Constructor for class com.actelion.research.util.hash.HashSetInt
- HashSetInt(List<Integer>) - Constructor for class com.actelion.research.util.hash.HashSetInt
- hashsize(long) - Static method in class com.actelion.research.util.BurtleHasher
- hashword(String, long) - Static method in class com.actelion.research.util.BurtleHasher
- hasMenuButton() - Method in class com.actelion.research.gui.dock.Dockable
- hasMoreLines() - Method in class com.actelion.research.io.StringReadChannel
- hasNeighbours(Coordinates, double) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- hasNext() - Method in class com.actelion.research.chem.io.RDFileParser
- hasOnlyFinite() - Method in class com.actelion.research.calc.Matrix
- hasSamePosition(PPNodeViz) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- hasStructureCoordinates() - Method in class com.actelion.research.chem.io.DWARFileParser
- hasStructureCoordinates2D() - Method in class com.actelion.research.chem.io.DWARFileParser
- hasStructureCoordinates3D() - Method in class com.actelion.research.chem.io.DWARFileParser
- hasStructures() - Method in class com.actelion.research.chem.io.DWARFileParser
-
If you don't read any records after calling this method, don't forget to call close() to close the underlying file.
- hasUnbalancedAtomCharge(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- hblaurie - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- HBOND_TERM - Static variable in class com.actelion.research.chem.docking.scoring.plp.PLPTerm
- HBTerm - Class in com.actelion.research.chem.docking.scoring.chemscore
- HeaderMouseAdapter - Class in com.actelion.research.gui.dock
- HeaderMouseAdapter(DockableHeader) - Constructor for class com.actelion.research.gui.dock.HeaderMouseAdapter
- HeaderPaintHelper - Class in com.actelion.research.gui
- HeaderPaintHelper() - Constructor for class com.actelion.research.gui.HeaderPaintHelper
- help() - Method in class com.actelion.research.util.CommandLineParser
- HELP - Static variable in class com.actelion.research.util.CommandLineParser
- HerschbachLaurie - Class in com.actelion.research.chem.forcefield.mmff.table
-
Table for Herschbach-Laurie version of Badger's rule.
- HerschbachLaurie(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.HerschbachLaurie
- HetNameParser - Class in com.actelion.research.chem.io.pdb.parser
-
HetNameParser
- HetNameParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.HetNameParser
- HetSynonymParser - Class in com.actelion.research.chem.io.pdb.parser
-
HetSynonymParser
- HetSynonymParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.HetSynonymParser
- hex2String(String) - Static method in class com.actelion.research.util.StringFunctions
- hg_step1(int, double[][]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- hg_step2(int, double[][], int[][], int[], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- hg_step3(int, int[][], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- hg_step4(int, double[][], int[][], int[], int[], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- hg_step5(int, int[][], int[], int[], int[]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- hg_step6(int, double[][], int[], int[], double) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- hgAlgorithm(double[][], String) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- HiDPIHelper - Class in com.actelion.research.gui.hidpi
- HiDPIHelper() - Constructor for class com.actelion.research.gui.hidpi.HiDPIHelper
- HiDPIIcon - Class in com.actelion.research.gui.hidpi
-
Created by thomas on 07/12/15.
- HiDPIIcon(Image, boolean) - Constructor for class com.actelion.research.gui.hidpi.HiDPIIcon
- HiDPIIconButton - Class in com.actelion.research.gui.hidpi
-
Created by sandert on 04/12/15.
- HiDPIIconButton(String, String, String) - Constructor for class com.actelion.research.gui.hidpi.HiDPIIconButton
-
Creates a button that, if image2 is given, toggles between two states indicated by two different button images.
- HiDPIIconButton(String, String, String, int, String) - Constructor for class com.actelion.research.gui.hidpi.HiDPIIconButton
-
Creates a button that, if image2 is given, toggles between two states indicated by two different button images.
- HiDPIToggleButton - Class in com.actelion.research.gui.hidpi
-
Created by thomas on 07/12/15.
- HiDPIToggleButton(String, String, String, String) - Constructor for class com.actelion.research.gui.hidpi.HiDPIToggleButton
-
Creates a button that, if image2 is given, toggles between two states indicated by two different button images.
- HiDPIUtil - Class in com.actelion.research.gui.hidpi
- HiDPIUtil() - Constructor for class com.actelion.research.gui.hidpi.HiDPIUtil
- HIGHLIGHT_ATOM_RADIUS - Static variable in class com.actelion.research.share.gui.editor.actions.DrawAction
- highlightAtom(StereoMolecule, int) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- hilite(Graphics) - Method in class com.actelion.research.chem.AbstractDrawingObject
- hilite(Graphics) - Method in class com.actelion.research.chem.reaction.ReactionArrow
- hilite(Graphics) - Method in class com.actelion.research.chem.TextDrawingObject
- Histogram - Class in com.actelion.research.calc.histogram
-
Histogram
- Histogram(double[], double, double, int) - Constructor for class com.actelion.research.calc.histogram.Histogram
- Histogram(double[], int) - Constructor for class com.actelion.research.calc.histogram.Histogram
- histogram2String(Matrix, int, int) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- HistogramMatchCalculator - Class in com.actelion.research.chem.descriptor.flexophore.completegraphmatcher
-
HistogramMatchCalculator
- HistogramMatchCalculator() - Constructor for class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.HistogramMatchCalculator
- hit(Rectangle, Shape, boolean) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- HOSE_CODE_CUT_C_SP3_SP3 - Static variable in class com.actelion.research.chem.contrib.HoseCodeCreator
- HoseCodeCreator - Class in com.actelion.research.chem.contrib
- HoseCodeCreator() - Constructor for class com.actelion.research.chem.contrib.HoseCodeCreator
- HS_BDIAGONAL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- HS_CROSS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- HS_DIAGCROSS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- HS_FDIAGONAL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- HS_HORIZONTAL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- HS_VERTICAL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- HungarianAlgorithm - Class in com.actelion.research.chem.descriptor.pharmacophoretree
- HungarianAlgorithm() - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- HYBRID - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- HYBRID_SHIFT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyShift
- Hydrogen - Static variable in class com.actelion.research.chem.PeriodicTable
- HydrogenHandler - Class in com.actelion.research.chem.contrib
- HydrogenHandler() - Constructor for class com.actelion.research.chem.contrib.HydrogenHandler
- hypot(double, double) - Static method in class com.actelion.research.calc.SingularValueDecomposition
I
- iAMPAC_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- IArrow - Interface in com.actelion.research.share.gui.editor.chem
-
Project: User: rufenec Date: 11/24/2014 Time: 3:28 PM
- IAtomPropertiesDialog - Interface in com.actelion.research.share.gui.editor.dialogs
-
Project: User: rufenec Date: 11/24/2014 Time: 5:03 PM
- IAtomQueryFeaturesDialog - Interface in com.actelion.research.share.gui.editor.dialogs
-
Project: User: rufenec Date: 11/24/2014 Time: 4:53 PM
- IBitArray - Interface in com.actelion.research.chem.properties.complexity
- IBitArrayFactory<T extends IBitArray> - Interface in com.actelion.research.chem.properties.complexity
- IBondQueryFeaturesDialog - Interface in com.actelion.research.share.gui.editor.dialogs
-
Project: User: rufenec Date: 11/24/2014 Time: 4:57 PM
- IChangeListener - Interface in com.actelion.research.share.gui.editor.listeners
-
Project: User: rufenec Date: 11/24/2014 Time: 3:25 PM
- IClipboardHandler - Interface in com.actelion.research.gui.clipboard
- IColor - Interface in com.actelion.research.share.gui.editor.geom
-
Project: User: rufenec Date: 11/24/2014 Time: 3:21 PM
- ICompleteGraph - Interface in com.actelion.research.util.graph.complete
-
ICompleteGraph
- ICursor - Interface in com.actelion.research.share.gui.editor.geom
-
Project: User: rufenec Date: 11/24/2014 Time: 3:21 PM
- id - Variable in class com.actelion.research.calc.statistics.median.ModelMedianDouble
- id - Variable in class com.actelion.research.calc.statistics.median.ModelMedianFloat
- id - Variable in class com.actelion.research.calc.statistics.median.ModelMedianInteger
- id - Variable in class com.actelion.research.calc.statistics.median.ModelMedianLong
- id - Variable in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- ID_FIELD - Static variable in class com.actelion.research.chem.SDFileMolecule
- IDABORT - com.actelion.research.share.gui.DialogResult
- IDCANCEL - com.actelion.research.share.gui.DialogResult
- idcode - Variable in class com.actelion.research.util.datamodel.IDCodeCoord
- IDCode() - Constructor for class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCode
- IDCODE_100 - Static variable in class com.actelion.research.chem.descriptor.flexophore.example.MatchFlexophoreNodesMain
- IDCODE_101 - Static variable in class com.actelion.research.chem.descriptor.flexophore.example.MatchFlexophoreNodesMain
- IDCodeCoord - Class in com.actelion.research.util.datamodel
-
IDCodeCoord Apr 12, 2012 MvK: Start implementation
- IDCodeCoord(int, String, String) - Constructor for class com.actelion.research.util.datamodel.IDCodeCoord
- IDCodeCoord(String) - Constructor for class com.actelion.research.util.datamodel.IDCodeCoord
- IDCodeCoord(String, String) - Constructor for class com.actelion.research.util.datamodel.IDCodeCoord
- IDCodeParser - Class in com.actelion.research.chem
- IDCodeParser() - Constructor for class com.actelion.research.chem.IDCodeParser
-
This default constructor creates molecules guaranteed to have 2D-atom-coordinates.
- IDCodeParser(boolean) - Constructor for class com.actelion.research.chem.IDCodeParser
- IDCodeParserWithoutCoordinateInvention - Class in com.actelion.research.chem
-
Typically you should use IDCodeParser instead of this class.
- IDCodeParserWithoutCoordinateInvention() - Constructor for class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- idcodeProperty() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- idcodeProperty() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- IDCodeWithName() - Constructor for class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCodeWithName
- idColumn - Variable in class com.actelion.research.chem.io.DWARFileParser.SpecialField
- iDEL_RE - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- IdentifiedObject<T> - Class in com.actelion.research.util.datamodel
-
IdentifiedObject Nov 2, 2011 MvK: Start implementation
- IdentifiedObject() - Constructor for class com.actelion.research.util.datamodel.IdentifiedObject
- IdentifiedObject(T, long) - Constructor for class com.actelion.research.util.datamodel.IdentifiedObject
- IDepictor<T> - Interface in com.actelion.research.share.gui.editor.chem
-
Project: User: rufenec Date: 11/24/2014 Time: 3:26 PM
- IDescriptorHandlerFlexophore - Interface in com.actelion.research.chem.descriptor.flexophore
- IDialog - Interface in com.actelion.research.share.gui.editor.dialogs
- iDICT_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- IDNO - com.actelion.research.share.gui.DialogResult
- IDOK - com.actelion.research.share.gui.DialogResult
- IdoScore - Class in com.actelion.research.chem.docking.scoring
- IdoScore(StereoMolecule, Set<Integer>, int[], MoleculeGrid) - Constructor for class com.actelion.research.chem.docking.scoring.IdoScore
- IDOSCORE - com.actelion.research.chem.docking.DockingEngine.ScoringFunction
- IDrawContext<T> - Interface in com.actelion.research.share.gui.editor.geom
-
Project: User: rufenec Date: 11/24/2014 Time: 3:22 PM
- IDrawingObject - Interface in com.actelion.research.share.gui.editor.chem
-
Project: User: rufenec Date: 11/24/2014 Time: 3:28 PM
- IDRETRY - com.actelion.research.share.gui.DialogResult
- IDYES - com.actelion.research.share.gui.DialogResult
- IFactory<S extends AMemorizedObject> - Interface in com.actelion.research.util.graph.complete
-
IFactory
- iGAST_HUCK - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- iGASTEIGER - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- iGAUSS80_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- iHUCKEL - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- IIdentifiedObject<T> - Interface in com.actelion.research.util.datamodel
-
IIdentifiedObject Nov 4, 2011 MvK: Start implementation
- IKeyCode - Interface in com.actelion.research.share.gui.editor.io
-
Project: User: rufenec Date: 11/24/2014 Time: 4:17 PM
- IKeyEvent - Interface in com.actelion.research.share.gui.editor.io
-
Project: User: rufenec Date: 11/24/2014 Time: 3:20 PM
- ImageClipboardHandler - Class in com.actelion.research.gui.clipboard
- ImageClipboardHandler() - Constructor for class com.actelion.research.gui.clipboard.ImageClipboardHandler
- ImageClipboardHandler.ImageSelection - Class in com.actelion.research.gui.clipboard
- ImageProvider<T> - Class in com.actelion.research.share.gui.editor
-
Created by rufenec on 08/05/15.
- ImageProvider() - Constructor for class com.actelion.research.share.gui.editor.ImageProvider
- ImageSelection(Image) - Constructor for class com.actelion.research.gui.clipboard.ImageClipboardHandler.ImageSelection
- iMMFF94_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- IMolDistHist - Interface in com.actelion.research.chem.descriptor.flexophore
- IMoleculeView - Interface in com.actelion.research.jfx.gui.chem
- IMouseEvent - Interface in com.actelion.research.share.gui.editor.io
-
Project: User: rufenec Date: 11/24/2014 Time: 3:19 PM
- IMPORTANT - Static variable in class com.actelion.research.chem.Molecule3D
- iMULLIKEN_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- in - Variable in class com.actelion.research.util.LittleEndianDataInputStream
- INCLUDE_ALL - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- INCLUDE_CATALYSTS - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- INCLUDE_COORDS - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- INCLUDE_DEFAULT - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- INCLUDE_DRAWING_OBJECTS - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- INCLUDE_MAPPING - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- INCLUDE_RXN_CODE_ONLY - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- INCLUSION - Static variable in class com.actelion.research.chem.phesa.VolumeGaussian
- increase(int, int, double) - Method in class com.actelion.research.calc.Matrix
- increaseNonCachableCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- INCREMENT - Static variable in class com.actelion.research.chem.prediction.CLogPPredictor
- incrementByte(int[], int) - Static method in class com.actelion.research.util.datamodel.IntVec
- incrementFrequency() - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- incrementFrequency() - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- incrementFrequencyOnePerMol() - Method in class com.actelion.research.chem.shredder.Fragment
- incrementFrequencySumAll() - Method in class com.actelion.research.chem.shredder.Fragment
- incrementHitCount() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache.CacheEntry
- IncrementTable - Class in com.actelion.research.chem.prediction
- IncrementTable() - Constructor for class com.actelion.research.chem.prediction.IncrementTable
- IncrementTable(String) - Constructor for class com.actelion.research.chem.prediction.IncrementTable
- index - Variable in class com.actelion.research.util.datamodel.IDCodeCoord
- index(int, int, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Torsion
-
Returns the index of a row for a given molecule and four connected atoms which form a torsion angle.
- index(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
-
Returns the index of a row for a given molecule and three connected atoms which form an angle.
- index(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Dfsb
-
Returns the index that a given set of three atoms have in the Dfsb table.
- index(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Stbn
-
Returns the index of a row for a given molecule and three connected atoms which form an angle.
- IndexCoordinates - Class in com.actelion.research.chem.descriptor.flexophore
- IndexCoordinates() - Constructor for class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
- IndexCoordinates(int, int, Coordinates) - Constructor for class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
- IndexHash - Class in com.actelion.research.chem.properties.complexity
- IndexHash() - Constructor for class com.actelion.research.chem.properties.complexity.IndexHash
- IndexHash(int) - Constructor for class com.actelion.research.chem.properties.complexity.IndexHash
- indexOf(byte[], byte) - Static method in class com.actelion.research.util.ArrayUtils
- indexOf(byte[], byte, int) - Static method in class com.actelion.research.util.ArrayUtils
- indexOf(int) - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
- indexOf(int) - Method in class com.actelion.research.util.IntQueue
- indexOf(int[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- indexOf(int[], int) - Static method in class com.actelion.research.util.ArrayUtils
- indexOf(int[], int, int) - Static method in class com.actelion.research.util.ArrayUtils
- indexOf(Object[], Object) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- indexOf(Object[], Object) - Static method in class com.actelion.research.util.ArrayUtils
- INFO - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- INFO_AMINO - Static variable in class com.actelion.research.chem.Molecule3D
- INFO_ATOMNAME - Static variable in class com.actelion.research.chem.Molecule3D
- INFO_ATOMSEQUENCE - Static variable in class com.actelion.research.chem.Molecule3D
- INFO_BFACTOR - Static variable in class com.actelion.research.chem.Molecule3D
- INFO_CHAINID - Static variable in class com.actelion.research.chem.Molecule3D
- INFO_DEFAULT - Static variable in class com.actelion.research.chem.descriptor.flexophore.PPNode
- INFO_DESCRIPTION - Static variable in class com.actelion.research.chem.Molecule3D
- INFO_INTERACTION_ATOM_TYPE - Static variable in class com.actelion.research.chem.Molecule3D
- INFO_PPP - Static variable in class com.actelion.research.chem.Molecule3D
- INFO_RESSEQUENCE - Static variable in class com.actelion.research.chem.Molecule3D
- informListeners() - Method in class com.actelion.research.gui.JChemistryView
- init() - Method in class com.actelion.research.chem.AbstractDepictor
- init() - Method in class com.actelion.research.chem.Depictor
- init() - Method in class com.actelion.research.chem.Depictor2D
- init() - Method in class com.actelion.research.chem.docking.scoring.idoscore.StrainTerm
- init() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- init() - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- init(int) - Method in class com.actelion.research.chem.CanonizerBaseValue
- init(LigandPose, double) - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- init(LigandPose, double) - Method in class com.actelion.research.chem.docking.scoring.ChemPLP
- init(LigandPose, double) - Method in class com.actelion.research.chem.docking.scoring.IdoScore
- init(StereoMolecule) - Method in class com.actelion.research.chem.mcs.RunBondVector2IdCode
- initHistogramArray(int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- initHistogramArray(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- initHistogramArray(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- INITIAL_SPLITS - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- initialCut(int, int, List<Integer>, List<Integer>, List<Integer>, List<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
-
a cut divides a edge into a target node and a source node: an edge is defined as a tuple of two nodes (a,b), a left cut results in node a being the source node and b being the target node: a-->--b a right cut results in the right node being the source node: a--<--b returns int array with source node as 0th element and target node as 1st element
- initialize() - Method in class com.actelion.research.chem.conf.BondRotationHelper
- initialize(double[], double, double, int) - Method in class com.actelion.research.calc.histogram.Histogram
- initialize(int) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Initializes the in memory torsion database by reading torsion list, associated torsion frequencies, torsion peak widths (ranges), and/or normalized 3-degree bins into memory.
- initialize(int) - Method in class com.actelion.research.util.BinaryDecoder
- initialize(int, int) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Initializes the in memory torsion database by reading torsion list, associated torsion frequencies, torsion peak widths (ranges), and/or normalized 3-degree bins into memory.
- initialize(StereoMolecule, boolean) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
Don't call this method directly.
- initialize(String) - Static method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
- initializeConformers(long, int) - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
-
Needs to be called, before getting individual conformers of the same molecule by getNextConformer().
- initializeConformers(StereoMolecule) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
One of the initializeConformers() methods needs to be called, before getting individual conformers of the same molecule by getNextConformer().
- initializeConformers(StereoMolecule, int, int, boolean) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
One of the initializeConformers() methods needs to be called, before getting individual conformers of the same molecule by getNextConformer().
- initializeExistingSet(int) - Method in class com.actelion.research.chem.DiversitySelector
- initialTransform(int) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
-
.
- initRND(byte, byte) - Method in class com.actelion.research.util.datamodel.ByteVec
- initRND(byte, byte, int, int) - Static method in class com.actelion.research.util.datamodel.ByteVec
- initRND(double[][]) - Method in class com.actelion.research.util.DoubleVec
-
The array contains the maximum and the minimum values for the initialisation of each field in the double vector.
- initRND(double, double) - Method in class com.actelion.research.util.DoubleVec
- injectNewSeed() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- iNO_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- InputObjectFracDimCalc - Class in com.actelion.research.chem.properties.fractaldimension
-
InputObjectFracDimCalc
- InputObjectFracDimCalc(InputObjectFracDimCalc) - Constructor for class com.actelion.research.chem.properties.fractaldimension.InputObjectFracDimCalc
- InputObjectFracDimCalc(StereoMolecule, long, String) - Constructor for class com.actelion.research.chem.properties.fractaldimension.InputObjectFracDimCalc
- inRingOfSize(MMFFMolecule, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
-
Returns true if the atom is in any ring of a given size.
- inRingOfSize(MMFFMolecule, int, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Angle
-
Checks if an angle is in a ring of given size.
- inRingOfSize(MMFFMolecule, int, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Torsion
-
Checks and returns the minimum ring size that a torsion is contained in.
- inRings(MMFFMolecule, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
-
Returns the number of rings that an atom is a member of in a molecule.
- inSameRing(MMFFMolecule, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
-
Returns true if two atoms are in the same ring of a given size.
- insertLigand(Molecule3D, Molecule3D, Coordinates) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- insideBounds(Coordinates[]) - Method in class com.actelion.research.chem.Coordinates
- INSTANCE - com.actelion.research.chem.io.pdb.converter.AminoAcidsLabeledContainer
- instantiate(String) - Static method in class com.actelion.research.chem.AbstractDrawingObject
- IntArray - Class in com.actelion.research.util.datamodel
- IntArray() - Constructor for class com.actelion.research.util.datamodel.IntArray
- IntArray(int) - Constructor for class com.actelion.research.util.datamodel.IntArray
- IntArray(int[]) - Constructor for class com.actelion.research.util.datamodel.IntArray
-
Shallow constructor.
- IntArray(IntArray) - Constructor for class com.actelion.research.util.datamodel.IntArray
-
Deep constructor.
- IntArrayComparator - Class in com.actelion.research.util
- IntArrayComparator() - Constructor for class com.actelion.research.util.IntArrayComparator
- intArrayToByteArray(int[]) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
- IntegerDouble - Class in com.actelion.research.util.datamodel
-
IntegerDouble Oct 24, 2011 MvK: Start implementation
- IntegerDouble() - Constructor for class com.actelion.research.util.datamodel.IntegerDouble
- IntegerDouble(int, double) - Constructor for class com.actelion.research.util.datamodel.IntegerDouble
- IntegerDouble(IntegerDouble) - Constructor for class com.actelion.research.util.datamodel.IntegerDouble
- INTERACTION_TYPE_NONE - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
- InteractionAtomTypeCalculator - Class in com.actelion.research.chem.interactionstatistics
- InteractionAtomTypeCalculator() - Constructor for class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- InteractionAtomTypeCalculator.AtomFlagCount - Enum in com.actelion.research.chem.interactionstatistics
- InteractionAtomTypeCalculator.AtomPropertyMask - Enum in com.actelion.research.chem.interactionstatistics
- InteractionAtomTypeCalculator.AtomPropertyShift - Enum in com.actelion.research.chem.interactionstatistics
- InteractionAtomTypeCalculator.FunctionalGroup - Enum in com.actelion.research.chem.interactionstatistics
- InteractionDescriptor(SplineFunction) - Constructor for class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable.InteractionDescriptor
- InteractionDistanceStatistics - Class in com.actelion.research.chem.interactionstatistics
- InteractionSimilarityTable - Class in com.actelion.research.chem.interactionstatistics
-
distance gives the distance of the point of highest potential.
- InteractionSimilarityTable.InteractionDescriptor - Class in com.actelion.research.chem.interactionstatistics
- InteractionTerm - Class in com.actelion.research.chem.docking.scoring.idoscore
-
ProteinLigandTerm is used to represent the energy between 2 atoms.
- InteractionTypeMap - Class in com.actelion.research.chem.descriptor.flexophore.generator
- InteractionTypeMap(double) - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.InteractionTypeMap
- intermediateColor(Color, Color, float) - Static method in class com.actelion.research.util.ColorHelper
-
Creates an intermediate color between color c1 and color c2 in the RGB color space.
- interpolate(double[], double[]) - Method in class com.actelion.research.util.SmoothingSplineInterpolator
- interrupt() - Method in class com.actelion.research.chem.forcefield.AbstractForceField
- interrupt() - Method in interface com.actelion.research.chem.forcefield.ForceField
- intersectClipRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- intersectClipRect(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMF
- intersects(IRectangle2D) - Method in interface com.actelion.research.share.gui.editor.geom.IRectangle2D
- IntQueue - Class in com.actelion.research.chem.descriptor.flexophore.calculator
-
Implementation for a FIFO of int.
- IntQueue - Class in com.actelion.research.util
-
Implementation for a FIFO of int.
- IntQueue() - Constructor for class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
-
Creeates a new Queue with an initial size of 100
- IntQueue() - Constructor for class com.actelion.research.util.IntQueue
-
Creeates a new Queue with an initial size of 100
- IntQueue(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
- IntQueue(int) - Constructor for class com.actelion.research.util.IntQueue
- intToByteArray(int) - Static method in class com.actelion.research.chem.phesa.EncodeFunctions
- intValue() - Method in class com.actelion.research.util.concurrent.AtomicFloat
- IntVec - Class in com.actelion.research.util.datamodel
- IntVec() - Constructor for class com.actelion.research.util.datamodel.IntVec
- IntVec(boolean[]) - Constructor for class com.actelion.research.util.datamodel.IntVec
-
Puts an boolean array into an int array.
- IntVec(int) - Constructor for class com.actelion.research.util.datamodel.IntVec
-
Don't forget to calculate the hash code after setting the bits!
- IntVec(int[]) - Constructor for class com.actelion.research.util.datamodel.IntVec
-
Deep copy, hash code is calculated.
- IntVec(int[], boolean) - Constructor for class com.actelion.research.util.datamodel.IntVec
-
If true each int contains only a 0 or a 1.
- IntVec(IntVec) - Constructor for class com.actelion.research.util.datamodel.IntVec
-
Deep copy, hash code is calculated.
- IntVec(List<Integer>) - Constructor for class com.actelion.research.util.datamodel.IntVec
- INumericalDataColumn - Interface in com.actelion.research.calc
- invalidateCoordinates() - Method in class com.actelion.research.chem.Canonizer
- invalidateHelperArrays(int) - Method in class com.actelion.research.chem.Molecule
-
Clears helperBits from mValidHelperArrays.
- invalidateStrain() - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- invent(StereoMolecule) - Method in class com.actelion.research.chem.coords.CoordinateInventor
-
Creates new atom 2D-coordinates for a molecule or a part of a molecule.
- invent(StereoMolecule, long[]) - Method in class com.actelion.research.chem.coords.CoordinateInventor
-
Creates new atom 2D-coordinates for a molecule or a part of a molecule.
- inventCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.IDCodeParser
- inventCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- InventorAngle - Class in com.actelion.research.chem.coords
-
Created by thomas on 9/23/16.
- InventorAngle(double, double) - Constructor for class com.actelion.research.chem.coords.InventorAngle
- InventorAngle(double, double, double, double) - Constructor for class com.actelion.research.chem.coords.InventorAngle
- InventorChain - Class in com.actelion.research.chem.coords
-
Created by thomas on 9/23/16.
- InventorChain(int) - Constructor for class com.actelion.research.chem.coords.InventorChain
- InventorCharge - Class in com.actelion.research.chem.coords
-
Created by thomas on 9/28/16.
- InventorCharge(InventorFragment, int, int) - Constructor for class com.actelion.research.chem.coords.InventorCharge
- InventorDefaultTemplateList - Class in com.actelion.research.chem.coords
- InventorDefaultTemplateList() - Constructor for class com.actelion.research.chem.coords.InventorDefaultTemplateList
- InventorFragment - Class in com.actelion.research.chem.coords
- InventorFragment(InventorFragment, int) - Constructor for class com.actelion.research.chem.coords.InventorFragment
- InventorFragment(StereoMolecule, int, int) - Constructor for class com.actelion.research.chem.coords.InventorFragment
- InventorTemplate - Class in com.actelion.research.chem.coords
- InventorTemplate(StereoMolecule, long[]) - Constructor for class com.actelion.research.chem.coords.InventorTemplate
- IO - Class in com.actelion.research.util
-
IO 2003 MvK: Start implementation
- IO() - Constructor for class com.actelion.research.util.IO
- IObjectiveCompleteGraph<T extends ICompleteGraph> - Interface in com.actelion.research.util.graph.complete
-
IObjectiveCompleteGraph
- Iodine - Static variable in class com.actelion.research.chem.PeriodicTable
- IonizableGroupDetector - Class in com.actelion.research.chem.phesa.pharmacophore
- IonizableGroupDetector(StereoMolecule) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.IonizableGroupDetector
- IonizableGroupDetector2D - Class in com.actelion.research.chem.descriptor.pharmacophoretree
- IonizableGroupDetector2D(StereoMolecule) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.IonizableGroupDetector2D
- IPharmacophorePoint - Interface in com.actelion.research.chem.phesa.pharmacophore
- IPharmacophorePoint.Functionality - Enum in com.actelion.research.chem.phesa.pharmacophore
- IPipeline<T> - Interface in com.actelion.research.util
-
IPipeline Interface to connect several Runable in a pipeline Mar 27, 2012 MvK: Start implementation Oct 9 2012 MvK: wereAllDataFetched() added.
- IPolygon - Interface in com.actelion.research.share.gui.editor.geom
-
Project: User: rufenec Date: 11/24/2014 Time: 4:45 PM
- IPPNode - Interface in com.actelion.research.chem.descriptor.flexophore
- IPPNodeSimilarity - Interface in com.actelion.research.chem.descriptor.flexophore.completegraphmatcher
-
IPPNodeSimilarity
- iPULLMAN - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- IReactionArrow - Interface in com.actelion.research.share.gui.editor.chem
-
Project: User: rufenec Date: 11/24/2014 Time: 5:49 PM
- IReactionMapper - Interface in com.actelion.research.chem.reaction
- IRectangle2D - Interface in com.actelion.research.share.gui.editor.geom
-
Project: User: rufenec Date: 11/24/2014 Time: 3:17 PM
- IS_JAVA_10 - Static variable in class com.actelion.research.gui.hidpi.HiDPIUtil
- IS_JAVA_11 - Static variable in class com.actelion.research.gui.hidpi.HiDPIUtil
- IS_JAVA_8 - Static variable in class com.actelion.research.gui.hidpi.HiDPIUtil
- IS_JAVA_8_OR_OLDER - Static variable in class com.actelion.research.gui.hidpi.HiDPIUtil
- IS_JAVA_9 - Static variable in class com.actelion.research.gui.hidpi.HiDPIUtil
- IS_VENDOR_APPLE - Static variable in class com.actelion.research.gui.hidpi.HiDPIUtil
- is3D() - Method in class com.actelion.research.chem.Molecule
- is3D(Molecule3D) - Static method in class com.actelion.research.chem.io.AbstractParser
- is64BitJRE() - Static method in class com.actelion.research.util.Platform
- isAcceptable(ArrayList<ConformationRule>) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- isAcceptor(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- isAcceptor(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- isAcceptor(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isAcceptor(StereoMolecule, int) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- isAcidicOxygen(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- isAcidicOxygenAtPhosphoricAcid(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- isActive() - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- isActive() - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- isAlcoholicOxygen(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isAliphatic(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- isAliphaticAtom(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isAlkaliMetal(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isAlkaline(int) - Static method in class com.actelion.research.chem.PeriodicTable
- isAlkylAmine(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- isAllDataIn() - Method in interface com.actelion.research.util.IPipeline
- isAllDataIn() - Method in class com.actelion.research.util.Pipeline
- isAllLetter(String) - Static method in class com.actelion.research.util.StringFunctions
- isAllLowerCase(String) - Static method in class com.actelion.research.util.StringFunctions
- isAllUpperCase(String) - Static method in class com.actelion.research.util.StringFunctions
- isAllylicAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isAltDown() - Method in interface com.actelion.research.share.gui.editor.io.IKeyEvent
- isAltDown() - Method in interface com.actelion.research.share.gui.editor.io.IMouseEvent
- isAmide(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- isAmideTypeBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Evaluates, whether bond is an amide bond, thio-amide, or amidine bond.
- isAmine(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- isAnimating() - Method in class com.actelion.research.gui.hidpi.HiDPIIconButton
- isAqua() - Static method in class com.actelion.research.gui.LookAndFeelHelper
- isAromatic() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- isAromatic(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- isAromatic(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- isAromatic(int) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- isAromatic(int) - Method in class com.actelion.research.chem.RingCollection
-
Return whether the ring is considered aromatic.
- isAromaticAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isAromaticBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isArylAmine(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- isAtomColorSupported() - Method in class com.actelion.research.gui.JDrawArea
- isAtomColorSupported() - Method in class com.actelion.research.share.gui.editor.Model
- isAtomConfigurationUnknown(int) - Method in class com.actelion.research.chem.Molecule
- isAtomFlag(int, int) - Method in class com.actelion.research.chem.Molecule3D
- isAtomicNoElectronegative(int) - Static method in class com.actelion.research.chem.Molecule
- isAtomicNoElectropositive(int) - Static method in class com.actelion.research.chem.Molecule
- isAtomMarkedForDeletion(int) - Method in class com.actelion.research.chem.Molecule
-
Checks whether this atom was marked to be deleted and not deleted yet.
- isAtomMember(int, int) - Method in class com.actelion.research.chem.RingCollection
- isAtomParityPseudo(int) - Method in class com.actelion.research.chem.Molecule
-
Pseudo paries are parities that indicate a relative configuration.
- isAtomStereoCenter(int) - Method in class com.actelion.research.chem.Molecule
-
Atoms with pseudo parities are not considered stereo centers.
- isAutoMappedAtom(int) - Method in class com.actelion.research.chem.Molecule
- isBackboneSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
-
A backbone search is a hash code comparison from encoding stereo and unsaturation depleted structures.
- isBasicNitrogen(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- isBINAPChiralityBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Checks whether bond is an axial chirality bond of the BINAP type.
- isBinary - Variable in class com.actelion.research.chem.descriptor.DescriptorInfo
- isBinaryFingerprint(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- isBitSet(int) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- isBitSet(int) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- isBitSet(int) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- isBitSet(int) - Method in class com.actelion.research.util.datamodel.IntVec
- isBitSet(int[], int) - Static method in class com.actelion.research.util.BitUtils
- isBitSet(int[], int) - Static method in class com.actelion.research.util.datamodel.IntVec
- isBitSet(int, int) - Static method in class com.actelion.research.util.datamodel.IntVec
- isBondBackgroundHilited(int) - Method in class com.actelion.research.chem.Molecule
-
Used for depiction only.
- isBondBridge(int) - Method in class com.actelion.research.chem.Molecule
- isBondForegroundHilited(int) - Method in class com.actelion.research.chem.Molecule
-
Used for depiction only.
- isBondMarkedForDeletion(int) - Method in class com.actelion.research.chem.Molecule
-
Checks whether this bond was marked to be deleted and not deleted yet.
- isBondMember(int, int) - Method in class com.actelion.research.chem.RingCollection
- isBondParityPseudo(int) - Method in class com.actelion.research.chem.Molecule
- isBondParityUnknownOrNone(int) - Method in class com.actelion.research.chem.Molecule
-
This hint/flag is set by CoordinateInventor for double bonds without given EZ-parity, because the new coordinates may imply a not intended EZ-parity.
- isCancelled() - Method in class com.actelion.research.gui.JDrawDialog
- isCapacityLimitBreakes() - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
-
If true not all index combinations were generated.
- isCapacityLimitBreakes() - Method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- isCapacityLimitBreakes() - Method in class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
-
If true not all index combinations where generated.
- isCapitalizedWord(String) - Static method in class com.actelion.research.util.StringFunctions
- isCarbonConnected2Hetero(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isCarbonExclusiveNode() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- isCarbonInteraction(int) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- isCarbonOnlyConnected2Hetero(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isCarbonTwoValencesMinimum(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isCarboxyC(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isCentralAlleneAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isChalcogene(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isChargeNeg(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- isChargePos(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- isCluster() - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
- isCommand() - Method in interface com.actelion.research.share.gui.editor.actions.Action
- isCommand() - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- isCommand() - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- isConclusive() - Method in class com.actelion.research.util.DateAnalysis
-
Call this only once after calling analyse() once or multiple times.
- isConnected2Hetero(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isConsiderAromaticRings() - Method in class com.actelion.research.chem.mcs.MCS
- isConsiderAromaticRings() - Method in class com.actelion.research.chem.mcs.MCSFast
- isConsiderRings() - Method in class com.actelion.research.chem.mcs.MCS
- isConsiderRings() - Method in class com.actelion.research.chem.mcs.MCSFast
- isControlDown() - Method in interface com.actelion.research.share.gui.editor.io.IKeyEvent
- isControlDown() - Method in interface com.actelion.research.share.gui.editor.io.IMouseEvent
- isCovered(long[], long[]) - Method in class org.openmolecules.chem.conf.gen.TorsionSetEliminationRule
-
Checks whether mask and data as elimination rule are covered by this rule.
- isCyanoN(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isDarkLookAndFeel() - Static method in class com.actelion.research.gui.LookAndFeelHelper
- isDataFlavorSupported(DataFlavor) - Method in class com.actelion.research.gui.clipboard.ImageClipboardHandler.ImageSelection
- isDataFlavorSupported(DataFlavor) - Method in class com.actelion.research.gui.dnd.MoleculeTransferable
- isDataFlavorSupported(DataFlavor) - Method in class com.actelion.research.gui.dnd.ReactionTransferable
- isDataFlavorSupported(DataFlavor) - Method in class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
- isDeletable() - Method in class com.actelion.research.chem.AbstractDrawingObject
- isDelocalized(int) - Method in class com.actelion.research.chem.RingCollection
-
Return whether the ring is considered delocalized, which are 6-membered aromatic rings with no preference concerning where the double bonds are located.
- isDelocalizedBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
A bond is considered delocalized, if it has different bond orders in different, but energetically equivalent mesomeric structures.
- isDescriptorShortName(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- isDonor(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- isDonor(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- isDonor(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isDonorHeavyAtom(StereoMolecule, int) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- isDonorHydrogen(StereoMolecule, int) - Static method in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- isDragFlavorSupported(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- isDragFlavorSupported(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- isDragFlavorSupported(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.SDFileMoleculeDropAdapter
- isDropOK(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- isDropOK(DropTargetDragEvent) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- isEarthAlkaliMetal(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isEditable() - Method in class com.actelion.research.gui.JChemistryView
- isEditable() - Method in class com.actelion.research.gui.JStructureView
- isEditable() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- isElectronegative(int) - Method in class com.actelion.research.chem.Molecule
- isElectropositive(int) - Method in class com.actelion.research.chem.Molecule
- isELUSIVE() - Static method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- isELUSIVE() - Static method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- isELUSIVE() - Static method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- isEmpty() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
- isEmpty() - Method in class com.actelion.research.chem.reaction.Reaction
- isEmpty() - Method in class com.actelion.research.util.IntQueue
- isEmpty() - Method in class com.actelion.research.util.Pipeline
- isEmptyString(String) - Static method in class com.actelion.research.share.gui.editor.actions.ChangeAtomPropertiesAction
- isEnabled() - Method in class org.openmolecules.chem.conf.so.ConformationRule
- isEnd() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- isEndOfRunReached() - Method in class com.actelion.research.chem.mcs.RunBondVector2IdCode
- isEtherOxygenAtAromatic(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isExactSearch() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
-
An exact search is a comparison of idcodes of standardized molecules with full stereo features.
- isExactSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
-
An exact search is a comparison of idcodes of standardized molecules with full stereo features.
- isExtensionListInDescription() - Method in class com.actelion.research.chem.io.CompoundFileFilter
-
Returns whether the extension list (.jpg, .gif, etc) should show up in the human readable description.
- isFinalized() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- isFixedDistance() - Method in class org.openmolecules.chem.conf.so.DistanceRule
- isFlatNitrogen(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Checks whether this nitrogen atom is flat, because it has a double bond, is member of an aromatic ring or is part of amide, an enamine or in resonance with an aromatic ring.
- isFlexible() - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- isFragment() - Method in class com.actelion.research.chem.ExtendedDepictor
- isFragment() - Method in class com.actelion.research.chem.Molecule
-
Molecule objects may represent complete molecules or sub-structure fragments, depending on, whether they are flagges as being a fragment or not.
- isFragment() - Method in class com.actelion.research.chem.reaction.Reaction
-
The naming of this method is in analogy to the corresponding method of the Molecule class.
- isFragment() - Method in class com.actelion.research.share.gui.editor.Model
- isFragmentIndexInMoleculeIndex() - Method in class com.actelion.research.chem.SSSearcherWithIndex
- isFragmentInMolecule() - Method in class com.actelion.research.chem.SSSearcher
-
Fastest check, whether the molecule contains the fragment.
- isFragmentInMolecule() - Method in class com.actelion.research.chem.SSSearcherWithIndex
- isFragmentInMolecule(int) - Method in class com.actelion.research.chem.SSSearcher
-
Fastest check, whether the molecule contains the fragment.
- isFragmentInMoleculeWithoutIndex() - Method in class com.actelion.research.chem.SSSearcherWithIndex
- isGDIFontDrawing() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- isGDIPenDrawing() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- isGDIPenWidthDrawing() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- isGraphSimilarity - Variable in class com.actelion.research.chem.descriptor.DescriptorInfo
- isGreaterThan(Angle) - Method in class com.actelion.research.util.Angle
-
Determines whether this angle is on the greater value side of angle a, i.e.
- isHalogene(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isHetero(ExtendedMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- ISimilarityCalculator<T> - Interface in com.actelion.research.chem.descriptor
- ISimilarityHandlerFactory - Interface in com.actelion.research.chem.descriptor
- isInAromaticRingOfSize(MMFFMolecule, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
-
Returns true if the atom is in an aromatic ring of given size.
- isInevitablePharmacophorePoint(int) - Method in interface com.actelion.research.chem.descriptor.flexophore.IMolDistHist
- isInevitablePharmacophorePoint(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- isInevitablePharmacophorePoint(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- isInFrontInTabbedPane(String) - Method in class com.actelion.research.gui.dock.JDockingPanel
- isInMesoFragment(int) - Method in class com.actelion.research.chem.CanonizerMesoHelper
- isInverted(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
- isIsolatedCarbon(StereoMolecule, int, int[]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isLargestFragmentOnly() - Method in class com.actelion.research.chem.StructureSearchSpecification
-
This setting is relevant for all search types except the substructure search.
- isLayouted() - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
- isLinear - Variable in class com.actelion.research.chem.forcefield.mmff.AngleBend
- isLinkNode() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- isLinux() - Static method in class com.actelion.research.util.Platform
- isMacintosh() - Static method in class com.actelion.research.util.Platform
- isMarked() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- isMarked(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- isMarkedAtom(int) - Method in class com.actelion.research.chem.Molecule
-
Atom marking may be used for any external purpose
- isMaxCapacityMatchListContainerReached() - Method in class com.actelion.research.chem.mcs.SubStructSearchExhaustiveTreeWalker
-
The sub structure search algortihm stops if the maximum capacity of the match list container is reached.
- isMaximized() - Method in class com.actelion.research.gui.dock.Dockable
- isMaximized() - Method in class com.actelion.research.gui.dock.JDockingPanel
- isMember(int) - Method in class com.actelion.research.chem.coords.InventorFragment
- isMemberOfNitroGroup(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- isMeso() - Method in class com.actelion.research.chem.CanonizerMesoHelper
- isMetalAtom(int) - Method in class com.actelion.research.chem.Molecule
- isMissingParenthesis(String) - Static method in class com.actelion.research.util.StringFunctions
- isModeQuery() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- isMoleculeInOrder() - Method in class com.actelion.research.chem.Molecule3D
- isMoleculeNext() - Method in class com.actelion.research.chem.io.RDFileParser
- isMoreGeneral(long[], long[]) - Method in class org.openmolecules.chem.conf.gen.TorsionSetEliminationRule
-
Checks whether mask and data constitute a more general rule than this and therefore include this.
- isMovable() - Method in class com.actelion.research.share.gui.Arrow
- isMovable() - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
- isNaN() - Method in class com.actelion.research.chem.Coordinates
- isNaturalAbundance(int) - Method in class com.actelion.research.chem.Molecule
- isNewSubstance() - Static method in class com.actelion.research.gui.LookAndFeelHelper
-
This is Substance from version 5
- isNewTorsionSet(TorsionSet) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- isNitrogenFamily(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isNitroGroupN(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomFunctionAnalyzer
- isNonsingular() - Method in class com.actelion.research.calc.LUDecomposition
-
Is the matrix nonsingular?
- isNoReactionSearch() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- isNoStereoSearch() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
-
A noStereo search is a hash code comparison from encoding stereo depleted structures.
- isNoStereoSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
-
A noStereo search is a hash code comparison from encoding stereo depleted structures.
- isNoStereoTautomerSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
-
A no-stereo-tautomer search is a hash code comparison from encoding stereo depleted generic tautomer structures.
- isNoStructureSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
- isOldSubstance() - Static method in class com.actelion.research.gui.LookAndFeelHelper
-
This is Substance version 3 or 4
- IsomericSmilesCreator - Class in com.actelion.research.chem
- IsomericSmilesCreator(StereoMolecule) - Constructor for class com.actelion.research.chem.IsomericSmilesCreator
-
Creates an IsomericSmilesCreator, which doesn't include atom mapping into generated smiles.
- IsomericSmilesCreator(StereoMolecule, boolean) - Constructor for class com.actelion.research.chem.IsomericSmilesCreator
-
Creates an IsomericSmilesCreator, which may include atom mapping numbers into generated smiles.
- isOnlyCarbon(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- isOnlyOneConformer() - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- isOnProductSide(double, double) - Method in class com.actelion.research.chem.reaction.ReactionArrow
- isOnProductSide(double, double) - Method in class com.actelion.research.share.gui.editor.Model
- isOnProductSide(float, float) - Method in class com.actelion.research.share.gui.Arrow
- isOnProductSide(float, float) - Method in interface com.actelion.research.share.gui.editor.chem.IArrow
- isOpen() - Method in class com.actelion.research.chem.io.CompoundFileParser
- isOptimize3D() - Method in class com.actelion.research.chem.io.AbstractParser
- isOrganicAtom(int) - Method in class com.actelion.research.chem.Molecule
- IsotopeHelper - Class in com.actelion.research.chem
- IsotopeHelper() - Constructor for class com.actelion.research.chem.IsotopeHelper
- isOverlap(SubGraphIndices) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- isOverlap(ListWithIntVec) - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- isOverlap(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- isOverlap(IBitArray) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- isOverlappingBits(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- isPerfectlyMapped() - Method in class com.actelion.research.chem.reaction.Reaction
-
Checks, whether all non-hydrogen atoms are mapped and whether every reactant atom has exactly one assigned product atom.
- isPiConsidered(int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
- isPseudoRotatableBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
In a consecutive sequence of sp-hybridized atoms multiple single bonds cause redundant torsions.
- isPurelyOrganic() - Method in class com.actelion.research.chem.Molecule
- isQuaQua() - Static method in class com.actelion.research.gui.LookAndFeelHelper
- isQueryInReaction() - Method in class com.actelion.research.chem.reaction.SRSearcher
-
Performs a reaction substructure search with the SSSearcher.cDefaultMatchMode
- isQueryInReaction(int) - Method in class com.actelion.research.chem.reaction.SRSearcher
- isReaction() - Method in class com.actelion.research.share.gui.editor.Model
- isReactionLayoutRequired() - Method in class com.actelion.research.chem.reaction.Reaction
- isReactionNext() - Method in class com.actelion.research.chem.io.RDFileParser
- isRegexInString(String, String) - Static method in class com.actelion.research.util.StringFunctions
- isRetronSearch() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- isRing() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- isRingAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isRingBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isRingExclusively(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isRingInMolecule(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isRotatableBond(int) - Method in class com.actelion.research.chem.conf.BondRotationHelper
- isSelected() - Method in class com.actelion.research.chem.AbstractDrawingObject
- isSelected() - Method in class com.actelion.research.gui.dock.Dockable
-
Answers if the panel is currently selected, i.e.
- isSelected() - Method in class com.actelion.research.gui.dock.TreeElement
- isSelected() - Method in class com.actelion.research.gui.dock.TreeLeaf
- isSelected() - Method in class com.actelion.research.share.gui.Arrow
- isSelected() - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
- isSelected() - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
- isSelectedAtom(int) - Method in class com.actelion.research.chem.Molecule
- isSelectedBond(int) - Method in class com.actelion.research.chem.Molecule
- isSetRingMMFFAromaticity(int) - Method in class com.actelion.research.chem.forcefield.mmff.MMFFMolecule
-
Returns true if the given ring has had its MMFF aromaticity flag set.
- isShiftDown() - Method in interface com.actelion.research.share.gui.editor.io.IKeyEvent
- isShiftDown() - Method in interface com.actelion.research.share.gui.editor.io.IMouseEvent
- isSimilaritySearch() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- isSimilaritySearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
- isSimpleHydrogen(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Uncharged hydrogen atoms with no isotop information nor with an attached custom label are considered simple and can usually be suppressed, effectively converting them from an explicit to an implicit hydrogen atom.
Note: This method returns true for uncharged, natural abundance hydrogens without custom labels even if they have a non-standard bonding situation (everything being different from having one single bonded non-simple-hydrogen neighbour, e.g. - isSingleConformationModeQuery() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- isSmallerThan(Angle) - Method in class com.actelion.research.util.Angle
-
Determines whether this angle is on the smaller value side of angle a, i.e.
- isSmallRingAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isSmallRingBond(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isStabilizedAtom(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- isStereoBond(int) - Method in class com.actelion.research.chem.Molecule
-
Checks whether bond is drawn as up/down single bond
- isStereoBond(int, int) - Method in class com.actelion.research.chem.Molecule
-
Checks whether bond is drawn as up/down single bond and is connected to atom with its pointed tip
- isSubreactionSearch() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- isSubstance() - Static method in class com.actelion.research.gui.LookAndFeelHelper
- isSubstructureSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
- isSulfoxyGroup(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isSupportedSearchType(ReactionSearchSpecification) - Method in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
-
Returns true if idcodes and/or hash codes for this particular search specification are directly available by the source, i.e.
- isSupportedSearchType(StructureSearchSpecification) - Method in interface com.actelion.research.chem.StructureSearchDataSource
-
Returns true if idcodes and/or hash codes for this particular search specification are directly available by the source, i.e.
- isSurroundedBy(Shape) - Method in class com.actelion.research.chem.AbstractDrawingObject
- isTautomerSearch() - Method in class com.actelion.research.chem.StructureSearchSpecification
-
A tautomer search is a hash code comparison from encoding generic tautomer structures.
- isTerminal() - Method in class com.actelion.research.chem.io.pdb.parser.Residue
- isTerminalC() - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- isThioEther(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isTransparent() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- IStructureNameResolver - Interface in com.actelion.research.chem.name
-
Created by thomas on 7/13/17.
- isUnix() - Static method in class com.actelion.research.util.Platform
- isUpperAndLowerCase(String) - Static method in class com.actelion.research.util.StringFunctions
- isUsed() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- isUsed() - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- isUserChange() - Method in class com.actelion.research.gui.DrawAreaEvent
- isValid() - Method in class com.actelion.research.chem.conf.TorsionDetail
- isValidBitIndex(int) - Method in class com.actelion.research.util.datamodel.IntVec
- isValidBitIndex(int[], int) - Static method in class com.actelion.research.util.BitUtils
- isValidSolution(SolutionCompleteGraph) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
-
If a single histogram is not matching the solution is invalid.
- isValidSolution(SolutionCompleteGraph) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- isValidSubstituentNameStart(String) - Static method in class com.actelion.research.chem.NamedSubstituents
- isValidType(int) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- isVector - Variable in class com.actelion.research.chem.descriptor.DescriptorInfo
- isVertical() - Method in class com.actelion.research.gui.dock.TreeFork
- isVisibleDockable() - Method in class com.actelion.research.gui.dock.Dockable
-
Answers if the panel is currently visible, i.e.
- isVoidTransformation() - Method in class com.actelion.research.chem.DepictorTransformation
- isWildcard(StereoMolecule, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- isWindows() - Static method in class com.actelion.research.util.Platform
- isWorseThan(SelfOrganizedConformer) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
-
Checks whether the total strain of this Conformer is larger than that of conformer, assuming that the calculated strain values are up-to-date.
- itemStateChanged(ItemEvent) - Method in class com.actelion.research.gui.JAtomQueryFeatureDialog
- iUSER_CHARGES - Static variable in class com.actelion.research.chem.io.Mol2FileParser
- IValidationListener - Interface in com.actelion.research.share.gui.editor.listeners
-
Project: User: rufenec Date: 11/24/2014 Time: 3:27 PM
J
- JAtomLabelDialog - Class in com.actelion.research.gui
- JAtomLabelDialog(Frame, ExtendedMolecule, int) - Constructor for class com.actelion.research.gui.JAtomLabelDialog
- JAtomQueryFeatureDialog - Class in com.actelion.research.gui
- JAtomQueryFeatureDialog(Dialog, ExtendedMolecule, int, boolean) - Constructor for class com.actelion.research.gui.JAtomQueryFeatureDialog
- JAtomQueryFeatureDialog(Frame, ExtendedMolecule, int, boolean) - Constructor for class com.actelion.research.gui.JAtomQueryFeatureDialog
- JBondQueryFeatureDialog - Class in com.actelion.research.gui
- JBondQueryFeatureDialog(Dialog, ExtendedMolecule, int) - Constructor for class com.actelion.research.gui.JBondQueryFeatureDialog
- JBondQueryFeatureDialog(Frame, ExtendedMolecule, int) - Constructor for class com.actelion.research.gui.JBondQueryFeatureDialog
- JBrowseButtons - Class in com.actelion.research.gui.hidpi
- JBrowseButtons(boolean, int, int, ActionListener) - Constructor for class com.actelion.research.gui.hidpi.JBrowseButtons
- JBrowseButtons(boolean, ActionListener) - Constructor for class com.actelion.research.gui.hidpi.JBrowseButtons
- JChemistryView - Class in com.actelion.research.gui
- JChemistryView(int) - Constructor for class com.actelion.research.gui.JChemistryView
-
Creates a new JChemistryView for showing a reaction or molecules.
- JChemistryView(int, int, int) - Constructor for class com.actelion.research.gui.JChemistryView
-
Creates a new JChemistryView for showing a reaction or molecules.
- JDockingPanel - Class in com.actelion.research.gui.dock
- JDockingPanel() - Constructor for class com.actelion.research.gui.dock.JDockingPanel
-
Creates a docking panel to which any Dockables may be added by the respective dock methods.
- JDrawArea - Class in com.actelion.research.gui
- JDrawArea(StereoMolecule, int) - Constructor for class com.actelion.research.gui.JDrawArea
- JDrawDialog - Class in com.actelion.research.gui
- JDrawDialog(Dialog, StereoMolecule) - Constructor for class com.actelion.research.gui.JDrawDialog
- JDrawDialog(Dialog, StereoMolecule, String) - Constructor for class com.actelion.research.gui.JDrawDialog
- JDrawDialog(Frame) - Constructor for class com.actelion.research.gui.JDrawDialog
- JDrawDialog(Frame, boolean) - Constructor for class com.actelion.research.gui.JDrawDialog
- JDrawDialog(Frame, boolean, String) - Constructor for class com.actelion.research.gui.JDrawDialog
- JDrawDialog(Frame, Reaction) - Constructor for class com.actelion.research.gui.JDrawDialog
- JDrawDialog(Frame, Reaction, String) - Constructor for class com.actelion.research.gui.JDrawDialog
- JDrawDialog(Frame, StereoMolecule) - Constructor for class com.actelion.research.gui.JDrawDialog
- JDrawDialog(Frame, StereoMolecule[]) - Constructor for class com.actelion.research.gui.JDrawDialog
- JDrawDialog(Frame, StereoMolecule[], String) - Constructor for class com.actelion.research.gui.JDrawDialog
- JDrawDialog(Frame, StereoMolecule, String) - Constructor for class com.actelion.research.gui.JDrawDialog
- JDrawPanel - Class in com.actelion.research.gui
- JDrawPanel(StereoMolecule) - Constructor for class com.actelion.research.gui.JDrawPanel
- JDrawPanel(StereoMolecule, boolean) - Constructor for class com.actelion.research.gui.JDrawPanel
- JDrawPanel(StereoMolecule, int) - Constructor for class com.actelion.research.gui.JDrawPanel
- JDrawToolbar - Class in com.actelion.research.gui
- JDrawToolbar(JDrawArea) - Constructor for class com.actelion.research.gui.JDrawToolbar
- JDrawToolbar(JDrawArea, int) - Constructor for class com.actelion.research.gui.JDrawToolbar
- JEditableChemistryView - Class in com.actelion.research.gui
- JEditableChemistryView(int) - Constructor for class com.actelion.research.gui.JEditableChemistryView
-
Creates a new JEditableChemistryView for showing & editing a reaction or molecule(s).
- JEditableStructureView - Class in com.actelion.research.gui
- JEditableStructureView() - Constructor for class com.actelion.research.gui.JEditableStructureView
- JEditableStructureView(int, int) - Constructor for class com.actelion.research.gui.JEditableStructureView
- JEditableStructureView(StereoMolecule) - Constructor for class com.actelion.research.gui.JEditableStructureView
- JEditableStructureView(StereoMolecule, int, int) - Constructor for class com.actelion.research.gui.JEditableStructureView
- JFileChooserOverwrite - Class in com.actelion.research.gui
- JFileChooserOverwrite() - Constructor for class com.actelion.research.gui.JFileChooserOverwrite
- JFXCanvasDepictor - Class in com.actelion.research.jfx.gui.chem
-
Project: User: rufenec Date: 10/12/11 Time: 6:00 PM
- JFXCanvasDepictor(StereoMolecule) - Constructor for class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- JFXCanvasDepictor(StereoMolecule, int) - Constructor for class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- JMessageBar - Class in com.actelion.research.gui
- JStructureView - Class in com.actelion.research.gui
- JStructureView() - Constructor for class com.actelion.research.gui.JStructureView
- JStructureView(int, int) - Constructor for class com.actelion.research.gui.JStructureView
- JStructureView(StereoMolecule) - Constructor for class com.actelion.research.gui.JStructureView
-
This creates a standard structure view where the displayed molecule is used for D&D and clipboard transfer after removing atom colors and bond highlights.
- JStructureView(StereoMolecule, int, int) - Constructor for class com.actelion.research.gui.JStructureView
-
This creates a standard structure view where the displayed molecule is used for D&D and clipboard transfer after removing atom colors and bond highlights.
- JStructureView(StereoMolecule, StereoMolecule) - Constructor for class com.actelion.research.gui.JStructureView
-
This creates a structure view that distinguishes between displayed molecule and the one being used for D&D and clipboard transfer.
- JStructureView(StereoMolecule, StereoMolecule, int, int) - Constructor for class com.actelion.research.gui.JStructureView
-
This creates a structure view that distinguishes between displayed molecule and the one being used for D&D and clipboard transfer.
- JTextDrawingObjectDialog - Class in com.actelion.research.gui
- JTextDrawingObjectDialog(Dialog, TextDrawingObject) - Constructor for class com.actelion.research.gui.JTextDrawingObjectDialog
- JTextDrawingObjectDialog(Frame, TextDrawingObject) - Constructor for class com.actelion.research.gui.JTextDrawingObjectDialog
K
- ka - Variable in class com.actelion.research.chem.forcefield.mmff.AngleBend
- ka(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
-
Returns 'ka' the force constant for a given index in the table.
- ka(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
-
Returns 'ka' given a molecule and three connected atoms which form an angle.
- KabschAlignment - Class in com.actelion.research.chem.alignment3d
-
described in: DOI 10.1002/jcc.20110 "Using Quaternions to Calculate RMSD"
- KabschAlignment(Conformer, Conformer) - Constructor for class com.actelion.research.chem.alignment3d.KabschAlignment
-
first conformer is the reference, second conformer is rotated and translated to minimize the RMSD
- KabschAlignment(Coordinates[], Coordinates[], int[][]) - Constructor for class com.actelion.research.chem.alignment3d.KabschAlignment
- kb - Variable in class com.actelion.research.chem.forcefield.mmff.BondStretch
- kb(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bndk
-
Returns 'kb' the force constant at a given index in the Bndk table.
- kb(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bond
-
Returns the 'kb' value at the given index from the Bond table.
- kb(MMFFMolecule, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bond
-
Returns 'kb' given a molecule and two atoms in that molecule that form a bond.
- kb(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Dfsb
-
Returns the equivalent 'kb' value for a given set of three atoms.
- Kb() - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
- Kb(double, double, double) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
- Kb(int) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
- kba(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Stbn
-
Returns 'kba' for a given index in the table.
- kba_ijk - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
- kba_kji - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
- kCDXObj_Bond - Static variable in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- kCDXObj_Fragment - Static variable in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- kCDXObj_Group - Static variable in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- kCDXObj_Node - Static variable in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- kCDXObj_Page - Static variable in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- KEEP_INITIAL_COORDINATES - Static variable in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- KEY_IS_ATOM_LABEL - Static variable in class com.actelion.research.share.gui.editor.Model
- KEY_IS_INVALID - Static variable in class com.actelion.research.share.gui.editor.Model
- KEY_IS_SUBSTITUENT - Static variable in class com.actelion.research.share.gui.editor.Model
- KEY_IS_VALID_START - Static variable in class com.actelion.research.share.gui.editor.Model
- keyPressed(KeyEvent) - Method in class com.actelion.research.gui.hidpi.JBrowseButtons
- keyPressed(KeyEvent) - Method in class com.actelion.research.gui.JDrawArea
- keyPressed(KeyEvent) - Method in class com.actelion.research.gui.JDrawDialog
- keyReleased(KeyEvent) - Method in class com.actelion.research.gui.hidpi.JBrowseButtons
- keyReleased(KeyEvent) - Method in class com.actelion.research.gui.JDrawArea
- keyReleased(KeyEvent) - Method in class com.actelion.research.gui.JDrawDialog
- KEYSTROKEFONTSIZE - Static variable in class com.actelion.research.share.gui.editor.actions.DrawAction
- keyTyped(KeyEvent) - Method in class com.actelion.research.gui.hidpi.JBrowseButtons
- keyTyped(KeyEvent) - Method in class com.actelion.research.gui.JDrawArea
- keyTyped(KeyEvent) - Method in class com.actelion.research.gui.JDrawDialog
L
- lassoColor() - Static method in class com.actelion.research.gui.JDrawArea
- lastHightlightPoint - Variable in class com.actelion.research.share.gui.editor.actions.AtomHighlightAction
- lastIndexOf(int[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- lastIndexOfNot(byte[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- layoutChildren() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- layoutContainer(Container) - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Method
- LEFT - Static variable in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Field
- LEN_INTEGER_BYTES - Static variable in class com.actelion.research.util.datamodel.IntVec
- length() - Method in interface com.actelion.research.chem.forcefield.mmff.Searchable
-
This function should return the total number of rows in a searchable table.
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Bndk
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Bond
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.CovRad
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Dfsb
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.HerschbachLaurie
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.OutOfPlane
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Stbn
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.Torsion
- length() - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
- length() - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Returns the length (or magnitude) of this vector.
- length() - Method in class com.actelion.research.util.datamodel.IntArray
- LIGAND - Static variable in class com.actelion.research.chem.Molecule3D
- LIGAND_GROUP - Static variable in class com.actelion.research.chem.io.pdb.parser.StructureAssembler
- LigandPose - Class in com.actelion.research.chem.docking
- LigandPose(Conformer, AbstractScoringEngine, double) - Constructor for class com.actelion.research.chem.docking.LigandPose
- LIMIT_NEIGHBOURS_SINCE_LAST_ADDED - Static variable in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- linear(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
-
Returns the linear bool of an atom given its MMFF type.
- LinearRegression - Class in com.actelion.research.calc.regression.linear.simple
-
LinearRegression 2009 MvK: Start implementation
- LinearRegression() - Constructor for class com.actelion.research.calc.regression.linear.simple.LinearRegression
- lineTo(int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- lineTo(int, int) - Method in class com.actelion.research.gui.wmf.WMF
- LINK_NODE - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- Linker - Class in com.actelion.research.chem.descriptor.flexophore.entity
-
Linker
- Linker(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- LIPO_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- listeners - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- ListInteger<T> - Class in com.actelion.research.chem.io.pdb.parser
-
ListInteger
- ListInteger(List<T>, int) - Constructor for class com.actelion.research.chem.io.pdb.parser.ListInteger
- ListWithIntVec - Class in com.actelion.research.chem.mcs
- ListWithIntVec() - Constructor for class com.actelion.research.chem.mcs.ListWithIntVec
- ListWithIntVec(int) - Constructor for class com.actelion.research.chem.mcs.ListWithIntVec
- ListWithIntVec(int, int) - Constructor for class com.actelion.research.chem.mcs.ListWithIntVec
- ListWithIntVec(ListWithIntVec) - Constructor for class com.actelion.research.chem.mcs.ListWithIntVec
- ListWithIntVecIdCode - Class in com.actelion.research.chem.properties.complexity
- ListWithIntVecIdCode(int) - Constructor for class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- ListWithIntVecIdCode(ListWithIntVec) - Constructor for class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
-
Flat constructor.
- ListWithIntVecIdCode(ListWithIntVecIdCode) - Constructor for class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
-
Deep constructor.
- LittleEndianDataInputStream - Class in com.actelion.research.util
- LittleEndianDataInputStream(InputStream) - Constructor for class com.actelion.research.util.LittleEndianDataInputStream
- LittleEndianDataOutputStream - Class in com.actelion.research.util
- LittleEndianDataOutputStream(OutputStream) - Constructor for class com.actelion.research.util.LittleEndianDataOutputStream
- load(File) - Method in class com.actelion.research.chem.io.AbstractParser
- load(String) - Method in class com.actelion.research.chem.io.AbstractParser
- load(String, Reader) - Method in class com.actelion.research.chem.io.AbstractParser
- loadCache(String) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
-
Loads pre-calculated rigid fragment coordinates from a cache file, which is either a text file created by the createCacheFiles() method, or a zip archive of the text file.
- loadDefaultCache() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
-
This loads the default cache file
- loadGroup(String) - Method in class com.actelion.research.chem.io.AbstractParser
- loadGroup(String, Reader) - Method in class com.actelion.research.chem.io.AbstractParser
- loadGroup(String, Reader, int, int) - Method in class com.actelion.research.chem.io.AbstractParser
- loadGroup(String, Reader, int, int) - Method in class com.actelion.research.chem.io.Mol2FileParser
- loadTable(String, Tables) - Static method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
-
Loads and registers a tables object with the ForceField class so it can be used by new ForceField instances.
- locateBonds() - Method in class com.actelion.research.chem.coords.InventorFragment
- locateDelocalizedDoubleBonds(boolean[]) - Method in class com.actelion.research.chem.AromaticityResolver
-
This method promotes all necessary bonds of the defined delocalized part of the molecule from single to double bonds in order to create a valid delocalized system of conjugated single and double bonds.
- locateDelocalizedDoubleBonds(boolean[], boolean, boolean) - Method in class com.actelion.research.chem.AromaticityResolver
-
This method promotes all necessary bonds of the defined delocalized part of the molecule from single to double bonds in order to create a valid delocalized system of conjugated single and double bonds.
- log() - Method in class com.actelion.research.calc.Matrix
-
Log function from the class Math .
- log2(int) - Static method in class com.actelion.research.calc.Logarithm
- Logarithm - Class in com.actelion.research.calc
-
Logarithm Mar 14, 2013 MvK Start implementation
- Logarithm() - Constructor for class com.actelion.research.calc.Logarithm
- longValue() - Method in class com.actelion.research.util.concurrent.AtomicFloat
- LookAndFeelHelper - Class in com.actelion.research.gui
- LookAndFeelHelper() - Constructor for class com.actelion.research.gui.LookAndFeelHelper
- lookupBondLength(StereoMolecule, int) - Static method in class com.actelion.research.chem.conf.BondLengthSet
-
Returns an estimate of the bond length based on atom and bond characteristics.
- lostOwnership(Clipboard, Transferable) - Method in class com.actelion.research.gui.clipboard.ImageClipboardHandler.ImageSelection
- lostOwnership(Clipboard, Transferable) - Method in class com.actelion.research.gui.dnd.MoleculeTransferable
- lostOwnership(Clipboard, Transferable) - Method in class com.actelion.research.gui.dnd.ReactionTransferable
- lostOwnership(Clipboard, Transferable) - Method in class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
- lowerQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianDouble
- lowerQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianFloat
- lowerQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianInteger
- lowerQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianLong
- LUDecomposition - Class in com.actelion.research.calc
-
LU Decomposition.
- LUDecomposition(Matrix) - Constructor for class com.actelion.research.calc.LUDecomposition
-
LU Decomposition Structure to access L, U and piv.
M
- main(String[]) - Static method in class com.actelion.research.calc.combinatorics.CombinationGenerator
- main(String[]) - Static method in class com.actelion.research.calc.filter.SlidingWindow
- main(String[]) - Static method in class com.actelion.research.calc.histogram.Histogram
- main(String[]) - Static method in class com.actelion.research.chem.contrib.DiastereoIDTest
- main(String[]) - Static method in class com.actelion.research.chem.contrib.HoseCodeCreator
- main(String[]) - Static method in class com.actelion.research.chem.contrib.testChiralDia
- main(String[]) - Static method in class com.actelion.research.chem.contrib.testDiaID
- main(String[]) - Static method in class com.actelion.research.chem.contrib.testHoses
- main(String[]) - Static method in class com.actelion.research.chem.descriptor.FingerPrintGenerator
- main(String[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- main(String[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.example.MatchFlexophoreNodesMain
- main(String[]) - Static method in class com.actelion.research.chem.descriptor.flexophore.generator.AtomTypeMap
- main(String[]) - Static method in exception com.actelion.research.chem.descriptor.flexophore.UnparametrizedAtomTypeException
- main(String[]) - Static method in class com.actelion.research.chem.io.Mol2FileParser
- main(String[]) - Static method in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMoleculeMain
- main(String[]) - Static method in class com.actelion.research.chem.SmilesParser
- main(String[]) - Static method in class com.actelion.research.gui.clipboard.ImageClipboardHandler
- main(String[]) - Static method in class com.actelion.research.util.BurtleHasher
- main(String[]) - Static method in class com.actelion.research.util.CommandLineParser
- main(String[]) - Static method in class com.actelion.research.util.convert.String2DoubleArray
- main(String[]) - Static method in class com.actelion.research.util.EncoderFloatingPointNumbers
- main(String[]) - Static method in class com.actelion.research.util.EncoderIntegerNumbers
- main(String[]) - Static method in class com.actelion.research.util.ErrorHashMap
- main(String[]) - Static method in class com.actelion.research.util.Formatter
- main(String[]) - Static method in class com.actelion.research.util.SizeOf
- main(String[]) - Static method in class com.actelion.research.util.StringFunctions
- main(String[]) - Static method in class org.openmolecules.chem.conf.so.StraightLineRule
-
Test code...
- makeColor(int, int, int) - Static method in class com.actelion.research.chem.SVGDepictor
- makeProteinFlexible(Molecule3D, Coordinates, double, boolean) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- makeProteinRigid(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- makeSkeleton(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- mAllAtoms - Variable in class com.actelion.research.chem.Molecule
- mAllBonds - Variable in class com.actelion.research.chem.Molecule
- mAllowedDragAction - Variable in class com.actelion.research.gui.JStructureView
- mAllowedDropAction - Variable in class com.actelion.research.gui.JStructureView
- manhattanBlockDistance(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
- manhattanBlockDistance(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- mapReaction(int, Point2D, Point2D) - Method in class com.actelion.research.share.gui.editor.Model
- mapReaction(Reaction, SSSearcher) - Method in interface com.actelion.research.chem.reaction.IReactionMapper
- mapReaction(Reaction, SSSearcher) - Method in class com.actelion.research.chem.reaction.MCSReactionMapper
- mapToolColor() - Static method in class com.actelion.research.gui.JDrawArea
- mArea - Variable in class com.actelion.research.gui.JDrawPanel
- markAtomForDeletion(int) - Method in class com.actelion.research.chem.Molecule
-
Marks this atom to be deleted in a later call to deleteMarkedAtomsAndBonds().
- markBondForDeletion(int) - Method in class com.actelion.research.chem.Molecule
-
Marks this bond to be deleted in a later call to deleteMarkedAtomsAndBonds().
- markDiastereotopicAtoms(StereoMolecule) - Static method in class com.actelion.research.chem.contrib.DiastereotopicAtomID
-
In order to debug we could number the group of diastereotopic atoms
- markLigand(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Find the most likely ligand (in term of size, rings, polar atoms) and mark it
- markLigand(Molecule3D, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Marks a numbered ligand
- markLigands(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Find the most likely ligands (in term of size)
- MarkushStructure - Class in com.actelion.research.chem
- MarkushStructure() - Constructor for class com.actelion.research.chem.MarkushStructure
- MarkushStructure(StereoMolecule[], int) - Constructor for class com.actelion.research.chem.MarkushStructure
- MASK_FIRST_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
- MASK_FIRST_SHORT - Static variable in class com.actelion.research.util.BitUtils
- MASK_FOURTH_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
- MASK_FOURTH_SHORT - Static variable in class com.actelion.research.util.BitUtils
- MASK_INVERSE_FIRST_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
- MASK_INVERSE_FOURTH_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
- MASK_INVERSE_SEC_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
- MASK_INVERSE_THIRD_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
- MASK_SEC_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
- MASK_SEC_SHORT - Static variable in class com.actelion.research.util.BitUtils
- MASK_THIRD_BYTE - Static variable in class com.actelion.research.util.datamodel.IntVec
- MASK_THIRD_SHORT - Static variable in class com.actelion.research.util.BitUtils
- maskByteWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- match(String, String) - Static method in class com.actelion.research.util.StringFunctions
- match(T) - Method in interface com.actelion.research.jfx.gui.misc.Selector
- MATCH_BALANCE - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- MATCH_NODE_NR_LIMIT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- MATCH_SIZE_LIMIT - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- matches(TorsionSetEliminationRule, double) - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- matchFirst(String, String) - Static method in class com.actelion.research.util.StringFunctions
- MatchFlexophoreNodesMain - Class in com.actelion.research.chem.descriptor.flexophore.example
- MatchFlexophoreNodesMain() - Constructor for class com.actelion.research.chem.descriptor.flexophore.example.MatchFlexophoreNodesMain
- matchReaction(Reaction) - Method in class com.actelion.research.chem.reaction.MCSReactionMapper
- matchSearch() - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
-
finds a set of balanced, high-scoring initial splits that are then used as an input for the extension match algorithm
- MathHelper - Class in com.actelion.research.chem.phesaflex
- mAtom - Variable in class com.actelion.research.chem.coords.InventorChain
- mAtom - Variable in class org.openmolecules.chem.conf.so.ConformationRule
- mAtomCharge - Variable in class com.actelion.research.chem.Molecule
- mAtomCustomLabel - Variable in class com.actelion.research.chem.Molecule
- mAtomFlags - Variable in class com.actelion.research.chem.Molecule
- mAtomicNo - Variable in class com.actelion.research.chem.Molecule
- mAtomList - Variable in class com.actelion.research.chem.Molecule
- mAtomList - Variable in class com.actelion.research.chem.Mutation
- mAtomMapNo - Variable in class com.actelion.research.chem.Molecule
- mAtomMass - Variable in class com.actelion.research.chem.Molecule
- mAtomQueryFeatures - Variable in class com.actelion.research.chem.Molecule
- mAtomX - Variable in class com.actelion.research.chem.coords.InventorFragment
- mAtomY - Variable in class com.actelion.research.chem.coords.InventorFragment
- Matrix - Class in com.actelion.research.calc
- Matrix() - Constructor for class com.actelion.research.calc.Matrix
- Matrix(boolean, double[]) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(boolean, int[]) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(boolean, List<Double>) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(byte[][]) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(double[][]) - Constructor for class com.actelion.research.calc.Matrix
-
Deep copy
- Matrix(double[][], boolean) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(float[][]) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(int[][]) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(int, int) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(Matrix) - Constructor for class com.actelion.research.calc.Matrix
- Matrix(List<DoubleVec>) - Constructor for class com.actelion.research.calc.Matrix
- MatrixBasedHistogram - Class in com.actelion.research.calc.histogram
-
MatrixBasedHistogram
- MatrixBasedHistogram() - Constructor for class com.actelion.research.calc.histogram.MatrixBasedHistogram
- max - Variable in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- max() - Method in class com.actelion.research.util.datamodel.DoubleArray
- max() - Method in class com.actelion.research.util.datamodel.IntArray
- max(byte[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- max(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- max(double[]) - Static method in class com.actelion.research.util.ArrayUtils
- max(double[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- max(float[]) - Static method in class com.actelion.research.util.ArrayUtils
- max(float[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- max(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- max(int[]) - Static method in class com.actelion.research.util.ArrayUtils
- max(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- max(Coordinates[]) - Static method in class com.actelion.research.chem.Coordinates
- max(String, String) - Static method in class com.actelion.research.util.StringFunctions
- MAX - Static variable in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
- MAX - Static variable in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- MAX_ALLOWED_COLLISION_INTENSITY - Static variable in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- MAX_ATOM_BITS - Static variable in class com.actelion.research.chem.SimpleCanonizer
- MAX_CONNATOMS - Static variable in class com.actelion.research.share.gui.editor.actions.DrawAction
- MAX_CONNATOMS - Static variable in class com.actelion.research.share.gui.editor.Model
- MAX_COUNT_VALUE - Static variable in class com.actelion.research.chem.descriptor.DescriptorEncoder
- MAX_DEFAULT_CURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- MAX_ID - Static variable in class com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator
- MAX_NUM_BITS - Static variable in class com.actelion.research.chem.properties.complexity.BitArray128
- MAX_NUM_BONDS - Static variable in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- MAX_NUM_HEAVY_ATOMS - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- MAX_NUM_NODES - Static variable in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- MAX_NUM_NODES_FLEXOPHORE - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophore
- MAX_NUM_SOLUTIONS - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- MAX_NUM_SOLUTIONS - Static variable in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- MAX_RING_SIZE - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
- MAX_SMALL_RING_SIZE - Static variable in class com.actelion.research.chem.RingCollection
- MAX_UNDO_SIZE - Static variable in class com.actelion.research.share.gui.editor.Model
- MAX_VAL_INTERACTION_TYPE - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
- maxConfs - Variable in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- maxDouble(List<Double>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- maximize(String) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
Toggle the maximization state of the dockable in the docking panel.
- maxInt(List<Integer>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- MAXMOLS - Static variable in class com.actelion.research.util.Sketch
- maxRange - Variable in class com.actelion.research.chem.descriptor.flexophore.DistHistHelper.RangeStatistics
- MAXSTEP - Static variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mBond - Variable in class com.actelion.research.chem.coords.InventorChain
- mBondAtom - Variable in class com.actelion.research.chem.Molecule
- mBondFlags - Variable in class com.actelion.research.chem.Molecule
- mBondQueryFeatures - Variable in class com.actelion.research.chem.Molecule
- mBondType - Variable in class com.actelion.research.chem.Molecule
- mChirality - Variable in class com.actelion.research.chem.Molecule
- mComponent - Variable in class com.actelion.research.gui.dock.TreeElement
- mCoordinates - Variable in class com.actelion.research.chem.Molecule
- MCS - Class in com.actelion.research.chem.mcs
- MCS() - Constructor for class com.actelion.research.chem.mcs.MCS
- MCS(int) - Constructor for class com.actelion.research.chem.mcs.MCS
- MCS(int, SSSearcher) - Constructor for class com.actelion.research.chem.mcs.MCS
- MCSFast - Class in com.actelion.research.chem.mcs
- MCSFast() - Constructor for class com.actelion.research.chem.mcs.MCSFast
- MCSFast(int) - Constructor for class com.actelion.research.chem.mcs.MCSFast
- MCSFunctions - Class in com.actelion.research.chem.mcs
- MCSFunctions() - Constructor for class com.actelion.research.chem.mcs.MCSFunctions
- MCSReactionMapper - Class in com.actelion.research.chem.reaction
- MCSReactionMapper() - Constructor for class com.actelion.research.chem.reaction.MCSReactionMapper
- mDepictor - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- MDHIndexTables - Class in com.actelion.research.chem.descriptor.flexophore
- mDiagnosticCollisionAtoms - Variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- mDiagnosticCollisionString - Variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- mDiagnosticTorsionString - Variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- mDim - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mDisplayMode - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- mDoLayoutMolecules - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- mDotProduct - Variable in class com.actelion.research.chem.DiversitySelector.DiversitySelectorRecord
- mDrawingObjectList - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- mDropAdapter - Variable in class com.actelion.research.gui.JStructureView
- MDYNE_A_TO_KCAL_MOL - Static variable in class com.actelion.research.chem.forcefield.mmff.Constants
- mean(Angle, Angle) - Static method in class com.actelion.research.util.Angle
-
Determines the mean angle between a1 and a2 on that side of the circle where a1 and a2 have the shorter connection.
- meanClust() - Static method in class com.actelion.research.util.datamodel.ByteVec
- median - Variable in class com.actelion.research.calc.statistics.median.ModelMedianDouble
- median - Variable in class com.actelion.research.calc.statistics.median.ModelMedianFloat
- median - Variable in class com.actelion.research.calc.statistics.median.ModelMedianInteger
- median - Variable in class com.actelion.research.calc.statistics.median.ModelMedianLong
- median() - Method in class com.actelion.research.util.datamodel.DoubleArray
- medianRange - Variable in class com.actelion.research.chem.descriptor.flexophore.DistHistHelper.RangeStatistics
- MedianStatisticFunctions - Class in com.actelion.research.calc.statistics.median
-
MedianStatisticFunctions Aug 5, 2011 MvK: Start implementation
- MedianStatisticFunctions() - Constructor for class com.actelion.research.calc.statistics.median.MedianStatisticFunctions
- merge(MolDistHistViz, MolDistHist) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
Deprecated.
- merge(SubGraphIndices) - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- merge(List<SubGraphIndices>) - Static method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
-
Merges fragments containing a common atom index.
- mergeOverlapping(List<SubGraphIndices>, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
-
Merges overlapping fragments.
- MERGEPAINT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_ALDUS_APM - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_ANIMATEPALETTE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_ARC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_BITBLT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CHORD - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CREATEBITMAP - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CREATEBITMAPINDIRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CREATEBRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CREATEBRUSHINDIRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CREATEFONTINDIRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CREATEPALETTE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CREATEPATTERNBRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CREATEPENINDIRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_CREATEREGION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_DELETEOBJECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_DIBBITBLT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_DIBCREATEPATTERNBRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_DIBSTRETCHBLT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_DRAWTEXT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_ELLIPSE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_ESCAPE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_EXCLUDECLIPRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_EXTFLOODFILL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_EXTTEXTOUT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_FILLREGION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_FLOODFILL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_FRAMEREGION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_INTERSECTCLIPRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_INVERTREGION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_LINETO - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_MOVETO - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_ANSI_FIXED_FONT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_ANSI_VAR_FONT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_BLACK_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_BLACK_PEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_DEFAULT_PALETTE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_DEVICE_DEFAULT_FONT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_DKGRAY_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_GRAY_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_HOLLOW_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_LTGRAY_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_NULL_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_NULL_PEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_OEM_FIXED_FONT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_SYSTEM_FIXED_FONT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_SYSTEM_FONT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_WHITE_BRUSH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OBJ_WHITE_PEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OFFSETCLIPRGN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OFFSETVIEWPORTORG - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_OFFSETWINDOWORG - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_PAINTREGION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_PATBLT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_PIE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_POLYBEZIER16 - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_POLYGON - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_POLYLINE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_POLYPOLYGON - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_REALIZEPALETTE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_RECTANGLE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_RESIZEPALETTE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_RESTOREDC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_ROUNDRECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SAVEDC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SCALEVIEWPORTEXT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SCALEWINDOWEXT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SELECTCLIPREGION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SELECTOBJECT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SELECTPALETTE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETBKCOLOR - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETBKMODE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETDIBTODEV - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETMAPMODE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETMAPPERFLAGS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETPALENTRIES - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETPIXEL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETPOLYFILLMODE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETRELABS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETROP2 - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETSTRETCHBLTMODE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETTEXTALIGN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETTEXTCHAREXTRA - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETTEXTCOLOR - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETTEXTJUSTIFICATION - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETVIEWPORTEXT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETVIEWPORTORG - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETWINDOWEXT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_SETWINDOWORG - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_STRETCHBLT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_STRETCHDIB - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- META_TEXTOUT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- MetaFile - Class in com.actelion.research.gui.wmf
- MetaFile() - Constructor for class com.actelion.research.gui.wmf.MetaFile
- METAL_TERM - Static variable in class com.actelion.research.chem.docking.scoring.plp.PLPTerm
- MetalTerm - Class in com.actelion.research.chem.docking.scoring.chemscore
- MetropolisMonteCarloHelper - Class in com.actelion.research.chem.phesaflex
- MetropolisMonteCarloHelper(StereoMolecule) - Constructor for class com.actelion.research.chem.phesaflex.MetropolisMonteCarloHelper
- MFCOMMENT - Static variable in class com.actelion.research.gui.wmf.WMF
- MFCOMMENT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- mFixedAtoms - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mFragment - Variable in class com.actelion.research.chem.SSSearcher
- mFragmentNoColor - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- mG - Variable in class com.actelion.research.chem.AbstractDepictor
- mGlobalAtom - Variable in class com.actelion.research.chem.coords.InventorFragment
- mGlobalBond - Variable in class com.actelion.research.chem.coords.InventorFragment
- mGlobalToLocalAtom - Variable in class com.actelion.research.chem.coords.InventorFragment
- mGrad - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- min - Variable in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- min() - Method in class com.actelion.research.util.datamodel.DoubleArray
- min(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- min(double[]) - Static method in class com.actelion.research.util.ArrayUtils
- min(double[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- min(float[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- min(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- min(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- min(Coordinates[]) - Static method in class com.actelion.research.chem.Coordinates
- min(String, String) - Static method in class com.actelion.research.util.StringFunctions
- MIN_BOND_LENGTH_SQUARE - Static variable in class com.actelion.research.share.gui.editor.Model
- MIN_NUM_ATOMS - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- MIN_NUM_NODES_SIM - Static variable in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- MINI_CUTOFF - Static variable in class com.actelion.research.chem.docking.DockingEngine
- minimise() - Method in class com.actelion.research.chem.forcefield.AbstractForceField
- minimise() - Method in interface com.actelion.research.chem.forcefield.ForceField
- minimise(int, double, double) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
-
Minimise the current molecule.
- minimumLayoutSize(Container) - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Method
- MinimumSpanningTree - Class in com.actelion.research.calc.graph
-
MinimumSpanningTree Kruskal's algorithm
- MinimumSpanningTree(Matrix) - Constructor for class com.actelion.research.calc.graph.MinimumSpanningTree
- MINLEN_FRAG - Static variable in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- minus(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
- minus(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- minus(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
- mIsEnabled - Variable in class org.openmolecules.chem.conf.so.ConformationRule
- mIsFragment - Variable in class com.actelion.research.chem.Molecule
- mIsInterrupted - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mIsMarkushStructure - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- mIsRacemate - Variable in class com.actelion.research.chem.Molecule
- mIsSelected - Variable in class com.actelion.research.chem.AbstractDrawingObject
- mix64(BurtleHasherABC) - Static method in class com.actelion.research.util.BurtleHasher
- mkdirs(File) - Static method in class com.actelion.research.util.IO
- mkdirs(String) - Static method in class com.actelion.research.util.IO
- mltb(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
-
Returns the MLTB type of an atom given its MMFF type.
- MM_ANISOTROPIC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- MM_ANISOTROPIC - Static variable in class com.actelion.research.gui.wmf.WMFGraphics
- MM_HIENGLISH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- MM_HIMETRIC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- MM_HITWIPS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- MM_ISOTROPIC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- MM_LOENGLISH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- MM_LOMETRIC - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- MM_TEXT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- mMaxAtoms - Variable in class com.actelion.research.chem.Molecule
- mMaxBonds - Variable in class com.actelion.research.chem.Molecule
- MMFF94 - Static variable in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
- MMFF94S - Static variable in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
- MMFF94SPLUS - Static variable in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
- MMFFMolecule - Class in com.actelion.research.chem.forcefield.mmff
-
MMFF molecule is a wrapper class for the ExtendedMolecule.
- MMFFMolecule(StereoMolecule) - Constructor for class com.actelion.research.chem.forcefield.mmff.MMFFMolecule
- mMol - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mMol - Variable in class com.actelion.research.gui.dnd.MoleculeTransferable
- mMolecule - Variable in class com.actelion.research.chem.SSSearcher
- mMolecule - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- mMutationType - Variable in class com.actelion.research.chem.Mutation
- mNewpos - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- MODE_ADD_NA_AND_CL - Static variable in class com.actelion.research.chem.MoleculeStandardizer
- MODE_ALLOW_CHARGE_CORRECTIONS - Static variable in class com.actelion.research.chem.reaction.Reactor
- MODE_ANGLES - Static variable in class com.actelion.research.chem.conf.TorsionDB
- MODE_BINS - Static variable in class com.actelion.research.chem.conf.TorsionDB
- MODE_BUFFER_HEAD_AND_TAIL - Static variable in class com.actelion.research.chem.io.DWARFileParser
- MODE_CONSIDER_MARKED_ATOMS - Static variable in class com.actelion.research.chem.coords.CoordinateInventor
- MODE_COORDINATES_PREFER_2D - Static variable in class com.actelion.research.chem.io.DWARFileParser
- MODE_COORDINATES_PREFER_3D - Static variable in class com.actelion.research.chem.io.DWARFileParser
- MODE_COORDINATES_REQUIRE_2D - Static variable in class com.actelion.research.chem.io.DWARFileParser
- MODE_COORDINATES_REQUIRE_3D - Static variable in class com.actelion.research.chem.io.DWARFileParser
- MODE_DRAWING_OBJECTS - Static variable in class com.actelion.research.gui.JDrawArea
- MODE_DRAWING_OBJECTS - Static variable in class com.actelion.research.share.gui.editor.Model
- MODE_EXTRACT_DETAILS - Static variable in class com.actelion.research.chem.io.DWARFileParser
- MODE_FULLY_MAP_REACTIONS - Static variable in class com.actelion.research.chem.reaction.Reactor
- MODE_GET_PARENT - Static variable in class com.actelion.research.chem.MoleculeStandardizer
- MODE_HARD_PPPOINTS - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophore
- MODE_KEEP_HYDROGEN_MAP - Static variable in class com.actelion.research.chem.MolfileParser
- MODE_KEEP_MARKED_ATOM_COORDS - Static variable in class com.actelion.research.chem.coords.CoordinateInventor
- MODE_LARGEST_FRAGMENT_ONLY - Static variable in class com.actelion.research.chem.StructureSearchSpecification
- MODE_MARKUSH_STRUCTURE - Static variable in class com.actelion.research.gui.JDrawArea
- MODE_MARKUSH_STRUCTURE - Static variable in class com.actelion.research.share.gui.editor.Model
- MODE_MULTIPLE_FRAGMENTS - Static variable in class com.actelion.research.gui.JDrawArea
- MODE_MULTIPLE_FRAGMENTS - Static variable in class com.actelion.research.share.gui.editor.Model
- MODE_PPNODE_SIMILARITY_COMPARISON - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- MODE_PREFER_MARKED_ATOM_COORDS - Static variable in class com.actelion.research.chem.coords.CoordinateInventor
- MODE_REACTION - Static variable in class com.actelion.research.gui.JDrawArea
- MODE_REACTION - Static variable in class com.actelion.research.share.gui.editor.Model
- MODE_REMOVE_DUPLICATE_PRODUCTS - Static variable in class com.actelion.research.chem.reaction.Reactor
- MODE_REMOVE_HYDROGEN - Static variable in class com.actelion.research.chem.coords.CoordinateInventor
- MODE_RETAIN_COORDINATES - Static variable in class com.actelion.research.chem.reaction.Reactor
- MODE_SKIP_DEFAULT_TEMPLATES - Static variable in class com.actelion.research.chem.coords.CoordinateInventor
- MODE_SMALL_AND_LARGE_RINGS - Static variable in class com.actelion.research.chem.RingCollection
- MODE_SMALL_AND_LARGE_RINGS_AND_AROMATICITY - Static variable in class com.actelion.research.chem.RingCollection
- MODE_SMALL_RINGS_AND_AROMATICITY - Static variable in class com.actelion.research.chem.RingCollection
- MODE_SMALL_RINGS_ONLY - Static variable in class com.actelion.research.chem.RingCollection
- MODE_SOFT_PPPOINTS - Static variable in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophore
- model - Variable in class com.actelion.research.share.gui.editor.actions.CommandAction
- model - Variable in class com.actelion.research.share.gui.editor.actions.DrawAction
- Model - Class in com.actelion.research.share.gui.editor
-
Project: User: rufenec Date: 1/24/13 Time: 5:02 PM
- Model(GeomFactory, int) - Constructor for class com.actelion.research.share.gui.editor.Model
- Model.AtomHighlightCallback - Interface in com.actelion.research.share.gui.editor
- Model.BondHighlightCallback - Interface in com.actelion.research.share.gui.editor
- ModelExhaustiveStatistics - Class in com.actelion.research.chem.properties.complexity
- ModelExhaustiveStatistics(int, int, int, double) - Constructor for class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- ModelMedianDouble - Class in com.actelion.research.calc.statistics.median
- ModelMedianDouble() - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianDouble
- ModelMedianDouble(double, double, double, int, int) - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianDouble
- ModelMedianDouble(ModelMedianDouble) - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianDouble
- ModelMedianFloat - Class in com.actelion.research.calc.statistics.median
- ModelMedianFloat() - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianFloat
- ModelMedianFloat(float, float, float, int, int) - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianFloat
- ModelMedianFloat(ModelMedianFloat) - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianFloat
- ModelMedianInteger - Class in com.actelion.research.calc.statistics.median
-
ModelMedianInteger Feb 9, 2012 MvK: Start implementation
- ModelMedianInteger() - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianInteger
- ModelMedianLong - Class in com.actelion.research.calc.statistics.median
-
ModelMedianInteger Feb 14, 2017 MvK: Start implementation
- ModelMedianLong() - Constructor for class com.actelion.research.calc.statistics.median.ModelMedianLong
- ModelParser - Class in com.actelion.research.chem.io.pdb.parser
-
ModelParser
- ModelParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.ModelParser
- ModelSampleFragments - Class in com.actelion.research.chem.mcs
- ModelSampleFragments(int) - Constructor for class com.actelion.research.chem.mcs.ModelSampleFragments
- ModelSampleFragments(int, int, int) - Constructor for class com.actelion.research.chem.mcs.ModelSampleFragments
- ModelSolutionSimilarity - Class in com.actelion.research.chem.descriptor.flexophore
- ModelSolutionSimilarity(SolutionCompleteGraph, float[]) - Constructor for class com.actelion.research.chem.descriptor.flexophore.ModelSolutionSimilarity
- mol - Variable in class com.actelion.research.chem.forcefield.mmff.Electrostatic
- mol - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
- mol - Variable in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- mol_ - Variable in class com.actelion.research.chem.AtomComparator
- Mol2FileParser - Class in com.actelion.research.chem.io
- Mol2FileParser() - Constructor for class com.actelion.research.chem.io.Mol2FileParser
- MolDistHist - Class in com.actelion.research.chem.descriptor.flexophore
- MolDistHist() - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- MolDistHist(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- MolDistHist(MolDistHist) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- MolDistHistEncoder - Class in com.actelion.research.chem.descriptor.flexophore
- MolDistHistEncoder() - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistEncoder
- MolDistHistViz - Class in com.actelion.research.chem.descriptor.flexophore
-
Class for Flexophore visualization and atom tracking.
- MolDistHistViz() - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- MolDistHistViz(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- MolDistHistViz(int, Molecule3D) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- MolDistHistViz(MolDistHist) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- MolDistHistViz(MolDistHistViz) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- MolDistHistVizEncoder - Class in com.actelion.research.chem.descriptor.flexophore
- MolDistHistVizEncoder() - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizEncoder
- MolDistHistVizFrag - Class in com.actelion.research.chem.descriptor.flexophore
- MolDistHistVizFrag() - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
- MolDistHistVizFrag(int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
- MolDistHistVizFrag(int, Molecule3D) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
- MolDistHistVizFrag(MolDistHist) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
- MolDistHistVizFrag(MolDistHistVizFrag) - Constructor for class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
- MolecularComplexityCalculator - Class in com.actelion.research.chem.properties.complexity
- MolecularComplexityCalculator() - Constructor for class com.actelion.research.chem.properties.complexity.MolecularComplexityCalculator
- MolecularFormula - Class in com.actelion.research.chem
- MolecularFormula(ExtendedMolecule) - Constructor for class com.actelion.research.chem.MolecularFormula
- MolecularVolume - Class in com.actelion.research.chem.phesa
- MolecularVolume(MolecularVolume) - Constructor for class com.actelion.research.chem.phesa.MolecularVolume
- MolecularVolume(MolecularVolume, Conformer) - Constructor for class com.actelion.research.chem.phesa.MolecularVolume
- MolecularVolume(StereoMolecule) - Constructor for class com.actelion.research.chem.phesa.MolecularVolume
- MolecularVolume(List<AtomicGaussian>, List<PPGaussian>, List<VolumeGaussian>, List<Coordinates>) - Constructor for class com.actelion.research.chem.phesa.MolecularVolume
- Molecule - Class in com.actelion.research.chem
- Molecule() - Constructor for class com.actelion.research.chem.Molecule
- Molecule() - Constructor for class com.actelion.research.gui.DefaultCompoundCollectionModel.Molecule
- Molecule(int, int) - Constructor for class com.actelion.research.chem.Molecule
- MOLECULE_DELIMITER - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- MOLECULE_DELIMITER_STRING - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- MOLECULE_FLAVORS - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
- molecule3D - Variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- Molecule3D - Class in com.actelion.research.chem
- Molecule3D() - Constructor for class com.actelion.research.chem.Molecule3D
- Molecule3D(int, int) - Constructor for class com.actelion.research.chem.Molecule3D
- Molecule3D(Molecule3D) - Constructor for class com.actelion.research.chem.Molecule3D
- Molecule3D(StereoMolecule) - Constructor for class com.actelion.research.chem.Molecule3D
- Molecule3DFunctions - Class in com.actelion.research.chem
- Molecule3DFunctions() - Constructor for class com.actelion.research.chem.Molecule3DFunctions
- MoleculeAutoMapper - Class in com.actelion.research.chem.reaction
- MoleculeAutoMapper(StereoMolecule) - Constructor for class com.actelion.research.chem.reaction.MoleculeAutoMapper
- moleculeChanged() - Method in class com.actelion.research.gui.JDrawArea
-
Use this to inform the JDrawArea after changing its molecule from outside.
- moleculeChanged(boolean) - Method in class com.actelion.research.gui.JDrawArea
-
Ideally don't use this from outside JDrawArea.
- MoleculeDataFormats - Class in com.actelion.research.jfx.dataformat
-
Deprecated.
- MoleculeDataFormats() - Constructor for class com.actelion.research.jfx.dataformat.MoleculeDataFormats
-
Deprecated.
- MoleculeDragAdapter - Class in com.actelion.research.gui.dnd
- MoleculeDragAdapter(Component) - Constructor for class com.actelion.research.gui.dnd.MoleculeDragAdapter
- MoleculeDropAdapter - Class in com.actelion.research.gui.dnd
- MoleculeDropAdapter() - Constructor for class com.actelion.research.gui.dnd.MoleculeDropAdapter
- MoleculeFilter - Interface in com.actelion.research.chem
- MoleculeGrid - Class in com.actelion.research.chem.io.pdb.converter
-
Class used to speed up the calculation of neighbours by creating a grid.
- MoleculeGrid(StereoMolecule) - Constructor for class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- MoleculeGrid(StereoMolecule, double, Coordinates) - Constructor for class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
-
Creates the Grid: Complexity O(nAtoms)
- MoleculeNeutralizer - Class in com.actelion.research.chem
- MoleculeNeutralizer() - Constructor for class com.actelion.research.chem.MoleculeNeutralizer
- moleculeQualifies(StereoMolecule) - Method in interface com.actelion.research.chem.MoleculeFilter
- MoleculeStandardizer - Class in com.actelion.research.chem
-
MoleculeStandardizer
- MoleculeStandardizer() - Constructor for class com.actelion.research.chem.MoleculeStandardizer
- MoleculeTransferable - Class in com.actelion.research.gui.dnd
- MoleculeTransferable(StereoMolecule) - Constructor for class com.actelion.research.gui.dnd.MoleculeTransferable
- MoleculeView - Class in com.actelion.research.jfx.gui.chem
-
Project: User: rufenec Date: 10/12/11 Time: 4:03 PM
- MoleculeView() - Constructor for class com.actelion.research.jfx.gui.chem.MoleculeView
- MoleculeView(StereoMolecule) - Constructor for class com.actelion.research.jfx.gui.chem.MoleculeView
- MoleculeViewSkin - Class in com.actelion.research.jfx.gui.chem
-
Project: User: rufenec Date: 10/12/11 Time: 4:10 PM
- MoleculeViewSkin(MoleculeView) - Constructor for class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- MolfileCreator - Class in com.actelion.research.chem
- MolfileCreator(ExtendedMolecule) - Constructor for class com.actelion.research.chem.MolfileCreator
-
This creates a new molfile version 2 from the given molecule.
- MolfileCreator(ExtendedMolecule, boolean) - Constructor for class com.actelion.research.chem.MolfileCreator
-
This creates a new molfile version 2 from the given molecule.
- MolfileCreator(ExtendedMolecule, boolean, double, StringBuilder) - Constructor for class com.actelion.research.chem.MolfileCreator
-
This creates a new molfile version 2 from the given molecule.
- MolfileCreator(ExtendedMolecule, boolean, StringBuilder) - Constructor for class com.actelion.research.chem.MolfileCreator
-
This creates a new molfile version 2 from the given molecule.
- MolfileParser - Class in com.actelion.research.chem
- MolfileParser() - Constructor for class com.actelion.research.chem.MolfileParser
-
Constructor of a MolFileParser, which will mirror Y,Z coordinates
- MolfileParser(int) - Constructor for class com.actelion.research.chem.MolfileParser
- MolfileV3Creator - Class in com.actelion.research.chem
-
This class generates an MDL molfile version 3.0 from a StereoMolecule as described by MDL in 'CTFile Formats June 2005'.
- MolfileV3Creator(StereoMolecule) - Constructor for class com.actelion.research.chem.MolfileV3Creator
-
This creates a new molfile version 3 from the given molecule.
- MolfileV3Creator(StereoMolecule, boolean) - Constructor for class com.actelion.research.chem.MolfileV3Creator
-
This creates a new molfile version 3 from the given molecule.
- MolfileV3Creator(StereoMolecule, boolean, double, StringBuilder) - Constructor for class com.actelion.research.chem.MolfileV3Creator
-
This creates a new molfile version 3 from the given molecule.
- MolfileV3Creator(StereoMolecule, boolean, StringBuilder) - Constructor for class com.actelion.research.chem.MolfileV3Creator
-
This creates a new molfile version 3 from the given molecule.
- moreRecordsAvailable() - Method in class com.actelion.research.chem.io.ODEFileParser
- mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
- mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
- mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
- mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
- mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JEditableChemistryView
- mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JEditableStructureView
- mouseClicked(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
- mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
- mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
- mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
- mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
- mouseDragged(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
- mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
- mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
- mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
- mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
- mouseEntered(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
- mouseExited(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
- mouseExited(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
- mouseExited(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
- mouseExited(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
- mouseExited(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
- mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
- mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
- mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
- mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
- mouseMoved(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
- mousePressed(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
- mousePressed(MouseEvent) - Method in class com.actelion.research.gui.dock.HeaderMouseAdapter
- mousePressed(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
- mousePressed(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
- mousePressed(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
- mousePressed(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
- mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.CompoundCollectionPane
- mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.dock.HeaderMouseAdapter
- mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.JChemistryView
- mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.JDrawArea
- mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.JDrawToolbar
- mouseReleased(MouseEvent) - Method in class com.actelion.research.gui.JStructureView
- move(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
- move(double, double) - Method in class com.actelion.research.chem.DepictorTransformation
- move(float, float) - Method in class com.actelion.research.share.gui.Arrow
- move(float, float) - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
- move(float, float) - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
- moveAtomWithUnboundedNeighbors(Conformer, int, double, double, double) - Method in class org.openmolecules.chem.conf.so.ConformationRule
- moveFieldToStart(String) - Method in class com.actelion.research.chem.SDFileMolecule
- moveGroup(Conformer, int, int[], double, double, double) - Method in class org.openmolecules.chem.conf.so.ConformationRule
-
Move one atom and all non-ring-bond substituents, provided attachment atom is not part of the notList.
- moveSubstituent(Conformer, int, int, double, double, double) - Method in class org.openmolecules.chem.conf.so.ConformationRule
-
Moves all atoms of the substituent connected to rootAtom starting with firstAtom.
- moveTo(int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- moveTo(int, int) - Method in class com.actelion.research.gui.wmf.WMF
- MOVETOL - Static variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mParent - Variable in class com.actelion.research.gui.dock.TreeElement
- mPoint - Variable in class com.actelion.research.chem.AbstractDrawingObject
- mPos - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mPriority - Variable in class com.actelion.research.chem.coords.InventorFragment
- mProbability - Variable in class com.actelion.research.chem.Mutation
- mProtectedFromDeletion - Variable in class com.actelion.research.chem.AbstractDrawingObject
- mProtectHydrogen - Variable in class com.actelion.research.chem.Molecule
- mReactantOrCoreCount - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- mReaction - Variable in class com.actelion.research.gui.dnd.ReactionTransferable
- mReader - Variable in class com.actelion.research.chem.io.CompoundFileParser
- mRigidFragment - Variable in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- mRotatableBond - Variable in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- MSDIFF_OFFSET - Static variable in class com.actelion.research.util.Sketch
- mSmiles - Variable in class com.actelion.research.chem.SmilesCreator
- mSpecifier1 - Variable in class com.actelion.research.chem.Mutation
- mSpecifier2 - Variable in class com.actelion.research.chem.Mutation
- mTables - Static variable in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
- mTimeInterval - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mToolBar - Variable in class com.actelion.research.gui.JDrawPanel
- mTotalEnergy - Variable in class com.actelion.research.chem.forcefield.AbstractForceField
- mTransformation - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- mTransformationReferenceX - Variable in class com.actelion.research.chem.AbstractDrawingObject
- mTransformationReferenceY - Variable in class com.actelion.research.chem.AbstractDrawingObject
- mTransformationValue1 - Variable in class com.actelion.research.chem.AbstractDrawingObject
- mTransformationValue2 - Variable in class com.actelion.research.chem.AbstractDrawingObject
- mult(byte[], byte[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
- mult(double) - Method in class com.actelion.research.util.datamodel.ByteVec
- mult(double) - Method in class com.actelion.research.util.datamodel.IntVec
- mult(double) - Method in class com.actelion.research.util.DoubleVec
- mult(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
- mult(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- mult(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
- MULT_FREQ - Static variable in class com.actelion.research.chem.descriptor.flexophore.PPNode
- multByteWise(int[], int[]) - Static method in class com.actelion.research.util.datamodel.IntVec
- multByteWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- multCols(Matrix) - Method in class com.actelion.research.calc.Matrix
- MultCoordFragIndex - Class in com.actelion.research.chem.descriptor.flexophore.generator
- MultCoordFragIndex(int[]) - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.MultCoordFragIndex
- multEl(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
-
Elementwise multiplication
- multEl(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Elementwise multiplication
- multEl(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
-
Elementwise multiplication
- MultipleNonOverlapSolution - Class in com.actelion.research.chem.properties.complexity
- MultipleNonOverlapSolution(int, FragmentDefinedByBondsIdCode, int) - Constructor for class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- MultipleNonOverlapSolution(MultipleNonOverlapSolution) - Constructor for class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- multiply(boolean, boolean, Matrix) - Method in class com.actelion.research.calc.Matrix
-
Multiplication of two matrices.
- multiply(double) - Method in class com.actelion.research.calc.Matrix
- multiply(int, Matrix, int) - Method in class com.actelion.research.calc.Matrix
- multiply(Matrix) - Method in class com.actelion.research.calc.Matrix
- multiply(Quaternion) - Method in class com.actelion.research.chem.phesa.Quaternion
-
convert Quaternion to a rotation matrix
- multiplyInverseMatrix(double[][], double[][], double[][]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- multiplyMatrix(double[][], double[][], double[][]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- multiplyValByVal(Matrix) - Method in class com.actelion.research.calc.Matrix
-
Value by value multiplication Matrices must have the same dimensions.
- mUseGraphics2D - Variable in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- mutate(StereoMolecule) - Method in class com.actelion.research.chem.Mutator
-
Does an in-place mutation of the molecule allowing any kind of mutation at any of the molecules non-selected atoms aiming for 4-24 non-H atoms with an optimum of 9 atoms.
- mutate(StereoMolecule, int, boolean) - Method in class com.actelion.research.chem.Mutator
-
Does an in-place mutation of the molecule allowing the defined mutation kinds at any of the molecules unselected atoms.
- mutate(StereoMolecule, ArrayList<Mutation>) - Method in class com.actelion.research.chem.Mutator
-
Selects a likely mutation from the list, performs the mutation and removes it from the list.
- Mutation - Class in com.actelion.research.chem
- Mutation() - Constructor for class com.actelion.research.chem.Mutation
- Mutation(int, int, int, int, int[], double) - Constructor for class com.actelion.research.chem.Mutation
- Mutation(int, int, int, int, int, double) - Constructor for class com.actelion.research.chem.Mutation
- MUTATION_ADD_ATOM - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_ANY - Static variable in class com.actelion.research.chem.Mutator
- MUTATION_CHANGE_ATOM - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_CHANGE_BOND - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_CHANGE_RING - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_CLOSE_RING - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_CLOSE_RING_AND_AROMATIZE - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_CUTOUT_ATOM - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_CUTOUT_SFRAGMENT - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_DELETE_ATOM - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_DELETE_BOND - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_DELETE_SUBSTITUENT - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_GROW - Static variable in class com.actelion.research.chem.Mutator
- MUTATION_INSERT_ATOM - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_INVERT_PARITY - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_KEEP_SIZE - Static variable in class com.actelion.research.chem.Mutator
- MUTATION_MIGRATE - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_SHRINK - Static variable in class com.actelion.research.chem.Mutator
- MUTATION_SWAP_SUBSTITUENT - Static variable in class com.actelion.research.chem.Mutation
- MUTATION_TOGGLE_AMID_SULFONAMID - Static variable in class com.actelion.research.chem.Mutation
- MutationBiasProvider - Interface in com.actelion.research.chem
- Mutator - Class in com.actelion.research.chem
- Mutator(AtomTypeList) - Constructor for class com.actelion.research.chem.Mutator
-
Creates a new Mutator that calculates probabilities of individual mutations from a given atom type list.
- Mutator(String) - Constructor for class com.actelion.research.chem.Mutator
-
Creates a new Mutator that calculates probabilities of individual mutations from a given atom type file.
- mValidHelperArrays - Variable in class com.actelion.research.chem.Molecule
- mValue - Variable in class com.actelion.research.chem.CanonizerBaseValue
- mWhere1 - Variable in class com.actelion.research.chem.Mutation
- mWhere2 - Variable in class com.actelion.research.chem.Mutation
N
- N - Variable in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable.InteractionDescriptor
- n_i(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
-
Returns 'N-i' from the table.
- N_SP2_TAUT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- name - Variable in class com.actelion.research.chem.descriptor.SimilarityCalculatorInfo
- name - Variable in class com.actelion.research.chem.io.DWARFileParser.SpecialField
- name(int) - Static method in class com.actelion.research.chem.PeriodicTable
- NAME_FIELD - Static variable in class com.actelion.research.chem.SDFileMolecule
- NamedSubstituents - Class in com.actelion.research.chem
- NamedSubstituents() - Constructor for class com.actelion.research.chem.NamedSubstituents
- nameToShortName(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- Native() - Constructor for class com.actelion.research.gui.DefaultCompoundCollectionModel.Native
- NativeClipboardAccessor - Class in com.actelion.research.gui.clipboard
- NativeClipboardAccessor() - Constructor for class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_ALDUSMETAFILE - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_BITMAP - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_CHEMDRAWINTERCHANGE - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_CTAB - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_DIB - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_EMBEDDEDSKETCH - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_IDCODE - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_METAFILE - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_MOLFILE - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_SERIALIZEMOLECULE - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_SERIALIZEREACTION - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- NC_SKETCH - Static variable in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- needsCoordinates - Variable in class com.actelion.research.chem.descriptor.DescriptorInfo
- needsLayout() - Method in class com.actelion.research.share.gui.editor.Model
- needsLayout(boolean) - Method in class com.actelion.research.share.gui.editor.Model
- NEG_CHARGE - com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint.Functionality
- negate() - Method in class com.actelion.research.chem.Coordinates
- negate() - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Returns this vector negated (signs swapped).
- neglectSpaceDelimitedCoordinates() - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
IDCodeParsers allow passing idcode and coordinates as one String with a space as separator in between.
- NEIGHBOURS_SHIFT - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyShift
- neutralizeChargedMolecule(StereoMolecule) - Method in class com.actelion.research.chem.MoleculeNeutralizer
-
Tries to neutralize all charged atoms of the molecule unless a charged atom has a neighbour atom with opposite charge.
- NewBondAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 1/28/13 Time: 1:28 PM
- NewBondAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.NewBondAction
- NewChainAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 3/26/13 Time: 3:42 PM
- NewChainAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.NewChainAction
- NEWLINE - Static variable in class com.actelion.research.chem.io.AbstractParser
- NEWLINE_REGEX - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- NEWLINE_STRING - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- newMMFF94(String) - Static method in class com.actelion.research.chem.forcefield.mmff.Tables
-
Returns a new MMFF94 table.
- next() - Method in class com.actelion.research.chem.io.CompoundFileParser
-
Advances the row counter to the next row
- next(String) - Static method in class com.actelion.research.util.IO
- next(String, DecimalFormat) - Static method in class com.actelion.research.util.IO
- nextClosing(String, int, char, char) - Static method in class com.actelion.research.util.StringFunctions
-
finds the next corresponding closing bracket char to the first open char
- nextClosingBracket(String, int) - Static method in class com.actelion.research.util.StringFunctions
-
finds the next balanced closing bracket "]" to the first open bracket "[" in the string.
- NITRO - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- Nitrogen - Static variable in class com.actelion.research.chem.PeriodicTable
- NONHNEIGHBOURS - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- NONPOLAR_TERM - Static variable in class com.actelion.research.chem.docking.scoring.plp.PLPTerm
- nonZero() - Method in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
-
Checks that at least one of the constants is non-zero.
- norm2() - Method in class com.actelion.research.calc.SingularValueDecomposition
-
Two norm
- norm2One() - Method in class com.actelion.research.util.datamodel.ByteVec
- norm2One() - Method in class com.actelion.research.util.datamodel.IntVec
- norm2One() - Method in class com.actelion.research.util.DoubleVec
- NORMAL - com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
- normalise() - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Normalises a vector.
- normalize() - Method in class com.actelion.research.chem.phesa.Quaternion
- normalize() - Method in class com.actelion.research.util.Angle
- normalizeAmbiguousBonds() - Method in class com.actelion.research.chem.ExtendedMolecule
-
Normalizes different forms of functional groups (e.g.
- normalizeCoordinates() - Method in class com.actelion.research.chem.coords.InventorTemplate
- normalizeEnantiomer() - Method in class com.actelion.research.chem.Canonizer
-
This normalizes all absolute tetrahedral-, allene- and atrop-parities within the molecule.
- normalizeESRGroups() - Method in class com.actelion.research.chem.CanonizerMesoHelper
-
If a meso fragment contains stereo atoms belonging to ESR groups then there may be an alternative way of specifying the same meso fragment because of the symmetry of the fragment.
- normalizeESRGroupSwappingAndRemoval(int[]) - Method in class com.actelion.research.chem.CanonizerMesoHelper
- normalizeID(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
- normalizeValue(double) - Static method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- normalizeValue(double) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerSkeletonSpheres
- normSquared() - Method in class com.actelion.research.chem.phesa.Quaternion
- NOSTEREO - com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
- NOSTEREO_TAUTOMER - com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
- NOT_SET - com.actelion.research.chem.forcefield.mmff.RingBoolean
- notifyVisibility(boolean) - Method in class com.actelion.research.gui.dock.Dockable
-
Method used by the JDockingPanel to inform the dockable when its visibility changes.
- NOTSRCCOPY - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- NOTSRCERASE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- NULL_MATCH_SCALING - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- NUM_BONDS_START_REGRESSION_SMALL_MOLECULE - Static variable in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
- NUM_BYTES_INTERACTION_TYPE - Static variable in class com.actelion.research.chem.descriptor.flexophore.PPNode
- NUM_CONFORMATIONS - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- number(String) - Static method in class com.actelion.research.chem.PeriodicTable
- NUMBER_ELEMENTS - Static variable in class com.actelion.research.chem.ExtendedMoleculeFunctions
O
- OBJECT_DELIMITER - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- OBJECT_DELIMITER_STRING - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- ObjectiveBlurFlexophoreHardMatchUncovered - Class in com.actelion.research.chem.descriptor.flexophore.completegraphmatcher
-
ObjectiveBlurFlexophoreHardMatchUncovered The weighting of the coverage is hard.
- ObjectiveBlurFlexophoreHardMatchUncovered() - Constructor for class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- ObjectiveBlurFlexophoreHardMatchUncovered(int, int, double, double) - Constructor for class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- ObjectiveExhaustiveStatistics - Class in com.actelion.research.chem.properties.complexity
- ObjectiveExhaustiveStatistics() - Constructor for class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
- OCCURENCE_CUTOFF - Static variable in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential
- OCCURENCE_CUTOFF - Static variable in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- ODE_EXTENSION - Static variable in class com.actelion.research.util.ConstantsDWAR
- ODEFileParser - Class in com.actelion.research.chem.io
- ODEFileParser(File) - Constructor for class com.actelion.research.chem.io.ODEFileParser
- ODEFileParser(Reader) - Constructor for class com.actelion.research.chem.io.ODEFileParser
- ODEFileParser(String) - Constructor for class com.actelion.research.chem.io.ODEFileParser
- OEM_CHARSET - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- onActionEnter() - Method in interface com.actelion.research.share.gui.editor.actions.Action
- onActionEnter() - Method in class com.actelion.research.share.gui.editor.actions.AtomMapAction
- onActionEnter() - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- onActionEnter() - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- onActionEnter() - Method in class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
- onActionLeave() - Method in interface com.actelion.research.share.gui.editor.actions.Action
- onActionLeave() - Method in class com.actelion.research.share.gui.editor.actions.AtomMapAction
- onActionLeave() - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- onActionLeave() - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- onAddBond(int, int) - Method in class com.actelion.research.share.gui.editor.actions.BondBaseAction
- onChange() - Method in interface com.actelion.research.share.gui.editor.listeners.IChangeListener
- onChangeBond(int) - Method in class com.actelion.research.share.gui.editor.actions.BondBaseAction
- onChangeBond(int) - Method in class com.actelion.research.share.gui.editor.actions.DownBondAction
- onChangeBond(int) - Method in class com.actelion.research.share.gui.editor.actions.UpBondAction
- onCommand() - Method in interface com.actelion.research.share.gui.editor.actions.Action
- onCommand() - Method in class com.actelion.research.share.gui.editor.actions.CleanAction
- onCommand() - Method in class com.actelion.research.share.gui.editor.actions.ClearAction
- onCommand() - Method in class com.actelion.research.share.gui.editor.actions.CopyAction
- onCommand() - Method in class com.actelion.research.share.gui.editor.actions.CutAction
- onCommand() - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- onCommand() - Method in class com.actelion.research.share.gui.editor.actions.PasteAction
- onCommand() - Method in class com.actelion.research.share.gui.editor.actions.UndoAction
- onDoubleClick(IMouseEvent) - Method in interface com.actelion.research.share.gui.editor.actions.Action
- onDoubleClick(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- onDoubleClick(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- onDoubleClick(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
- onDrag(Point2D) - Method in class com.actelion.research.share.gui.editor.actions.AddRingAction
- onDrag(Point2D) - Method in class com.actelion.research.share.gui.editor.actions.BondHighlightAction
- onDrag(Point2D) - Method in class com.actelion.research.share.gui.editor.actions.NewChainAction
- onDragBegin(DragGestureEvent) - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- onDragBegin(DragGestureEvent) - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- onDragEnter() - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- onDragEnter() - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- onDragEnter() - Method in class com.actelion.research.gui.JChemistryView
- onDragEnter() - Method in class com.actelion.research.gui.JStructureView
- onDragExit() - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- onDragExit() - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- onDragExit() - Method in class com.actelion.research.gui.JChemistryView
- onDragExit() - Method in class com.actelion.research.gui.JStructureView
- onDragOver() - Method in class com.actelion.research.gui.dnd.MoleculeDragAdapter
- onDragOver() - Method in class com.actelion.research.gui.dnd.ReactionDragAdapter
- onDragOver() - Method in class com.actelion.research.gui.JChemistryView
- onDragOver() - Method in class com.actelion.research.gui.JStructureView
- onDrawAtom(int, String, double, double) - Method in class com.actelion.research.chem.AbstractDepictor
- onDrawAtom(int, String, double, double) - Method in class com.actelion.research.chem.SVGDepictor
- onDrawBond(int, double, double, double, double) - Method in class com.actelion.research.chem.AbstractDepictor
- onDrawBond(int, double, double, double, double) - Method in class com.actelion.research.chem.SVGDepictor
- onDrop() - Method in class com.actelion.research.gui.JChemistryView
- onDrop() - Method in class com.actelion.research.gui.JStructureView
- onDropMolecule(StereoMolecule, Point) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- onDropReaction(Reaction, Point) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- ONE_FOUR - com.actelion.research.chem.forcefield.mmff.Separation.Relation
- ONE_ONE - com.actelion.research.chem.forcefield.mmff.Separation.Relation
- ONE_THREE - com.actelion.research.chem.forcefield.mmff.Separation.Relation
- ONE_TWO - com.actelion.research.chem.forcefield.mmff.Separation.Relation
- ONE_X - com.actelion.research.chem.forcefield.mmff.Separation.Relation
- onHighlight(int, boolean) - Method in interface com.actelion.research.share.gui.editor.Model.AtomHighlightCallback
- onHighlight(int, boolean) - Method in interface com.actelion.research.share.gui.editor.Model.BondHighlightCallback
- onKeyPressed(IKeyEvent) - Method in interface com.actelion.research.share.gui.editor.actions.Action
- onKeyPressed(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.AtomHighlightAction
- onKeyPressed(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.AtomMapAction
- onKeyPressed(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.BondHighlightAction
- onKeyPressed(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- onKeyPressed(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- onKeyPressed(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
- onKeyReleased(IKeyEvent) - Method in interface com.actelion.research.share.gui.editor.actions.Action
- onKeyReleased(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- onKeyReleased(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- onKeyReleased(IKeyEvent) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
- onMouseDown(IMouseEvent) - Method in interface com.actelion.research.share.gui.editor.actions.Action
-
Handles Mouse down events
- onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.AddRingAction
- onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ArrowAction
- onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.AtomHighlightAction
- onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.BondHighlightAction
- onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.NewChainAction
- onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
- onMouseDown(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
- onMouseMove(IMouseEvent, boolean) - Method in interface com.actelion.research.share.gui.editor.actions.Action
- onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.ArrowAction
- onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.AtomHighlightAction
- onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.AtomMapAction
- onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.BondHighlightAction
- onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
- onMouseMove(IMouseEvent, boolean) - Method in class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
- onMouseUp(IMouseEvent) - Method in interface com.actelion.research.share.gui.editor.actions.Action
-
Handles the MouseUp event
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.AddRingAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ArrowAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.AtomMapAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.BondBaseAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ChangeAtomAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ChangeAtomPropertiesAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ChangeChargeAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.DeleteAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.NewChainAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.UnknownParityAction
- onMouseUp(IMouseEvent) - Method in class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
- oop - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- OPAQUE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- openDocument(String) - Static method in class com.actelion.research.util.Platform
-
Given a filename, open this file with the default application
- openReader(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
- optimalDist - Variable in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable.InteractionDescriptor
- optimalStrength - Variable in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable.InteractionDescriptor
- optimize(Evaluable) - Method in class com.actelion.research.chem.optimization.OptimizerLBFGS
-
Optimization routine using the limited Broyden-Fletcher-Goldfarb-Shanno algorithm
- optimize(SelfOrganizedConformer, int, double, double) - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- OPTIMIZE_RIGID_FRAGS - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
- optimize3D - Variable in class com.actelion.research.chem.io.AbstractParser
- optimizeAtomCoordinates(int) - Method in class com.actelion.research.chem.coords.InventorFragment
- OptimizerLBFGS - Class in com.actelion.research.chem.optimization
-
taken from DD_chem3d, small changes necessary because a different output structure is needed it returns not only a value (the objective function), but the transformation array for achieving the best alignment
- OptimizerLBFGS(int, double) - Constructor for class com.actelion.research.chem.optimization.OptimizerLBFGS
- OR(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Makes an logical OR and calculates the hash code.
- OR(List<IntVec>) - Static method in class com.actelion.research.util.datamodel.IntVec
-
Makes an logical OR and calculates the hash code.
- order - Variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree.BiGramInt
- org.openmolecules.chem.conf.gen - package org.openmolecules.chem.conf.gen
- org.openmolecules.chem.conf.so - package org.openmolecules.chem.conf.so
- originalToExtendedAtom(int) - Method in class org.openmolecules.chem.conf.gen.RigidFragment
- OUT_CHARACTER_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- OUT_DEFAULT_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- OUT_DEVICE_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- OUT_RASTER_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- OUT_SEPARATOR_COL - Static variable in class com.actelion.research.calc.Matrix
- OUT_SEPARATOR_ROW - Static variable in class com.actelion.research.calc.Matrix
- OUT_STRING_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- OUT_STROKE_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- OUT_TT_PRECIS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- OutOfPlane - Class in com.actelion.research.chem.forcefield.mmff
-
Out of plane energy term class.
- OutOfPlane - Class in com.actelion.research.chem.forcefield.mmff.table
- OutOfPlane(Tables, MMFFMolecule, int, int, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.OutOfPlane
-
Construct a new out of plane energy term.
- OutOfPlane(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.OutOfPlane
- overlapDistance(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
- Oxygen - Static variable in class com.actelion.research.chem.PeriodicTable
P
- p - Static variable in class com.actelion.research.chem.phesa.MolecularVolume
- PACKAGE_DATAWARRIOR_IDORSIA - Static variable in class com.actelion.research.util.ConstantsDWAR
- paint(IDrawContext) - Method in interface com.actelion.research.share.gui.editor.actions.Action
- paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.ArrowAction
- paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.AtomHighlightAction
- paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.AtomMapAction
- paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.BondBaseAction
- paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.BondHighlightAction
- paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.CommandAction
- paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.NewChainAction
- paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.SelectionAction
- paint(IDrawContext) - Method in class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
- paint(IDrawContext<T>) - Method in interface com.actelion.research.share.gui.editor.chem.IDepictor
- paint(Graphics) - Method in class com.actelion.research.chem.ExtendedDepictor
- paint(Graphics) - Method in class com.actelion.research.gui.dock.JDockingPanel
- paint(Object) - Method in class com.actelion.research.chem.AbstractDepictor
- paint(Object) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- paint(T) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- paintBorder(Component, Graphics, int, int, int, int) - Method in class com.actelion.research.gui.dock.ShadowBorder
- paintComponent(Graphics) - Method in class com.actelion.research.gui.dock.DockableHeader
- paintComponent(Graphics) - Method in class com.actelion.research.gui.JChemistryView
- paintComponent(Graphics) - Method in class com.actelion.research.gui.JDrawArea
- paintComponent(Graphics) - Method in class com.actelion.research.gui.JDrawToolbar
- paintComponent(Graphics) - Method in class com.actelion.research.gui.JEditableChemistryView
- paintComponent(Graphics) - Method in class com.actelion.research.gui.JEditableStructureView
- paintComponent(Graphics) - Method in class com.actelion.research.gui.JStructureView
- paintDrawingObjects(Graphics) - Method in class com.actelion.research.chem.ExtendedDepictor
- paintDrawingObjects(T) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- paintFragmentNumbers(Graphics) - Method in class com.actelion.research.chem.ExtendedDepictor
- paintFragmentNumbers(T) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- paintIcon(Component, Graphics, int, int) - Method in class com.actelion.research.gui.hidpi.HiDPIIcon
- paintStructures(Object) - Method in class com.actelion.research.chem.ExtendedDepictor
- paintStructures(T) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- pairMatch(String, String) - Static method in class com.actelion.research.chem.descriptor.flexophore.example.MatchFlexophoreNodesMain
- PAR_CLEAVE_RINGS - Static variable in class com.actelion.research.chem.mcs.MCS
- PAR_CLEAVE_RINGS - Static variable in class com.actelion.research.chem.mcs.MCSFast
- PAR_KEEP_AROMATIC_RINGS - Static variable in class com.actelion.research.chem.mcs.MCS
- PAR_KEEP_AROMATIC_RINGS - Static variable in class com.actelion.research.chem.mcs.MCSFast
- PAR_KEEP_RINGS - Static variable in class com.actelion.research.chem.mcs.MCS
- PAR_KEEP_RINGS - Static variable in class com.actelion.research.chem.mcs.MCSFast
- PARA_TAG_HISTOGRAM_SIMILARITY_THRESH - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- PARA_TAG_MODE_MATCH - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- PARA_TAG_MODE_SINGLE_CONFORMATION_QUERY - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- PARA_TAG_PPNODE_SIMILARITY_THRESH - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- ParameterizedStringList - Class in com.actelion.research.chem.prediction
- ParameterizedStringList() - Constructor for class com.actelion.research.chem.prediction.ParameterizedStringList
- parent - Variable in class com.actelion.research.chem.io.DWARFileParser.SpecialField
- parse(Reaction, BufferedReader) - Method in class com.actelion.research.chem.io.RXNFileParser
- parse(Reaction, BufferedReader, boolean) - Method in class com.actelion.research.chem.io.RXNFileParser
- parse(Reaction, File) - Method in class com.actelion.research.chem.io.RXNFileParser
- parse(Reaction, File, boolean) - Method in class com.actelion.research.chem.io.RXNFileParser
- parse(Reaction, String) - Method in class com.actelion.research.chem.io.RXNFileParser
- parse(Reaction, String, boolean) - Method in class com.actelion.research.chem.io.RXNFileParser
- parse(StereoMolecule, byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Parses the idcode and populates the given molecule to represent the passed idcode.
- parse(StereoMolecule, byte[]) - Method in class com.actelion.research.chem.SmilesParser
- parse(StereoMolecule, byte[], boolean, boolean) - Method in class com.actelion.research.chem.SmilesParser
- parse(StereoMolecule, byte[], byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Parses the idcode and populates the given molecule to represent the passed idcode.
- parse(StereoMolecule, byte[], byte[], int, int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Parses the idcode and populates the given molecule to represent the passed idcode.
- parse(StereoMolecule, byte[], int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Parses the idcode and populates the given molecule to represent the passed idcode.
- parse(StereoMolecule, byte[], int, int) - Method in class com.actelion.research.chem.SmilesParser
- parse(StereoMolecule, byte[], int, int, boolean, boolean) - Method in class com.actelion.research.chem.SmilesParser
- parse(StereoMolecule, BufferedReader) - Method in class com.actelion.research.chem.MolfileParser
- parse(StereoMolecule, File) - Method in class com.actelion.research.chem.MolfileParser
- parse(StereoMolecule, String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Parses the idcode and populates the given molecule to represent the passed idcode.
- parse(StereoMolecule, String) - Method in class com.actelion.research.chem.MolfileParser
- parse(StereoMolecule, String) - Method in class com.actelion.research.chem.SmilesParser
-
Parses the given smiles into the molecule, creates proper atom coordinates to reflect correct double bond geometries and translates tetrahedral and allene parities into up/down-bonds.
- parse(StereoMolecule, StringBuffer) - Method in class com.actelion.research.chem.MolfileParser
- parse(StereoMolecule, String, String) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
Parses the idcode and populates the given molecule to represent the passed idcode.
- parse(BufferedInputStream) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- parse(BufferedReader) - Method in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- parse(File) - Method in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- parse(String[]) - Method in class com.actelion.research.util.CommandLineParser
- parse(List<String>, int, List<AtomRecord>, List<AtomRecord>) - Method in class com.actelion.research.chem.io.pdb.parser.ModelParser
- parseCoordinates(byte[], int, StereoMolecule, Coordinates[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
-
This method parses an id-coordinate string (new format only) and writes the coordinates into a Coordinates array.
- parseDate(String) - Static method in class com.actelion.research.util.Formatter
- parseDateTime(String) - Static method in class com.actelion.research.util.Formatter
- parseInteger(InputStream) - Static method in class com.actelion.research.util.datamodel.IntArray
- parseInteger(String, String) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- parseLong(InputStream) - Static method in class com.actelion.research.chem.properties.complexity.BitArray128
- parseMapping(byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- parseMapping(byte[], int) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- parseReaction(byte[]) - Method in class com.actelion.research.chem.SmilesParser
- parseString(InputStream) - Static method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- parseString(InputStream) - Static method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- paste() - Static method in class com.actelion.research.jfx.gui.misc.ClipboardHelper
- PASTE_AND_DROP_OPTION_ALLOW_FRAGMENT_STATE_CHANGE - Static variable in class com.actelion.research.gui.JChemistryView
- PASTE_AND_DROP_OPTION_KEEP_ATOM_COLORS - Static variable in class com.actelion.research.gui.JChemistryView
- PASTE_AND_DROP_OPTION_KEEP_BOND_HIGHLIGHTING - Static variable in class com.actelion.research.gui.JChemistryView
- PASTE_AND_DROP_OPTION_LAYOUT_REACTION - Static variable in class com.actelion.research.gui.JChemistryView
- PASTE_AND_DROP_OPTION_REMOVE_CATALYSTS - Static variable in class com.actelion.research.gui.JChemistryView
- PASTE_AND_DROP_OPTION_REMOVE_DRAWING_OBJECTS - Static variable in class com.actelion.research.gui.JChemistryView
- PasteAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 5/16/13 Time: 3:39 PM
- PasteAction(Model, Dimension) - Constructor for class com.actelion.research.share.gui.editor.actions.PasteAction
- pasteImage() - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
- pasteImage() - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- pasteImage() - Static method in class com.actelion.research.gui.clipboard.ImageClipboardHandler
- pasteMolecule() - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Get one Molecule from the Clipboard.
- pasteMolecule() - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- pasteMolecule() - Method in class com.actelion.research.share.gui.editor.actions.PasteAction
- pasteMolecule(boolean) - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
- pasteMolecule(double, double) - Method in class com.actelion.research.share.gui.editor.Model
- pasteMolecules() - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Get one or more Molecule(s) from the Clipboard.
- pasteMolecules() - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- pasteReaction() - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Get a Reaction from the Clipboard
- pasteReaction() - Method in interface com.actelion.research.gui.clipboard.IClipboardHandler
- pasteReaction() - Method in class com.actelion.research.share.gui.editor.actions.PasteAction
- pasteReaction(double, double) - Method in class com.actelion.research.share.gui.editor.Model
- pasteReactionWindowsNative() - Method in class com.actelion.research.gui.clipboard.ClipboardHandler
- pasteText() - Static method in class com.actelion.research.gui.clipboard.TextClipboardHandler
- PAT_NOT_ALPHANUMERIC - Static variable in class com.actelion.research.util.StringFunctions
- PAT_WHITESPACE - Static variable in class com.actelion.research.util.StringFunctions
- PATCOPY - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PATINVERT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PATPAINT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PATTERN_NF_DWAR - Static variable in class com.actelion.research.util.ConstantsDWAR
- PATTERN_NF_DWAR4 - Static variable in class com.actelion.research.util.ConstantsDWAR
- PDBCoordEntryFile - Class in com.actelion.research.chem.io.pdb.parser
-
PDBCoordEntryFile
- PDBCoordEntryFile() - Constructor for class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- PDBFileParser - Class in com.actelion.research.chem.io.pdb.parser
-
PDBFileParser
- PDBFileParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- peek() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
-
Peek the first element of the Queue (do not increment the queue index)
- peek() - Method in class com.actelion.research.util.IntQueue
-
Peek the first element of the Queue (do not increment the queue index)
- perceivedBrightness(Color) - Static method in class com.actelion.research.util.ColorHelper
-
This is a color's perceived brightness by the human eye
- performMutation(StereoMolecule, Mutation) - Method in class com.actelion.research.chem.Mutator
-
Performs the given mutation on the molecule, updates atom coordinates, and updates stereo bonds to reflect lost or new stereo centers.
- PeriodicTable - Class in com.actelion.research.chem.forcefield.mmff
- PeriodicTable - Class in com.actelion.research.chem
- PERIPHERY_WEIGHT - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- PharmacophoreCalculator - Class in com.actelion.research.chem.phesa.pharmacophore
- PharmacophoreNode - Class in com.actelion.research.chem.descriptor.pharmacophoretree
-
A PharmacophoreNode represents a node in a PharmacophoreTree.
- PharmacophoreNode(List<Integer>, int[][], double[], boolean, boolean) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- PharmacophoreNode(List<Integer>, int[][], double[], int, boolean, boolean) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- PharmacophoreNode(List<Integer>, int[], List<Double>, List<Double>, int) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- PharmacophorePointFactory - Class in com.actelion.research.chem.phesa.pharmacophore
- PharmacophorePointFactory() - Constructor for class com.actelion.research.chem.phesa.pharmacophore.PharmacophorePointFactory
- PharmacophoreTree - Class in com.actelion.research.chem.descriptor.pharmacophoretree
-
A PharmacophoreTree closely follows the concepts of FeatureTrees as described by Rarey and Dixon (DOI:10.1023/a:1008068904628).
- PharmacophoreTree(List<PharmacophoreNode>, List<int[]>) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- PharmacophoreTree.BiGramInt - Class in com.actelion.research.chem.descriptor.pharmacophoretree
-
container of an undirected edge
- PharmacophoreTreeGenerator - Class in com.actelion.research.chem.descriptor.pharmacophoretree
-
Generates a PharmacophoreTree from a StereoMolecule.
- PharmGraphGenerator - Class in com.actelion.research.chem.descriptor.pharmacophoregraph
- PharmGraphGenerator() - Constructor for class com.actelion.research.chem.descriptor.pharmacophoregraph.PharmGraphGenerator
- PHESA - com.actelion.research.chem.docking.DockingEngine.StartPosition
- PheSAAlignment - Class in com.actelion.research.chem.phesa
- PheSAAlignment(MolecularVolume, MolecularVolume) - Constructor for class com.actelion.research.chem.phesa.PheSAAlignment
- PheSAAlignment(MolecularVolume, MolecularVolume, double) - Constructor for class com.actelion.research.chem.phesa.PheSAAlignment
- PheSAAlignment(StereoMolecule, StereoMolecule) - Constructor for class com.actelion.research.chem.phesa.PheSAAlignment
- PheSAAlignment(StereoMolecule, StereoMolecule, double) - Constructor for class com.actelion.research.chem.phesa.PheSAAlignment
- PheSAAlignment.axis - Enum in com.actelion.research.chem.phesa
- PheSAAlignment.PheSAResult - Class in com.actelion.research.chem.phesa
- PheSAAlignmentOptimizer - Class in com.actelion.research.chem.alignment3d
- PheSABindingHypothesis - Class in com.actelion.research.chem.phesa
- PheSABindingHypothesis(List<StereoMolecule>) - Constructor for class com.actelion.research.chem.phesa.PheSABindingHypothesis
- PheSABindingHypothesis(List<StereoMolecule>, int) - Constructor for class com.actelion.research.chem.phesa.PheSABindingHypothesis
- PheSAMolecule - Class in com.actelion.research.chem.phesa
- PheSAMolecule() - Constructor for class com.actelion.research.chem.phesa.PheSAMolecule
- PheSAMolecule(StereoMolecule, MolecularVolume) - Constructor for class com.actelion.research.chem.phesa.PheSAMolecule
- PheSAMolecule(StereoMolecule, ArrayList<MolecularVolume>) - Constructor for class com.actelion.research.chem.phesa.PheSAMolecule
- PheSAResult(StereoMolecule, StereoMolecule, double) - Constructor for class com.actelion.research.chem.phesa.PheSAAlignment.PheSAResult
- PHOSPHONATE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- Phosphorus - Static variable in class com.actelion.research.chem.PeriodicTable
- PI - Static variable in class com.actelion.research.util.Sketch
- pie(int, int, int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- pie(int, int, int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMF
- pilp(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
-
Returns the PILP type of an atom given its MMFF type.
- Pipeline<T> - Class in com.actelion.research.util
-
Pipeline Enables concurrent access to a queue.
- Pipeline() - Constructor for class com.actelion.research.util.Pipeline
- Pipeline(List<T>) - Constructor for class com.actelion.research.util.Pipeline
-
The 'all data in' flag is set true.
- PlaneRule - Class in org.openmolecules.chem.conf.so
- PlaneRule(int[], StereoMolecule) - Constructor for class org.openmolecules.chem.conf.so.PlaneRule
- Platform - Class in com.actelion.research.util
-
Requires JRE 1.6
- Platform() - Constructor for class com.actelion.research.util.Platform
- PLATFORM_NAME_DATAWARRIOR - Static variable in class com.actelion.research.util.ConstantsDWAR
- PLPTerm - Class in com.actelion.research.chem.docking.scoring.plp
-
piecewise linear potential (PLP) as described in doi:10.1021/ci800298z parameters from model 3 (M3)
- plus(Matrix) - Method in class com.actelion.research.calc.Matrix
- plus(ByteVec, ByteVec) - Static method in class com.actelion.research.util.datamodel.ByteVec
- plus(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- plus(DoubleVec, DoubleVec) - Static method in class com.actelion.research.util.DoubleVec
- PointDouble - Class in com.actelion.research.util.datamodel
- PointDouble() - Constructor for class com.actelion.research.util.datamodel.PointDouble
- PointDouble(double, double) - Constructor for class com.actelion.research.util.datamodel.PointDouble
- PointDouble(Point) - Constructor for class com.actelion.research.util.datamodel.PointDouble
- PointUtils - Class in com.actelion.research.util
- PointUtils() - Constructor for class com.actelion.research.util.PointUtils
- PolarSurfaceAreaPredictor - Class in com.actelion.research.chem.prediction
-
This class predicts the topological polar surface area (TPSA) of a molecule as a sum of contributions of its polar atom-types.
- PolarSurfaceAreaPredictor() - Constructor for class com.actelion.research.chem.prediction.PolarSurfaceAreaPredictor
- pollAll() - Method in class com.actelion.research.util.Pipeline
- pollAllWithWait() - Method in class com.actelion.research.util.Pipeline
-
all data in flag has to be set.
- pollData() - Method in class com.actelion.research.util.Pipeline
- polygon(int[], int[], int) - Method in class com.actelion.research.gui.wmf.MetaFile
- polygon(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMF
- Polygon - Class in com.actelion.research.share.gui
- Polygon() - Constructor for class com.actelion.research.share.gui.Polygon
- polyline(int[], int[], int) - Method in class com.actelion.research.gui.wmf.MetaFile
- polyline(int[], int[], int) - Method in class com.actelion.research.gui.wmf.WMF
- Polynome(double[]) - Constructor for class com.actelion.research.util.FastSpline.Polynome
- polypolygon(Polygon[]) - Method in class com.actelion.research.gui.wmf.MetaFile
- polypolygon(Polygon[]) - Method in class com.actelion.research.gui.wmf.WMF
- pop() - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
-
Pop the first element of the Queue
- pop() - Method in class com.actelion.research.util.IntQueue
-
Pop the first element of the Queue
- popUndo() - Method in class com.actelion.research.share.gui.editor.Model
- PopupProvider - Interface in com.actelion.research.gui.dock
- POS_CHARGE - com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint.Functionality
- PositionConstraint - Class in com.actelion.research.chem.forcefield.mmff
- PositionConstraint(StereoMolecule, double, double) - Constructor for class com.actelion.research.chem.forcefield.mmff.PositionConstraint
- PotentialEnergyTerm - Interface in com.actelion.research.chem.potentialenergy
- pow(double) - Method in class com.actelion.research.calc.Matrix
- power - Variable in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
- PPGaussian - Class in com.actelion.research.chem.phesa.pharmacophore
- PPGaussian(int, IPharmacophorePoint) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
- PPGaussian(PPGaussian) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
- PPNode - Class in com.actelion.research.chem.descriptor.flexophore
- PPNode() - Constructor for class com.actelion.research.chem.descriptor.flexophore.PPNode
- PPNode(PPNode) - Constructor for class com.actelion.research.chem.descriptor.flexophore.PPNode
- PPNodeRGroup - Class in com.actelion.research.chem.descriptor.flexophore.entity
-
PPNodeStructure
- PPNodeRGroup() - Constructor for class com.actelion.research.chem.descriptor.flexophore.entity.PPNodeRGroup
- PPNodeRGroup(PPNode, String) - Constructor for class com.actelion.research.chem.descriptor.flexophore.entity.PPNodeRGroup
- PPNodeSimilarity - Class in com.actelion.research.chem.descriptor.flexophore.completegraphmatcher
-
PPNodeSimilarity
- PPNodeSimilarity(int, int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
-
This constructor is used for parallel mode.
- PPNodeViz - Class in com.actelion.research.chem.descriptor.flexophore
-
Pharmacophore node with information about corresponding atoms in the molecule used for construction.
- PPNodeViz() - Constructor for class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- PPNodeViz(PPNode) - Constructor for class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- PPNodeViz(PPNodeViz) - Constructor for class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- PPNodeVizTriangle - Class in com.actelion.research.chem.descriptor.flexophore
- PPNodeVizTriangle(PPNodeViz, PPNodeViz, PPNodeViz) - Constructor for class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- PPTriangle - Class in com.actelion.research.chem.phesa.pharmacophore
- PPTriangle(IPharmacophorePoint, IPharmacophorePoint, IPharmacophorePoint, double, double, double, Coordinates) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.PPTriangle
- PPTriangleCreator - Class in com.actelion.research.chem.phesa.pharmacophore
- PPTriangleMatcher - Class in com.actelion.research.chem.phesa.pharmacophore
- PPTriangleMatcher.AlignmentResult - Class in com.actelion.research.chem.phesa.pharmacophore
- ppWeight - Variable in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- predictAtomSequence(StereoMolecule, int, int[], int[]) - Static method in class com.actelion.research.chem.conf.BondRotationHelper
- preferredLayoutSize(Container) - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Method
- PREFIX_OUTPUT - Static variable in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMoleculeMain
- PREOPTIMIZED - Static variable in class com.actelion.research.chem.Molecule3D
- preProcess(Conformer, MolecularVolume) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
-
Move COM of the molecular volume to the origin of the lab-frame and orient molecules so that their principal moments of inertia coincide with the 3 axis of the coordinate system
- PRINT_DEBUG_INDEXES - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- PRINT_ELIMINATION_RULES_WITH_STRUCTURES - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- PRINT_EXIT_REASON - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- PRINT_TORSION_AND_FRAGMENT_LIKELYHOODS - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- printAtomType(long) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- printAtomType(StereoMolecule, int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- printContent(byte[], byte[]) - Method in class com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention
- printMutationList(ArrayList<Mutation>, boolean) - Method in class com.actelion.research.chem.Mutator
- printStatus() - Method in class com.actelion.research.gui.dock.TreeElement
- printStatus() - Method in class com.actelion.research.gui.dock.TreeFork
- printStatus() - Method in class com.actelion.research.gui.dock.TreeLeaf
- printStatus() - Method in class com.actelion.research.gui.dock.TreeRoot
- printTime(double) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- process(InputObjectFracDimCalc) - Method in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMolecule
- process(Pipeline<StereoMolecule>, int, boolean, boolean) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorParallizer
- process(List<StereoMolecule>, File) - Method in class com.actelion.research.chem.mcs.ExhaustiveMCSGeneratorParallel
- processMolecule(StereoMolecule, TreeSet<String>) - Method in class com.actelion.research.chem.AtomTypeList
- PRODUCT_IDENTIFIER - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- ProgressController - Interface in com.actelion.research.calc
- ProgressListener - Interface in com.actelion.research.calc
- PROOF_QUALITY - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PropertyCalculator - Class in com.actelion.research.chem
- PropertyCalculator(StereoMolecule) - Constructor for class com.actelion.research.chem.PropertyCalculator
- PROTEIN_GROUP - Static variable in class com.actelion.research.chem.io.pdb.parser.StructureAssembler
- ProteinSynthesizer - Class in com.actelion.research.chem.io.pdb.parser
- ProteinSynthesizer() - Constructor for class com.actelion.research.chem.io.pdb.parser.ProteinSynthesizer
- PS_DASH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PS_DASHDOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PS_DASHDOTDOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PS_DOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PS_INSIDEFRAME - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PS_NULL - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PS_SOLID - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- PURITY_FIELD - Static variable in class com.actelion.research.chem.SDFileMolecule
- push(int) - Method in class com.actelion.research.chem.descriptor.flexophore.calculator.IntQueue
-
Push an element on top of the queue
- push(int) - Method in class com.actelion.research.util.IntQueue
-
Push an element on top of the queue
- pushUndo() - Method in class com.actelion.research.share.gui.editor.Model
- putContent(Clipboard) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- putImage(Image) - Static method in class com.actelion.research.gui.clipboard.ClipboardHandler
-
Deprecated.You may use ImageClipboardHandler.copyImage for consistency reasons
Q
- qualifiesAsAmideTypeBond(int) - Method in class com.actelion.research.chem.RingCollection
-
Checks, whether this bond may contribute pi-electrons from an amide-resonance to an aromatic ring.
- Quaternion - Class in com.actelion.research.chem.phesa
- Quaternion(double, double, double, double) - Constructor for class com.actelion.research.chem.phesa.Quaternion
- Quaternion(Coordinates, double) - Constructor for class com.actelion.research.chem.phesa.Quaternion
- quickExp(double) - Method in class com.actelion.research.chem.phesa.QuickMathCalculator
- QuickMathCalculator - Class in com.actelion.research.chem.phesa
R
- r_star(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
-
Returns 'R*' which is derived from the table.
- r0 - Variable in class com.actelion.research.chem.forcefield.mmff.BondStretch
- r0(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bndk
-
Returns 'r0' the ideal bond length at a given index in the Bndk table.
- r0(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bond
-
Returns the 'r0' value at the given index from the Bond table.
- r0(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.CovRad
-
Returns the 'r0' (or covRad) parameter from the table given an index.
- r0(MMFFMolecule, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Bond
-
Returns 'r0' given a molecule and two atoms in that molecule that form a bond.
- r0i - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
- r0k - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
- R2_BLACK - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_COPYPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_MASKNOTPENNOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_MASKPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_MASKPENNOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_MERGENOTPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_MERGEPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_MERGEPENNOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_NOP - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_NOT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_NOTCOPYPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_NOTMASKPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_NOTMERGEPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_NOTXORPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_WHITE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- R2_XORPEN - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- RAD2DEG - Static variable in class com.actelion.research.chem.forcefield.mmff.Constants
- random() - Static method in class com.actelion.research.chem.Coordinates
- RANDOM - com.actelion.research.chem.docking.DockingEngine.StartPosition
- RANDOM - Static variable in class com.actelion.research.util.datamodel.ByteVec
- randomPerturbation(Random) - Method in class com.actelion.research.chem.docking.LigandPose
- randomVectorInSphere(Random) - Static method in class com.actelion.research.chem.docking.DockingUtils
- range() - Method in class com.actelion.research.calc.statistics.median.ModelMedianDouble
- range() - Method in class com.actelion.research.calc.statistics.median.ModelMedianFloat
- range() - Method in class com.actelion.research.calc.statistics.median.ModelMedianInteger
- range() - Method in class com.actelion.research.calc.statistics.median.ModelMedianLong
- RANGE_HISTOGRAM - Static variable in class com.actelion.research.chem.descriptor.flexophore.generator.ConstantsFlexophoreGenerator
-
Range histogram in Angstrom.
- RangeStatistics() - Constructor for class com.actelion.research.chem.descriptor.flexophore.DistHistHelper.RangeStatistics
- rank() - Method in class com.actelion.research.calc.SingularValueDecomposition
-
Effective numerical matrix rank
- RDFileParser - Class in com.actelion.research.chem.io
-
Quick and dirty RD-File parser that reads non-hierarchical RD-Files.
- RDFileParser(File) - Constructor for class com.actelion.research.chem.io.RDFileParser
- RDFileParser(Reader) - Constructor for class com.actelion.research.chem.io.RDFileParser
- RDFileParser(String) - Constructor for class com.actelion.research.chem.io.RDFileParser
- Reaction - Class in com.actelion.research.chem.reaction
- Reaction() - Constructor for class com.actelion.research.chem.reaction.Reaction
- Reaction(Reaction) - Constructor for class com.actelion.research.chem.reaction.Reaction
- Reaction(StereoMolecule[], int) - Constructor for class com.actelion.research.chem.reaction.Reaction
- Reaction(String) - Constructor for class com.actelion.research.chem.reaction.Reaction
- REACTION_CENTER_LONG_COUNT - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- REACTION_CENTER_WEIGHT - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP
- REACTION_FLAVORS - Static variable in class com.actelion.research.chem.dnd.ChemistryFlavors
- REACTION_TYPE_NOMOLS - Static variable in class com.actelion.research.chem.ChemistryHelper
- REACTION_TYPE_NOPRODUCTS - Static variable in class com.actelion.research.chem.ChemistryHelper
- REACTION_TYPE_NORMAL - Static variable in class com.actelion.research.chem.ChemistryHelper
- REACTION_TYPE_REACTANTS - Static variable in class com.actelion.research.chem.ChemistryHelper
- ReactionArrow - Class in com.actelion.research.chem.reaction
- ReactionArrow() - Constructor for class com.actelion.research.chem.reaction.ReactionArrow
- ReactionArrow(String) - Constructor for class com.actelion.research.chem.reaction.ReactionArrow
- ReactionDragAdapter - Class in com.actelion.research.gui.dnd
- ReactionDragAdapter(Component) - Constructor for class com.actelion.research.gui.dnd.ReactionDragAdapter
- ReactionDropAdapter - Class in com.actelion.research.gui.dnd
- ReactionDropAdapter() - Constructor for class com.actelion.research.gui.dnd.ReactionDropAdapter
- ReactionEncoder - Class in com.actelion.research.chem.reaction
- ReactionSearch - Class in com.actelion.research.chem.reaction
- ReactionSearch(ReactionSearchSpecification, ReactionSearchDataSource, StructureSearchController, ProgressController) - Constructor for class com.actelion.research.chem.reaction.ReactionSearch
-
This contructs a new structure search, which upon calling start() runs a multithreaded structure search on the structure rows provided by dataSource.
- ReactionSearchDataSource - Interface in com.actelion.research.chem.reaction
- ReactionSearchSpecification - Class in com.actelion.research.chem.reaction
- ReactionSearchSpecification(int, String[], long[][], long[][], long[][]) - Constructor for class com.actelion.research.chem.reaction.ReactionSearchSpecification
-
Creates a complete specification for a reaction substructure search with one or more query generic reactions.
- ReactionSearchSpecification(int, String[], long[][], long[][], long[][], float, float) - Constructor for class com.actelion.research.chem.reaction.ReactionSearchSpecification
-
Creates a complete specification for a reaction similarity search with one or more query reactions.
- ReactionSearchSpecification(String[], long[][]) - Constructor for class com.actelion.research.chem.reaction.ReactionSearchSpecification
-
Creates a complete specification for a retron search with one or more query retron substructures.
- ReactionTransferable - Class in com.actelion.research.gui.dnd
- ReactionTransferable(Reaction) - Constructor for class com.actelion.research.gui.dnd.ReactionTransferable
- Reactor - Class in com.actelion.research.chem.reaction
- Reactor(Reaction) - Constructor for class com.actelion.research.chem.reaction.Reactor
-
Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants.
- Reactor(Reaction, boolean) - Constructor for class com.actelion.research.chem.reaction.Reactor
-
Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants.
- Reactor(Reaction, boolean, boolean, int, boolean) - Constructor for class com.actelion.research.chem.reaction.Reactor
-
Deprecated.
- Reactor(Reaction, int, int) - Constructor for class com.actelion.research.chem.reaction.Reactor
-
Constructs a Reactor that is able to build products from a generic reaction (transformation) and a list of real world reactants.
- read() - Method in class com.actelion.research.util.BinaryDecoder
- read(byte[], int, int) - Method in class com.actelion.research.util.LittleEndianDataInputStream
- read(File) - Static method in class com.actelion.research.util.datamodel.IntVec
- read(File) - Static method in class com.actelion.research.util.datamodel.ScorePoint
- read(File) - Static method in class com.actelion.research.util.IO
- read(InputStream) - Static method in class com.actelion.research.chem.mcs.ListWithIntVec
- read(InputStream) - Static method in class com.actelion.research.chem.properties.complexity.BitArray128
- read(InputStream) - Static method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- read(InputStream) - Static method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- read(InputStream) - Static method in class com.actelion.research.util.datamodel.IntArray
- read(InputStream) - Static method in class com.actelion.research.util.datamodel.IntVec
- read(InputStream) - Static method in class com.actelion.research.util.IO
- read(String) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- read(String) - Static method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- read(String) - Static method in class com.actelion.research.util.datamodel.IntArray
- read(String) - Method in class com.actelion.research.util.datamodel.IntVec
- readBetweenTags(String, String, String, Vector<String>) - Static method in class com.actelion.research.util.IO
- readBitStringDense(File) - Static method in class com.actelion.research.util.datamodel.IntVec
- readBitStringDense(String) - Static method in class com.actelion.research.util.datamodel.IntVec
- readBoolean() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readByte() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readChar() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readContent(Clipboard) - Static method in class com.actelion.research.jfx.gui.misc.ClipboardHelper
- readDouble() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readDoubleArray(String) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- readDoubleArray(String, String) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- readEncoded(String, String) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizEncoder
- readFile(String) - Static method in class com.actelion.research.chem.forcefield.mmff.Csv
-
Read a file at location 'path' and parse it as a CSV file.
- readFloat() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readFromFile() - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- readFromTag(String, String, Vector<String>) - Static method in class com.actelion.research.util.IO
-
Reads all lines after a given tag and stores the lines as Strings in a vector object.
- readFully(byte[]) - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readFully(byte[], int, int) - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readIDCodesFromFile() - Method in class com.actelion.research.chem.io.CompoundFileHelper
- readIDCodesFromFile(File) - Method in class com.actelion.research.chem.io.CompoundFileHelper
-
Reads all compounds as idcode list from the given file.
- readIDCodesWithNamesFromFile(File, boolean) - Method in class com.actelion.research.chem.io.CompoundFileHelper
-
Reads all compounds as idcode list with identifiers from the given file.
- readInput(String) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- readInt() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readIntArray(String) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
-
Separator is ','.
- readIntArray(String, String) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- readIntsFile(String) - Static method in class com.actelion.research.chem.forcefield.mmff.Csv
-
A helper function that casts and returns a CSV file consisting entirely of ints on all rows and columns.
- readLine() - Method in class com.actelion.research.io.StringReadChannel
- readLine() - Method in class com.actelion.research.util.LittleEndianDataInputStream
-
Deprecated.
- readLine(InputStream) - Static method in class com.actelion.research.util.IO
- readLine(Reader) - Static method in class com.actelion.research.util.IO
- readLine(FileChannel) - Static method in class com.actelion.research.util.IO
- readLines2DoubleArray(File) - Static method in class com.actelion.research.util.IO
- readLines2IntArray(File) - Static method in class com.actelion.research.util.IO
-
Reads a file that contains one int per line.
- readLines2List(File) - Static method in class com.actelion.research.util.IO
- readLines2List(InputStream) - Static method in class com.actelion.research.util.IO
-
The stream is not closed.
- readLines2List(List<File>) - Static method in class com.actelion.research.util.IO
- readListIntger(File) - Static method in class com.actelion.research.util.IO
- readLong() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readNodes(String) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
-
reads a MolDistHist from the toString() method.
- readSerialized(File) - Static method in class com.actelion.research.calc.Matrix
- readShort() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readStructuresFromFile(boolean) - Method in class com.actelion.research.chem.io.CompoundFileHelper
- readStructuresFromFile(File, boolean) - Method in class com.actelion.research.chem.io.CompoundFileHelper
- readUnsignedByte() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readUnsignedShort() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readUTF() - Method in class com.actelion.research.util.LittleEndianDataInputStream
- readUTF(DataInput) - Static method in class com.actelion.research.util.LittleEndianDataInputStream
- readXMLElement(Element) - Static method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- readXMLElement(Element) - Static method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- readXMLElement(Element) - Static method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- realize() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
-
Resizes the node array to the needed length.
- realize() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- realize() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
-
May be called after finishing adding new interaction types.
- recalculateCoordPPPoints() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
Recalculates the coordinates off the pharmacophore nodes.
- recentException - Variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- receptorConf - Variable in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- receycle(IBitArray) - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- rect - Variable in class com.actelion.research.share.gui.Arrow
- rectangle(int, int, int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- rectangle(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMF
- RED - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
- redistribute() - Method in class com.actelion.research.gui.dock.JDockingPanel
- reduce(List<Integer>) - Method in class com.actelion.research.util.datamodel.IntVec
-
Removes all values with no corresponding index in the list.
- reduce(Vector<Integer>) - Method in class com.actelion.research.util.datamodel.ByteVec
- reduce(Vector<Integer>) - Method in class com.actelion.research.util.DoubleVec
- REGEX_FILE_EXTENSION - Static variable in class com.actelion.research.util.ConstantsDWAR
- REGEX_META_CHARACTERS - Static variable in class com.actelion.research.util.StringFunctions
- registerAtomHighlightCallback(Model.AtomHighlightCallback) - Method in class com.actelion.research.share.gui.editor.Model
- registerBondHighlightCallback(Model.BondHighlightCallback) - Method in class com.actelion.research.share.gui.editor.Model
- registerDragEvent() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- regress() - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- rel - Variable in class com.actelion.research.chem.forcefield.mmff.Electrostatic
- relocateView(String, String, int, float) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
May be overriden to catch user initiated drag&drop
- RemarkParser - Class in com.actelion.research.chem.io.pdb.parser
-
RemarkParser
- RemarkParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.RemarkParser
- remove(int) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- remove(int) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- remove(int) - Method in class com.actelion.research.util.hash.HashSetInt
- remove(int) - Method in class com.actelion.research.util.SortedList
- remove(Point2D) - Method in interface com.actelion.research.share.gui.editor.geom.IPolygon
- remove(Point2D) - Method in class com.actelion.research.share.gui.Polygon
- removeAll() - Method in class com.actelion.research.util.SortedList
- removeAllAtomsWithoutNeighbours(Molecule3D) - Static method in class com.actelion.research.chem.Molecule3DFunctions
- removeAllStrings() - Method in class com.actelion.research.chem.SortedStringList
- removeAtomColors() - Method in class com.actelion.research.chem.Molecule
- removeAtomCustomLabels() - Method in class com.actelion.research.chem.Molecule
-
This removes all custom labels from the atoms.
- removeAtomMarkers() - Method in class com.actelion.research.chem.Molecule
- removeAtomSelection() - Method in class com.actelion.research.chem.Molecule
- removeBondHiliting() - Method in class com.actelion.research.chem.Molecule
- removeCatalysts() - Method in class com.actelion.research.chem.reaction.Reaction
- removeChangeListener(IChangeListener) - Method in class com.actelion.research.share.gui.editor.Model
- removeCharacter(StringBuilder, char) - Static method in class com.actelion.research.util.StringFunctions
- removeCharacter(String, char) - Static method in class com.actelion.research.util.StringFunctions
- removeCol(int) - Method in class com.actelion.research.calc.Matrix
- removeCompoundCollectionListener(CompoundCollectionListener) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- removeCompoundCollectionListener(CompoundCollectionListener) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- removeContent(Dockable, boolean) - Method in class com.actelion.research.gui.dock.TreeLeaf
-
undockes and removes a Dockable from the docking tree and from the component tree
- removeDescriptors() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- removeDescriptors() - Method in class com.actelion.research.chem.StructureSearchSpecification
- removeDoubletsInt(List<int[]>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- removeDoubletsIntOrderIndepend(List<int[]>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
-
Removes arrays which contains identical integer.
- removeDrawingObjects() - Method in class com.actelion.research.chem.reaction.Reaction
- removeExplicitHydrogens() - Method in class com.actelion.research.chem.ExtendedMolecule
-
Removes all plain explicit hydrogens atoms from the molecule, converting them effectively to implicit ones.
- removeExplicitHydrogens(boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Removes all plain explicit hydrogens atoms from the molecule, converting them effectively to implicit ones.
- removeExtension(String) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
-
Provided that filePath has a recognized extension, then the extension is removed.
- removeInevitablePharmacophorePoint(int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- removeLast() - Method in class com.actelion.research.util.datamodel.IntArray
- removeLayoutComponent(Component) - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Method
- removeLigand(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- removeLonePairs(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- removeMapping(Reaction) - Method in class com.actelion.research.chem.reaction.MCSReactionMapper
- removeMappingNo(int) - Method in class com.actelion.research.chem.Molecule
- removeNode(PharmacophoreNode) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
- removePathAndExtension(String) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
-
Provided that fileName has a leading file path, then path and separator are removed.
- removeProgressListener(ProgressListener) - Method in class com.actelion.research.calc.DataProcessor
- removeQueryFeatures() - Method in class com.actelion.research.chem.Molecule
-
Removes any query features from the molecule
- removeStructureListener(StructureListener) - Method in class com.actelion.research.gui.JChemistryView
- removeStructureListener(StructureListener) - Method in class com.actelion.research.gui.JStructureView
- removeSubstructureFromMolecule(StereoMolecule, StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- removeSubStructures(List<StereoMolecule>) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
-
Removes all molecules that are a substructure of one of the molecules in the input list.
- removeSubstructuresFromMolecule(StereoMolecule, List<StereoMolecule>) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
-
Deletes the substructures, if found, in the molecule.
- removeValidationListener(IValidationListener) - Method in class com.actelion.research.share.gui.editor.Model
- removeValue(int) - Method in class com.actelion.research.util.datamodel.IntArray
-
Computational expensive operation!
- removeWater(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- removeWater(Molecule3D, boolean) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- removeWaterSalts(Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- removeWildcards(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- removeWithLeaf(TreeLeaf) - Method in class com.actelion.research.gui.dock.TreeContainer
- removeWithLeaf(TreeLeaf) - Method in class com.actelion.research.gui.dock.TreeFork
- removeWithLeaf(TreeLeaf) - Method in class com.actelion.research.gui.dock.TreeRoot
- renumberESRGroups(int) - Method in class com.actelion.research.chem.Molecule
-
For the given ESR type (AND or OR) renumbers all group indexes starting from 0.
- reorderAtoms() - Method in class com.actelion.research.chem.Molecule3D
-
Reorganizes atom indexes, so that moveable atoms are first
- repairLig(StereoMolecule) - Static method in class com.actelion.research.chem.docking.DockingUtils
- replaceAtoms(ExtendedMolecule[], int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- replaceAtoms(ExtendedMolecule, int, int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- replaceChildElement(TreeElement, TreeElement) - Method in class com.actelion.research.gui.dock.TreeContainer
- replaceChildElement(TreeElement, TreeElement) - Method in class com.actelion.research.gui.dock.TreeFork
- replaceChildElement(TreeElement, TreeElement) - Method in class com.actelion.research.gui.dock.TreeRoot
- replaceLigand(Molecule3D, Molecule3D) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- replaceLigand(Molecule3D, Molecule3D, Coordinates) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Replaces the preoptimized ligand in mol
- REPTerm - Class in com.actelion.research.chem.docking.scoring.plp
-
repulsive term, see PLPTerm for reference
- reset() - Method in class com.actelion.research.chem.mcs.ContainerListWithIntVec
- reset() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- reset() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- reset() - Method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- reset() - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- reset() - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- reset() - Method in class com.actelion.research.util.datamodel.IntArray
- reset() - Method in class com.actelion.research.util.graph.complete.AMemorizedObject
- reset() - Method in class com.actelion.research.util.graph.complete.ContainerMemory
- reset() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- reset() - Method in class com.actelion.research.util.Pipeline
-
Sets all to 0 and allDataIn to false..
- reset(int) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
-
Clears the hash map with the records that contain the given number of bits set.
- resetAllCounters() - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
- resetFragments(Reaction) - Method in class com.actelion.research.chem.reaction.MCSReactionMapper
- resetInevitablePharmacophorePoints() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- resetInfoColor() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- resetInfoColor() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- Residue - Class in com.actelion.research.chem.io.pdb.parser
-
ModelGroupAtoms handles a group of atoms, e.g.
- Residue(List<AtomRecord>) - Constructor for class com.actelion.research.chem.io.pdb.parser.Residue
- resize(boolean[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- resize(boolean[][], int, int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- resize(boolean[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- resize(byte[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- resize(double[][], int, int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- resize(double[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- resize(int) - Method in class com.actelion.research.util.datamodel.IntVec
- resize(int[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- resize(int[], int) - Static method in class com.actelion.research.util.datamodel.IntArray
- resize(int, int) - Method in class com.actelion.research.calc.Matrix
-
Resizes the matrix, the old data are written to the new matrix, if possible.
- resize(Object, int) - Static method in class com.actelion.research.util.ArrayUtils
-
Resize an array
- resize(String[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
-
Resize an array of Object
- resolve(String) - Static method in class com.actelion.research.chem.name.StructureNameResolver
- resolveLocal(String) - Method in interface com.actelion.research.chem.name.IStructureNameResolver
-
Local and typically quick name resolution
- resolveLocal(String) - Static method in class com.actelion.research.chem.name.StructureNameResolver
-
If a IStructureNameResolver instance was instantiated and given to this class, then that is asked to try to resolve the given chemical name, i.e.
- resolveRemote(String) - Method in interface com.actelion.research.chem.name.IStructureNameResolver
-
Typically remote server based name resolution that requires a network round trip
- resolveRemote(String) - Static method in class com.actelion.research.chem.name.StructureNameResolver
-
If a IStructureNameResolver instance was instantiated and given to this class, then that is asked to try to resolve the given chemical name, i.e.
- resolveRemote(String[]) - Method in interface com.actelion.research.chem.name.IStructureNameResolver
-
Remote server based name resolution of multiple names packed into one network round trip
- resolveRemote(String[]) - Static method in class com.actelion.research.chem.name.StructureNameResolver
-
If a IStructureNameResolver instance was instantiated and given to this class, then that is asked to try to resolve the given chemical name list, i.e.
- RESOURCE_AAS_LABELED - Static variable in class com.actelion.research.chem.io.pdb.converter.ConstantsAminoAcidsLabeled
- restore() - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- restore() - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- restoreState() - Method in class com.actelion.research.gui.JDrawArea
- restrainedRelaxation(StereoMolecule, double) - Method in class com.actelion.research.chem.phesaflex.FlexibleShapeAlignment
- ResultFracDimCalc - Class in com.actelion.research.chem.properties.fractaldimension
-
ResultFracDimCalc
- ResultFracDimCalc(InputObjectFracDimCalc) - Constructor for class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- ResultFragmentsStatistic - Class in com.actelion.research.chem.properties.complexity
- ResultFragmentsStatistic(StereoMolecule, List<ModelExhaustiveStatistics>) - Constructor for class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- ResultObjective - Class in com.actelion.research.chem.properties.complexity
- ResultObjective() - Constructor for class com.actelion.research.chem.properties.complexity.ResultObjective
- RETAIN_REACTANT_AND_PRODUCT_ORDER - Static variable in class com.actelion.research.chem.reaction.ReactionEncoder
- retrieveHighestValuesFrom2DArray(double[][], double[], int[][]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeUtils
- retrieveProtein() - Method in class com.actelion.research.chem.io.pdb.parser.ProteinSynthesizer
- reverse(byte[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
- reverse(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- reverse(Object[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- RGROUPS - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
- RIGHT - Static variable in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Field
- RIGID - Static variable in class com.actelion.research.chem.Molecule3D
- RigidFragment - Class in org.openmolecules.chem.conf.gen
- RigidFragment(int, int[], int[], int[], int[], Conformer[], double[]) - Constructor for class org.openmolecules.chem.conf.gen.RigidFragment
- RigidFragmentCache - Class in org.openmolecules.chem.conf.gen
-
This class implements a thread-save, concurrent cache of rigid fragments' 3D-atom-coordinates.
- RigidFragmentCache.CacheEntry - Class in org.openmolecules.chem.conf.gen
- RigidFragmentProvider - Class in org.openmolecules.chem.conf.gen
-
An instance of this class is used by any ConformerGenerator to hand out one or multiple 3D-coordinate sets for rigid fragments within a molecules.
- RigidFragmentProvider(long, RigidFragmentCache, boolean) - Constructor for class org.openmolecules.chem.conf.gen.RigidFragmentProvider
- rik2 - Variable in class com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionTerm
- RingBoolean - Enum in com.actelion.research.chem.forcefield.mmff
- RingCollection - Class in com.actelion.research.chem
- RingCollection(ExtendedMolecule, int) - Constructor for class com.actelion.research.chem.RingCollection
-
Generates the complete set of small rings, which don't contain metal atoms and have up to 7 members.
If mode includes LARGE_RINGS, then it determines for every atom and bond the size of the smallest ring, which they are a member of.
If mode includes AROMATICITY then every small ring is checked, whether it is aromatic. - RingCollection(ExtendedMolecule, int, int) - Constructor for class com.actelion.research.chem.RingCollection
-
Generates the complete set of small rings, which don't contain metal atoms and have up to 7 members.
If mode includes LARGE_RINGS, then it determines for every atom and bond the size of the smallest ring, which they are a member of.
If mode includes AROMATICITY then every small ring is checked, whether it is aromatic. - ringIsMMFFAromatic(int) - Method in class com.actelion.research.chem.forcefield.mmff.MMFFMolecule
-
Determine if a ring is aromatic according to MMFF criteria.
- ringIsMMFFAromatic(MMFFMolecule, int) - Static method in class com.actelion.research.chem.forcefield.mmff.type.Atom
-
Determine if a ring is aromatic according to MMFF criteria.
- RISK_NAME - Static variable in class com.actelion.research.chem.prediction.ToxicityPredictor
- rot(long, long) - Static method in class com.actelion.research.util.BurtleHasher
- RotatableBond - Class in org.openmolecules.chem.conf.gen
-
A RotatableBond knows the two rigid fragments within a molecule that are connected by this bond.
- RotatableBond(StereoMolecule, int, int[], int[], int, RigidFragment[], Random) - Constructor for class org.openmolecules.chem.conf.gen.RotatableBond
- RotatableBond(StereoMolecule, int, int[], int[], int, RigidFragment[], Random, boolean) - Constructor for class org.openmolecules.chem.conf.gen.RotatableBond
- rotate(double) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- rotate(double[][]) - Method in class com.actelion.research.chem.Coordinates
- rotate(double, double, double) - Method in class com.actelion.research.chem.coords.InventorFragment
- rotate(double, double, double) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- rotate(Coordinates, double) - Method in class com.actelion.research.chem.Coordinates
- rotateAroundBond(int, double, Conformer, boolean) - Method in class com.actelion.research.chem.conf.BondRotationHelper
-
rotate torsion angle of a conformer
- rotateAtom(Conformer, int, int, Coordinates, double) - Method in class org.openmolecules.chem.conf.so.ConformationRule
- rotateBond(Molecule3D, int, int, double) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
-
Make sure the parity of mol match the one from ref, otherwise fix it.
- rotateC(double[][]) - Method in class com.actelion.research.chem.Coordinates
- rotateLigand(Molecule3D, double, Coordinates, Coordinates) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- rotateMol(Conformer, double[]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- rotateMol(Conformer, Matrix) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- rotateMol(Conformer, Quaternion, double[]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- rotateMol(StereoMolecule, double[]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- rotateMol(StereoMolecule, double[][]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- rotateMol(StereoMolecule, Matrix) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- rotateMol(StereoMolecule, Quaternion, double[]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- rotateShift(Matrix) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- rotateSmallerSide(int, double) - Method in class com.actelion.research.chem.conf.BondRotationHelper
- rotateTo(Conformer, short) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
-
Rotate the smaller side of the molecule around this bond to reach the defined torsion angle.
- rotateToIndex(Conformer, int) - Method in class org.openmolecules.chem.conf.gen.RotatableBond
-
Rotate the smaller side of the molecule around this bond to reach the torsion angle defined by torsionIndex.
- roundRect(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- roundRect(int, int, int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMF
- row(int) - Static method in class com.actelion.research.chem.forcefield.mmff.PeriodicTable
-
Returns which row in the periodic table an atom with given atomic number is in.
- row2Matrix(int, int) - Method in class com.actelion.research.calc.Matrix
- rowFromESRType(int) - Static method in class com.actelion.research.share.gui.editor.Model
- rowQualifies(int) - Method in interface com.actelion.research.chem.StructureSearchController
-
If the structure search specification is part of a broader criteria list, then this method determines, whether all other, i.e.
- rows() - Method in class com.actelion.research.calc.Matrix
- rowtm(int) - Static method in class com.actelion.research.chem.forcefield.mmff.PeriodicTable
-
Returns which row in the periodic table an atom is in with transition metals having their row number multiplied by 10.
- rstar_ij - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
- RULE_NAME - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
- RULE_TYPE_BINAP - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
- RULE_TYPE_DISTANCE - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
- RULE_TYPE_LINE - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
- RULE_TYPE_PLANE - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
- RULE_TYPE_STEREO - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
- RULE_TYPE_TORSION - Static variable in class org.openmolecules.chem.conf.so.ConformationRule
- run() - Method in class com.actelion.research.chem.mcs.RunBondVector2IdCode
- run_minimiser(int, double, double) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
- RunBondVector2IdCode - Class in com.actelion.research.chem.mcs
- RunBondVector2IdCode(int, Pipeline<IBitArray>, Pipeline<FragmentDefinedByBondsIdCode>) - Constructor for class com.actelion.research.chem.mcs.RunBondVector2IdCode
- RXN_CODE_TAG - Static variable in class com.actelion.research.chem.io.RXNFileCreator
- RXN_CODE_TAG - Static variable in class com.actelion.research.chem.io.RXNFileV3Creator
- RXNFileCreator - Class in com.actelion.research.chem.io
- RXNFileCreator(Reaction) - Constructor for class com.actelion.research.chem.io.RXNFileCreator
- RXNFileCreator(Reaction, String) - Constructor for class com.actelion.research.chem.io.RXNFileCreator
- RXNFileParser - Class in com.actelion.research.chem.io
- RXNFileParser() - Constructor for class com.actelion.research.chem.io.RXNFileParser
- RXNFileV3Creator - Class in com.actelion.research.chem.io
- RXNFileV3Creator(Reaction) - Constructor for class com.actelion.research.chem.io.RXNFileV3Creator
- RXNFileV3Creator(Reaction, String) - Constructor for class com.actelion.research.chem.io.RXNFileV3Creator
S
- s(T, T) - Static method in class com.actelion.research.chem.forcefield.mmff.Search
-
Function used in swapping variables in one line.
- s(T, T) - Static method in class com.actelion.research.chem.forcefield.mmff.table.Torsion
- save() - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- save() - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- save(Molecule3D, Writer) - Method in class com.actelion.research.chem.io.AbstractParser
- save(Molecule3D, Writer) - Method in class com.actelion.research.chem.io.Mol2FileParser
- save(Molecule3D, String) - Method in class com.actelion.research.chem.io.AbstractParser
- save(List<Molecule3D>, int, Writer) - Method in class com.actelion.research.chem.io.Mol2FileParser
-
Writes also the partial charges
- save(List<Molecule3D>, Writer) - Method in class com.actelion.research.chem.io.AbstractParser
-
If not subclassed, save the files separately
- save(List<Molecule3D>, Writer) - Method in class com.actelion.research.chem.io.Mol2FileParser
- save(List<Molecule3D>, String) - Method in class com.actelion.research.chem.io.AbstractParser
- saveRXNFile(Reaction) - Method in class com.actelion.research.chem.io.CompoundFileHelper
- sbmb(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
-
Returns the SBMB type of an atom given its MMFF type.
- ScaffoldHelper - Class in com.actelion.research.chem
- ScaffoldHelper() - Constructor for class com.actelion.research.chem.ScaffoldHelper
- scale(double) - Method in class com.actelion.research.chem.AbstractDrawingObject
- scale(double) - Method in class com.actelion.research.chem.Coordinates
- scale(double) - Method in class com.actelion.research.chem.TextDrawingObject
- scale(double, double) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- scale(float) - Method in class com.actelion.research.share.gui.Arrow
- scale(float) - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
- scale(float) - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
- scale(float, float) - Method in class com.actelion.research.share.gui.editor.Model
- scale(int) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
-
This is a convenience method that scales the passed int value with getUIScaleFactor() and returns the rounded result.
- scale(BufferedImage) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
- SCALE - Static variable in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
- scaleC(double) - Method in class com.actelion.research.chem.Coordinates
- scaleCoords(double) - Method in class com.actelion.research.chem.Molecule
- ScaledEditorKit - Class in com.actelion.research.gui.hidpi
- ScaledEditorKit() - Constructor for class com.actelion.research.gui.hidpi.ScaledEditorKit
- ScaledHTML - Class in com.actelion.research.gui.hidpi
- ScaledHTML() - Constructor for class com.actelion.research.gui.hidpi.ScaledHTML
- ScaledStyleSheet - Class in com.actelion.research.gui.hidpi
- ScaledStyleSheet() - Constructor for class com.actelion.research.gui.hidpi.ScaledStyleSheet
- scaleInto(Reaction, double, double, double, double, double) - Static method in class com.actelion.research.chem.ChemistryHelper
- scaleIntoF(Reaction, double, double, double, double, double) - Static method in class com.actelion.research.chem.ChemistryHelper
- scaleIntoOld(Reaction, double, double, double, double, double) - Static method in class com.actelion.research.chem.ChemistryHelper
- scaleRetinaAndUI(int) - Static method in class com.actelion.research.gui.hidpi.HiDPIHelper
-
This is a convenience method that scales the passed int value with getUIScaleFactor() and with getRetinaScaleFactor() and returns the rounded result.
- ScorePoint - Class in com.actelion.research.util.datamodel
- ScorePoint() - Constructor for class com.actelion.research.util.datamodel.ScorePoint
- ScorePoint(int, int) - Constructor for class com.actelion.research.util.datamodel.ScorePoint
- ScorePoint(int, int, double) - Constructor for class com.actelion.research.util.datamodel.ScorePoint
- ScorePoint(Point) - Constructor for class com.actelion.research.util.datamodel.ScorePoint
- ScorePoint(Point, double) - Constructor for class com.actelion.research.util.datamodel.ScorePoint
- ScrollPaneAutoScrollerWhenDragging - Class in com.actelion.research.gui
- ScrollPaneAutoScrollerWhenDragging(JScrollPane, boolean) - Constructor for class com.actelion.research.gui.ScrollPaneAutoScrollerWhenDragging
- Sdf - Class in com.actelion.research.chem.forcefield.mmff
-
The Sdf class provides helper functions for dealing with the SDF file format.
- Sdf() - Constructor for class com.actelion.research.chem.forcefield.mmff.Sdf
- SDF_EXTENSION - Static variable in class com.actelion.research.util.ConstantsDWAR
- Sdf.OnMolecule - Interface in com.actelion.research.chem.forcefield.mmff
- SDFileMolecule - Class in com.actelion.research.chem
- SDFileMolecule() - Constructor for class com.actelion.research.chem.SDFileMolecule
- SDFileMolecule(Molecule) - Constructor for class com.actelion.research.chem.SDFileMolecule
- SDFileMolecule(SDFileMolecule) - Constructor for class com.actelion.research.chem.SDFileMolecule
- SDFileMoleculeDropAdapter - Class in com.actelion.research.gui.dnd
- SDFileMoleculeDropAdapter() - Constructor for class com.actelion.research.gui.dnd.SDFileMoleculeDropAdapter
- SDFileMoleculeTransferable - Class in com.actelion.research.gui.dnd
- SDFileMoleculeTransferable(StereoMolecule, StructureInfo) - Constructor for class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
- SDFileParser - Class in com.actelion.research.chem.io
- SDFileParser(File) - Constructor for class com.actelion.research.chem.io.SDFileParser
- SDFileParser(File, String[]) - Constructor for class com.actelion.research.chem.io.SDFileParser
- SDFileParser(Reader) - Constructor for class com.actelion.research.chem.io.SDFileParser
- SDFileParser(Reader, String[]) - Constructor for class com.actelion.research.chem.io.SDFileParser
- SDFileParser(String) - Constructor for class com.actelion.research.chem.io.SDFileParser
- SDFileParser(String, String[]) - Constructor for class com.actelion.research.chem.io.SDFileParser
- SE_RESIZE - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- Search - Class in com.actelion.research.chem.forcefield.mmff
-
The search class provides binary searching on arrays.
- Search() - Constructor for class com.actelion.research.chem.forcefield.mmff.Search
- SEARCH_TYPE_NOT_SUPPORTED - Static variable in interface com.actelion.research.chem.reaction.ReactionSearchDataSource
- SEARCH_TYPE_NOT_SUPPORTED - Static variable in interface com.actelion.research.chem.StructureSearchDataSource
- Searchable - Interface in com.actelion.research.chem.forcefield.mmff
-
Interface that must be implemented for array objects that can be searched by the binary search function.
- SEED - Static variable in class com.actelion.research.chem.docking.LigandPose
- select(long[][], int) - Method in class com.actelion.research.chem.DiversitySelector
- selectDockable(Dockable) - Method in class com.actelion.research.gui.dock.JDockingPanel
- selectFileToOpen(String, int) - Method in class com.actelion.research.chem.io.CompoundFileHelper
- selectFileToOpen(String, int) - Method in class com.actelion.research.gui.FileHelper
- selectFileToOpen(String, int, String) - Method in class com.actelion.research.gui.FileHelper
-
Shows a file-open-dialog, lets the user choose and returns the selected file.
- selectFileToSave(String, int, String) - Method in class com.actelion.research.chem.io.CompoundFileHelper
- selectFileToSave(String, int, String) - Method in class com.actelion.research.gui.FileHelper
-
Shows a file-save-dialog, lets the user choose and return the file's path and name.
- selectFragmentByAtom(int) - Method in class com.actelion.research.share.gui.editor.Model
- SELECTION_COLOR - Static variable in class com.actelion.research.chem.AbstractDrawingObject
- SelectionAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 1/24/13 Time: 5:57 PM
- SelectionAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.SelectionAction
- selectionColor() - Static method in class com.actelion.research.gui.JDrawArea
- selectObject(int) - Method in class com.actelion.research.gui.wmf.MetaFile
- selectObject(int) - Method in class com.actelion.research.gui.wmf.WMF
- selectOption(String, String, String[]) - Method in class com.actelion.research.chem.io.CompoundFileHelper
- selectOption(String, String, String[]) - Method in class com.actelion.research.gui.FileHelper
- Selector<T> - Interface in com.actelion.research.jfx.gui.misc
-
Created with IntelliJ IDEA.
- SelfOrganizedConformer - Class in org.openmolecules.chem.conf.so
- SelfOrganizedConformer(StereoMolecule) - Constructor for class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- SEP - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizEncoder
- SEP - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- SEP - Static variable in class com.actelion.research.util.IO
- SEP - Static variable in class com.actelion.research.util.StringFunctions
- SEP_LINE - Static variable in class com.actelion.research.util.ConstantsDWAR
- SEP_PARAMETER - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- SEP_VALUE - Static variable in class com.actelion.research.util.ConstantsDWAR
- Separation - Class in com.actelion.research.chem.forcefield.mmff
-
The Separation class is an efficient storage of an adjacency matrix representing how many degrees of separation there are between any two atoms.
- Separation(MMFFMolecule) - Constructor for class com.actelion.research.chem.forcefield.mmff.Separation
-
Constructs a new separation table for a molecule.
- Separation.Relation - Enum in com.actelion.research.chem.forcefield.mmff
-
Relation class shows the relationship between two atoms A1 and A2.
- SEPARATOR_ATOMS - Static variable in class com.actelion.research.chem.descriptor.flexophore.PPNode
- serializeCache(String, int) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
-
Writes for every distinct fragment: one idcode, multiple encoded coordinate sets, multiple conformer likelihoods
- serialVersionUID - Static variable in exception com.actelion.research.chem.descriptor.flexophore.UnparametrizedAtomTypeException
- serialVersionUID - Static variable in class com.actelion.research.gui.JAtomLabelDialog
- set(boolean[], boolean) - Static method in class com.actelion.research.util.ArrayUtils
- set(byte) - Method in class com.actelion.research.util.datamodel.ByteVec
- set(byte[], byte) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
-
Flat copy from node into this.
- set(double) - Method in class com.actelion.research.calc.Matrix
- set(double) - Method in class com.actelion.research.util.DoubleVec
- set(double[]) - Method in class com.actelion.research.util.DoubleVec
- set(double[][]) - Method in class com.actelion.research.calc.Matrix
- set(double[][], double) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- set(double[], double) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- set(double, double) - Method in class com.actelion.research.util.datamodel.PointDouble
- set(double, double, double) - Method in class com.actelion.research.chem.Coordinates
- set(float) - Method in class com.actelion.research.util.concurrent.AtomicFloat
- set(float[][], float) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- set(float[], float) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- set(int) - Method in class com.actelion.research.util.datamodel.IntVec
-
Don't forget to set the hash code!
- set(int[]) - Method in class com.actelion.research.util.DoubleVec
- set(int[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- set(int[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- set(int, byte) - Method in class com.actelion.research.util.datamodel.ByteVec
-
Hash value has to be recalculated!
- set(int, double) - Method in class com.actelion.research.util.DoubleVec
- set(int, int) - Method in class com.actelion.research.util.datamodel.IntArray
- set(int, int) - Method in class com.actelion.research.util.datamodel.IntVec
-
Don't forget to set the hash code!
- set(int, int, double) - Method in class com.actelion.research.calc.Matrix
- set(int, int, double) - Method in class com.actelion.research.util.DoubleVec
- set(int, int, String) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- set(short[][], short) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- set(Matrix) - Method in class com.actelion.research.calc.Matrix
- set(Matrix, int) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- set(Coordinates) - Method in class com.actelion.research.chem.Coordinates
-
Copies x,y,z from c to this
- set(ExtendedMolecule, int) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorAtoms
- set(ExtendedMolecule, int) - Method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- set(ExtendedMolecule, int) - Method in class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
- set(Molecule3D) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- set(StereoMolecule, StereoMolecule) - Method in class com.actelion.research.chem.mcs.MCS
-
mol should contain equal or more bonds than frag.
- set(StereoMolecule, StereoMolecule) - Method in class com.actelion.research.chem.mcs.MCSFast
- set(StereoMolecule, StereoMolecule, boolean[]) - Method in class com.actelion.research.chem.mcs.MCS
-
mol should contain equal or more bonds than frag.
- set(IntVec) - Method in class com.actelion.research.util.datamodel.IntVec
-
Don't forget to set the hash code!
- set(PointDouble) - Method in class com.actelion.research.util.datamodel.PointDouble
- set(String, String) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.PPNodeRGroup
- set(String, String, String) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- set(List<PPNodeViz>) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- set(T, T) - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- setAccessory(Component) - Method in class com.actelion.research.gui.JDrawDialog
- setActive(boolean) - Method in class com.actelion.research.gui.dnd.MoleculeDropAdapter
- setActive(boolean) - Method in class com.actelion.research.gui.dnd.ReactionDropAdapter
- setAlignment(int, int) - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Sets the Alignment attribute of the VerticalFlowLayout object
- setAllAtomFlag(int, boolean) - Method in class com.actelion.research.chem.Molecule3D
- setAllAtoms(int) - Method in class com.actelion.research.chem.Molecule
-
Low level method for constructing/modifying a molecule from scratch.
- setAllBonds(int) - Method in class com.actelion.research.chem.Molecule
-
Low level method for constructing/modifying a molecule from scratch.
- setAllDataIn() - Method in class com.actelion.research.util.Pipeline
- setAllDataIn(boolean) - Method in interface com.actelion.research.util.IPipeline
- setAllDataIn(boolean) - Method in class com.actelion.research.util.Pipeline
-
has to be set true or
wereAllDataFetched()
will never become true. - setAllowDropOrPasteWhenDisabled(boolean) - Method in class com.actelion.research.gui.JChemistryView
- setAllowFragmentStatusChangeOnPasteOrDrop(boolean) - Method in class com.actelion.research.gui.JStructureView
-
When fragment status change on drop is allowed then dropping a fragment (molecule) on a molecule (fragment) inverts the status of the view's chemical object.
- setAllowQueryFeatures(boolean) - Method in class com.actelion.research.gui.JDrawArea
-
If set to false then any query features will be removed from the molecule and any functionality that allows to define atom- or bond-query features won't be available.
- setAllowQueryFeatures(boolean) - Method in class com.actelion.research.gui.JEditableStructureView
- setAnisou(String) - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- setArea(double) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- setAromatic(boolean) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- setArrIndexParentNodes(int[]) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizFrag
- setArrNode(byte[]) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- setAssignParitiesToNitrogen(boolean) - Method in class com.actelion.research.chem.StereoMolecule
-
This is a policy setting for this StereoMolecule as molecule container.
- setAtomAbnormalValence(int, int) - Method in class com.actelion.research.chem.Molecule
-
Set an atom's maximum valance to be different from the default one.
- setAtomAmino(int, String) - Method in class com.actelion.research.chem.Molecule3D
- setAtomBfactor(int, double) - Method in class com.actelion.research.chem.Molecule3D
- setAtomChainId(int, String) - Method in class com.actelion.research.chem.Molecule3D
- setAtomCharge(int, int) - Method in class com.actelion.research.chem.Molecule
- setAtomCIPParity(int, int) - Method in class com.actelion.research.chem.Molecule
-
The atom Cahn-Ingold-Prelog parity is a calculated property available above/equal helper level cHelperCIP.
- setAtomColor(int, int) - Method in class com.actelion.research.chem.Molecule
- setAtomColorSupported(boolean) - Method in class com.actelion.research.gui.JDrawArea
- setAtomColorSupported(boolean) - Method in class com.actelion.research.share.gui.editor.Model
- setAtomConfigurationUnknown(int, boolean) - Method in class com.actelion.research.chem.Molecule
-
This is a user applied information, rather than a calculated value.
- setAtomCustomLabel(int, byte[]) - Method in class com.actelion.research.chem.Molecule
-
If a custom atom label is set, a molecule depiction displays the custom label instead of the original one.
- setAtomCustomLabel(int, String) - Method in class com.actelion.research.chem.Molecule
-
If a custom atom label is set, a molecule depiction displays the custom label instead of the original one.
- setAtomDescription(int, String) - Method in class com.actelion.research.chem.Molecule3D
- setAtomESR(int, int, int) - Method in class com.actelion.research.chem.Molecule
-
This is MDL's enhanced stereo representation (ESR).
- setAtomFlag(int, int, boolean) - Method in class com.actelion.research.chem.Molecule3D
- setAtomFlags(int, int) - Method in class com.actelion.research.chem.Molecule3D
- setAtomicNo(int) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- setAtomicNo(int, int) - Method in class com.actelion.research.chem.Molecule
-
Set an atom's atomic number and defines the isotop to be natural abundance.
- setAtomId(int) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- setAtomIndexConnectionFlexophorePoint(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
- setAtomIndexFirstLinkerAtom(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
- setAtomList(int, int[]) - Method in class com.actelion.research.chem.Molecule
-
Defines a list of allowed/excluded atomic numbers for sub-structure matching.
- setAtomList(int, int[], boolean) - Method in class com.actelion.research.chem.Molecule
-
Defines an atom list as query feature for substructure search
- setAtomMapNo(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
-
Defines an atom mapping number within the context of a reaction.
- setAtomMarker(int, boolean) - Method in class com.actelion.research.chem.Molecule
-
Atom marking may be used for any external purpose
- setAtomMass(int, int) - Method in class com.actelion.research.chem.Molecule
-
Set atom to specific isotop or to have a natural isotop distribution
- setAtomName(int, String) - Method in class com.actelion.research.chem.Molecule3D
- setAtomParity(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
-
The atom parity is a calculated property available above/equal helper level cHelperParities.
- setAtomQueryFeature(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
-
Introduce or remove an atom query feature and make sure, the molecule is flagged to be a sub-structure fragment (see setFragment()).
- setAtomRadical(int, int) - Method in class com.actelion.research.chem.Molecule
-
Sets an atom's radical state as singulet,dublet,triplet or none
- setAtoms(List<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- setAtomSelection(int, boolean) - Method in class com.actelion.research.chem.Molecule
- setAtomSequence(int, int) - Method in class com.actelion.research.chem.Molecule3D
- setAtomStereoCenter(int, boolean) - Method in class com.actelion.research.chem.Molecule
-
An atom is considered a stereo center, if it is a stereo center in at least in one of the molecule configurations represented by the ESR definitions.
- setAtomText(String[]) - Method in class com.actelion.research.chem.AbstractDepictor
-
Defines additional atom text to be displayed in top right position of some/all atom label.
- setAtomText(String[]) - Method in class com.actelion.research.gui.JDrawArea
-
Defines additional atom text to be displayed in top right position of some/all atom label.
- setAtomText(String[]) - Method in class com.actelion.research.gui.JStructureView
-
Defines additional atom text to be displayed in top right position of some/all atom labels.
- setAtomX(int, double) - Method in class com.actelion.research.chem.Molecule
- setAtomY(int, double) - Method in class com.actelion.research.chem.Molecule
- setAtomZ(int, double) - Method in class com.actelion.research.chem.Molecule
- setAttachedHydrogenCount(int, int) - Method in class com.actelion.research.chem.Molecule3D
-
Defines a number of attached hydrogens without known 3D-coordinates
- setAuthor(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setAuxiliaryInfo(String, Object) - Method in class com.actelion.research.chem.Molecule3D
- setAverageBondLength(Reaction, double) - Static method in class com.actelion.research.chem.ChemistryHelper
- setBackground(Color) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setBackground(Color) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setBackgroundColor(Color) - Static method in class com.actelion.research.gui.JMessageBar
- setBackgroundColor(Color) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- setBackgroundColor(Color) - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- setBase(IMolDistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- setBase(T) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- setBiasProvider(MutationBiasProvider) - Method in class com.actelion.research.chem.Mutator
- setBiasReference(StereoMolecule) - Method in interface com.actelion.research.chem.MutationBiasProvider
- setBit(int) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- setBit(int) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- setBit(int) - Method in class com.actelion.research.util.datamodel.IntVec
-
Counts from the left to the right Don't forget to set the hash code!
- setBit(int[], int) - Static method in class com.actelion.research.util.BitUtils
- setBit(int[], int) - Static method in class com.actelion.research.util.datamodel.IntVec
- setBits(int, int) - Method in class com.actelion.research.util.datamodel.IntVec
- setBKColor(Color) - Method in class com.actelion.research.gui.wmf.MetaFile
- setBKColor(Color) - Method in class com.actelion.research.gui.wmf.WMF
- setBKMode(int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setBKMode(int) - Method in class com.actelion.research.gui.wmf.WMF
- setBondAtom(int, int, int) - Method in class com.actelion.research.chem.Molecule
- setBondBackgroundHiliting(int, boolean) - Method in class com.actelion.research.chem.Molecule
-
Used for depiction only.
- setBondCIPParity(int, int) - Method in class com.actelion.research.chem.Molecule
-
The bond Cahn-Ingold-Prelog parity is a calculated property available above/equal helper level cHelperCIP.
- setBondESR(int, int, int) - Method in class com.actelion.research.chem.Molecule
-
MDL's enhanced stereo representation for BINAP type of stereo bonds.
- setBondForegroundHiliting(int, boolean) - Method in class com.actelion.research.chem.Molecule
-
Used for depiction only.
- setBondIndex(IntVec) - Method in class com.actelion.research.chem.mcs.SubStructSearchBondIndex
- setBondOrder(int, int) - Method in class com.actelion.research.chem.Molecule
-
Sets the bond type based on bond order without stereo orientation.
- setBondOrder(int, int) - Method in class com.actelion.research.chem.Molecule3D
- setBondParity(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
-
The bond parity is a calculated property available above/equal helper level cHelperParities.
- setBondParityUnknownOrNone(int) - Method in class com.actelion.research.chem.Molecule
-
This hint/flag is set by CoordinateInventor for double bonds without given EZ-parity, because the new coordinates may imply a not intended EZ-parity.
- setBondQueryFeature(int, int, boolean) - Method in class com.actelion.research.chem.Molecule
- setBondsMolecule(int) - Method in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- setBondTorsion(int, short) - Method in class com.actelion.research.chem.conf.Conformer
-
Sets the current bond torsion to be retrieved later.
- setBondType(int, int) - Method in class com.actelion.research.chem.Molecule
-
Defines a bond type combining bod order and stereo orientation.
- setBorderColor(Color) - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- setBrushFillStyle(int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setBrushHatch(int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setBrushPattern(Image) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setBusyColor(Color) - Static method in class com.actelion.research.gui.JMessageBar
- setByte(int[], int, int) - Static method in class com.actelion.research.util.datamodel.IntVec
- setByte(int, int) - Method in class com.actelion.research.util.datamodel.IntVec
-
Counts from the left to the right Don't forget to set the hash code!
- setBytes(int[], int) - Static method in class com.actelion.research.util.datamodel.IntVec
- setBytes(int, int, int) - Method in class com.actelion.research.util.datamodel.IntVec
- setCache(RigidFragmentCache) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentProvider
- setCaveat(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setCenter(Coordinates) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- setCenter(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
- setChargeAtom(int) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- setChiralDrawPosition(int) - Method in class com.actelion.research.gui.JStructureView
- setChirality(int) - Method in class com.actelion.research.chem.Molecule
-
Sets the overall chirality of the molecule taking into account: Recognition of stereo centers and stereo bonds, defined ESR features, meso detection.
- setCIPParities() - Method in class com.actelion.research.chem.Canonizer
- setCisPep(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setClassification(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setClip(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setClip(int, int, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setClip(Shape) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setClip(Shape) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setClipBoardData(String, byte[]) - Static method in class com.actelion.research.gui.clipboard.ClipboardHandler
- setClipBoardData(String, byte[]) - Static method in class com.actelion.research.gui.clipboard.NativeClipboardAccessor
- setClipboardHandler(IClipboardHandler) - Method in class com.actelion.research.gui.CompoundCollectionPane
-
call this in order to get clipboard support
- setClipboardHandler(IClipboardHandler) - Method in class com.actelion.research.gui.JDrawArea
-
Call this after initialization to get clipboard support
- setClipboardHandler(IClipboardHandler) - Method in class com.actelion.research.gui.JStructureView
-
Call this in order to get clipboard support: setClipboardHandler(new ClipboardHandler());
- setClipRgn() - Method in class com.actelion.research.gui.wmf.MetaFile
- setClipRgn() - Method in class com.actelion.research.gui.wmf.WMF
- setCol(int, double) - Method in class com.actelion.research.calc.Matrix
- setCol(int, double[]) - Method in class com.actelion.research.calc.Matrix
- setCollectFragmentIdCodes(boolean) - Method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- setCollisionIntensity(double, double[][]) - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- setColName(int, String) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- setColor(int) - Method in class com.actelion.research.chem.AbstractDepictor
- setColor(Color) - Method in class com.actelion.research.chem.AbstractDepictor
- setColor(Color) - Method in class com.actelion.research.chem.Depictor
- setColor(Color) - Method in class com.actelion.research.chem.Depictor2D
- setColor(Color) - Method in class com.actelion.research.chem.SVGDepictor
- setColor(Color) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setColor(Color) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setColor(Color) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- setColorMCS2Molecule(StereoMolecule, StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- setColorMolecule(StereoMolecule, int[]) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- setColorMoleculeFromBondIndex(StereoMolecule, int[], int) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- setColors(Color, Color) - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
-
Colors to be passed to Depictor.
- setComposite(Composite) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setCompound(int, T) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- setCompound(int, T) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- setCompound(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setCompoundFilter(MoleculeFilter) - Method in class com.actelion.research.gui.CompoundCollectionPane
- setCompoundList(Collection<T>) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- setCompoundList(Collection<T>) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- setConformationMode(int) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- setContent(Reaction) - Method in class com.actelion.research.gui.JChemistryView
- setContent(Reaction) - Method in class com.actelion.research.gui.JEditableChemistryView
- setContent(Reaction, DrawingObjectList) - Method in class com.actelion.research.gui.JChemistryView
- setContent(Reaction, DrawingObjectList) - Method in class com.actelion.research.gui.JEditableChemistryView
- setContent(StereoMolecule) - Method in class com.actelion.research.gui.JChemistryView
- setContent(StereoMolecule[]) - Method in class com.actelion.research.gui.JChemistryView
- setContent(StereoMolecule[]) - Method in class com.actelion.research.gui.JEditableChemistryView
- setContent(StereoMolecule[], DrawingObjectList) - Method in class com.actelion.research.gui.JChemistryView
- setContent(StereoMolecule[], DrawingObjectList) - Method in class com.actelion.research.gui.JEditableChemistryView
- setContent(StereoMolecule, DrawingObjectList) - Method in class com.actelion.research.gui.JChemistryView
- setContentMinimumSize(Dimension) - Method in class com.actelion.research.gui.dock.Dockable
-
Sets the minimum size of the encapsulated content component and sets the minimum width of the dockable header.
- setCoord(Coordinates) - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
- setCoordinates(double, double) - Method in class com.actelion.research.chem.TextDrawingObject
- setCoordinates(double, double, double) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setCoordinates(double, double, double, double) - Method in class com.actelion.research.chem.reaction.ReactionArrow
- setCoordinates(float, float, float, float) - Method in interface com.actelion.research.share.gui.editor.chem.IArrow
- setCoordinates(int, Coordinates) - Method in class com.actelion.research.chem.conf.Conformer
-
Copies x,y,z from coords into this atom's coordinates
- setCoordinates(int, Coordinates) - Method in class com.actelion.research.chem.Molecule3D
- setCoordinates(Coordinates) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setCoordinates(String) - Method in class com.actelion.research.chem.shredder.Fragment3D
- setCoordinatesNull() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setCoordinatesNull(StereoMolecule) - Static method in class com.actelion.research.chem.ExtendedMoleculeFunctions
- setCoordinatesReplace(int, Coordinates) - Method in class com.actelion.research.chem.conf.Conformer
-
Replaces the atom's Coordinates object by the given one
- setCreateFragments(boolean) - Method in class com.actelion.research.gui.CompoundCollectionPane
-
Defines whether new created structures are fragments of molecules.
- setCryst1(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setCurrentDirectory(File) - Static method in class com.actelion.research.chem.io.CompoundFileHelper
- setCurrentTool(int) - Method in class com.actelion.research.gui.JDrawToolbar
- setCustomTemplateList(List<InventorTemplate>) - Method in class com.actelion.research.chem.coords.CoordinateInventor
-
By providing a custom template list containing substructures with predefined atom coordinates, any occurence of any of these substructures will receive the relative atom coordinates of the provided template, unless the substructure shares more than one atom with a previously found substructure or the substructure shares more than one atom with the non marked atoms and mode is MODE_????_MARKED_ATOM_COORDS.
- setData(String, Object) - Method in class com.actelion.research.chem.StructureInfo
- setData(T) - Method in class com.actelion.research.util.datamodel.IdentifiedObject
- setData(T) - Method in interface com.actelion.research.util.datamodel.IIdentifiedObject
- setDateDeposition(Date) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setDBRef(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setDBRef1DBRef2(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setDefaultAverageBondLength(double) - Static method in class com.actelion.research.chem.Molecule
-
When the molecule adds a new bond to a new atom or a new ring, then atoms are positioned such that the lengths of the new bonds are equal to the average length of existing bonds.
- setDeletable(boolean) - Method in class com.actelion.research.chem.AbstractDrawingObject
- setDescription(String) - Method in class com.actelion.research.chem.io.CompoundFileFilter
-
Sets the human readable description of this filter.
- setDescriptorHandlerFactory(DescriptorHandlerFactory) - Method in class com.actelion.research.chem.io.CompoundFileParser
-
If a requested descriptor is not available in a particuar compound record, the parser can create one itself, provided its DescriptorHandlerFactory knows the descriptor name.
- setDirectionality(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
- setDirectionality(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
- setDirectionality(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- setDirectionality(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
- setDirectionality(Coordinates) - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
- setDirectionality(Coordinates) - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
- setDisableBorder(boolean) - Method in class com.actelion.research.gui.JStructureView
- setDiscreteFunction(double[]) - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
- setDisplayMode(int) - Method in class com.actelion.research.chem.AbstractDepictor
- setDisplayMode(int) - Method in class com.actelion.research.chem.ExtendedDepictor
- setDisplayMode(int) - Method in class com.actelion.research.gui.JChemistryView
- setDisplayMode(int) - Method in class com.actelion.research.gui.JDrawArea
- setDisplayMode(int) - Method in class com.actelion.research.gui.JStructureView
-
Sets the display mode for the Depictor.
- setDisplayMode(int) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- setDisplayMode(int) - Method in interface com.actelion.research.share.gui.editor.chem.IDepictor
- setDisplayMode(int) - Method in class com.actelion.research.share.gui.editor.Model
- setDisplaySize(Dimension) - Method in class com.actelion.research.share.gui.editor.Model
- setDistanceHistogram(byte[]) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- setDistanceTables(List<double[][]>) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
The distance tables which were generated from the conformations.
- setDistHist(int, int, byte[]) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- setDistHists(byte[], int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
-
Flat copy
- setDouble(double) - Method in class com.actelion.research.util.datamodel.IntegerDouble
- setDrawingObjects(DrawingObjectList) - Method in class com.actelion.research.chem.reaction.Reaction
- setDrawingObjects(DrawingObjectList) - Method in class com.actelion.research.gui.JDrawArea
- setE0(double) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- setEditable(boolean) - Method in class com.actelion.research.gui.CompoundCollectionPane
-
Defines, whether the list and individual structures can be edited.
- setEditable(boolean) - Method in class com.actelion.research.gui.JChemistryView
- setEditable(boolean) - Method in class com.actelion.research.gui.JStructureView
- setEditable(boolean) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- setElectronegativity(double) - Method in class com.actelion.research.chem.Element
- setELUSIVE(boolean) - Static method in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorBonds
- setELUSIVE(boolean) - Static method in class com.actelion.research.chem.properties.complexity.ContainerBitArray
- setELUSIVE(boolean) - Static method in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- setEnabled(boolean) - Method in class com.actelion.research.gui.CompoundCollectionPane
- setEnabled(boolean) - Method in class com.actelion.research.gui.JChemistryView
- setEnabled(boolean) - Method in class com.actelion.research.gui.JStructureView
- setEnabled(boolean) - Method in class org.openmolecules.chem.conf.so.ConformationRule
- setEnd(boolean) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setEnergy(double) - Method in class com.actelion.research.chem.conf.Conformer
- setErrorColor(Color) - Static method in class com.actelion.research.gui.JMessageBar
- setESRType(int) - Method in class com.actelion.research.share.gui.editor.Model
- setExistingSet(long[][]) - Method in class com.actelion.research.chem.DiversitySelector
- setExpdata(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setExtension(String) - Method in class com.actelion.research.gui.JFileChooserOverwrite
- setExtensionListInDescription(boolean) - Method in class com.actelion.research.chem.io.CompoundFileFilter
-
Determines whether the extension list (.jpg, .gif, etc) should show up in the human readable description.
- setFactorIsomorphSymmetric(double) - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- setFactorTextSize(double) - Method in class com.actelion.research.chem.AbstractDepictor
-
Sets a multiplication factor to the text size of all labels.
- setFieldData(String, String) - Method in class com.actelion.research.chem.SDFileMolecule
- setFileSupport(int) - Method in class com.actelion.research.gui.CompoundCollectionPane
-
Defines, whether the popup menu contains 'Open' and/or 'Save' items.
- setFill(long) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- setFill(long) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- setFixedAtoms(int[]) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
- setFixedAtoms(int[]) - Method in interface com.actelion.research.chem.forcefield.ForceField
- setFlat(double[][]) - Method in class com.actelion.research.calc.Matrix
- setFlatness(double) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setFlexible(boolean) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- setFont(Font) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setFont(Font) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setFont(String, double, boolean) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- setFont(String, double, boolean) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- setFontEscapement(int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setForegroundColor(Color, Color) - Method in class com.actelion.research.chem.AbstractDepictor
-
If the foreground color is set, the molecule is drawn in the foreground color except for non carbon atoms, which are drawn in atomicNo specific colors.
- setForegroundColor(Color, Color) - Method in class com.actelion.research.chem.ExtendedDepictor
- setForegroundColor(Color, Color) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- setFragment(boolean) - Method in class com.actelion.research.chem.Molecule
-
Molecule objects may represent complete molecules or sub-structure fragments, depending on, whether they are flagges as being a fragment or not.
- setFragment(boolean) - Method in class com.actelion.research.chem.reaction.Reaction
-
Sets all reactants and products of this reaction to the given fragment state, i.e.
- setFragment(boolean) - Method in class com.actelion.research.share.gui.editor.Model
- setFragment(byte[], int[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
-
Deprecated.
- setFragment(byte[], long[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- setFragment(StereoMolecule) - Method in class com.actelion.research.chem.mcs.SubStructSearchBondIndex
- setFragment(StereoMolecule) - Method in class com.actelion.research.chem.mcs.SubStructSearchExhaustiveTreeWalker
- setFragment(StereoMolecule) - Method in class com.actelion.research.chem.SSSearcher
-
Defines the fragment to be used in isFragmentInMolecule(...) or findFragmentInMolecule(...).
- setFragment(StereoMolecule, int[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
-
Deprecated.
- setFragment(StereoMolecule, long[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- setFragment(String, int[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
-
Deprecated.
- setFragment(String, long[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- setFragmentNoColor(long) - Method in interface com.actelion.research.share.gui.editor.chem.IDepictor
- setFragmentNoColor(C) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- setFragmentNoColor(Color) - Method in class com.actelion.research.chem.ExtendedDepictor
- setFragmentNoColor(Color) - Method in class com.actelion.research.gui.JChemistryView
- setFragments(int) - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- setFragments(StereoMolecule[]) - Method in class com.actelion.research.gui.JDrawArea
- setFragments(StereoMolecule[]) - Method in class com.actelion.research.share.gui.editor.Model
- setFrequency(int) - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- setFrequency(int) - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- setFrequencyOnePerMol(int) - Method in class com.actelion.research.chem.shredder.Fragment
- setFrequencySumAll(int) - Method in class com.actelion.research.chem.shredder.Fragment
- setFunctionalities(int[]) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- setGDIFillBrush() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setGDIFont() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setGDIFontDrawing(boolean) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setGDIHollowBrush() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setGDIPen() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setGDIPenDrawing(boolean) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setGDIPenWidthDrawing(boolean) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setGrowBoost(double) - Method in class com.actelion.research.chem.Mutator
- setHash(int) - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- setHash(int) - Method in class com.actelion.research.chem.properties.complexity.IndexHash
- setHeight(double) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- setHelix(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setHelperValidity(int) - Method in class com.actelion.research.chem.Molecule
-
Use this method with extreme care.
- setHet(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setHetAtomRecords(List<AtomRecord>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setHgap(int) - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Sets the Hgap attribute of the VerticalFlowLayout object
- setHiliteBondSet(int[]) - Method in class com.actelion.research.gui.JDrawArea
- setHmId_Formula(HashMap<String, String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setHmId_Name(HashMap<String, String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setHmId_Site(HashMap<String, String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setHmId_Synonyms(HashMap<String, String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setHorizontalFill(boolean) - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Sets the Hfill attribute of the VerticalFlowLayout object
- setHydrogenProtection(boolean) - Method in class com.actelion.research.chem.Molecule
-
Fragment's query features are checked for consistency and normalized during helper array creation.
- setId(int) - Method in class com.actelion.research.chem.io.pdb.parser.ListInteger
- setId(long) - Method in class com.actelion.research.util.datamodel.IdentifiedObject
- setId(long) - Method in interface com.actelion.research.util.datamodel.IIdentifiedObject
- setID(int) - Method in class com.actelion.research.calc.Matrix
- setID(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setIdcode(String) - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- setIdCode(String) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- setIdCode(String) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- setIdCode(String) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.PPNodeRGroup
- setIdCode(String) - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- setIDCode(String) - Method in class com.actelion.research.gui.JStructureView
- setIDCode(String, String) - Method in class com.actelion.research.gui.JStructureView
- setIdentifier(int) - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- setIdFlexophorePoint1(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- setIdFlexophorePoint2(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.Linker
- setImageProvider(ImageProvider) - Method in class com.actelion.research.share.gui.editor.Model
- setIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
- setIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setIndex(int) - Method in class com.actelion.research.chem.properties.complexity.IndexHash
- setIndexOriginalAtom(int) - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
- setIndexSphereVisualization(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setInstance(IStructureNameResolver) - Static method in class com.actelion.research.chem.name.StructureNameResolver
- setInteger(int) - Method in class com.actelion.research.util.datamodel.IntegerDouble
- setInteractionAtomType(int, int) - Method in class com.actelion.research.chem.Molecule3D
- setInteractionType(byte[]) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- setInteractionTypes(Molecule3D) - Static method in class com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator
- setInternalDragAndDropIsMove(boolean) - Method in class com.actelion.research.gui.CompoundCollectionPane
-
Defines the behaviour for internal drag&drop.
- setJrnl(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setKeywords(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setL1(long) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- setL2(long) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- setLambda(double) - Method in class com.actelion.research.util.SmoothingSplineInterpolator
- setLargestFragmentOnly(boolean) - Method in class com.actelion.research.chem.StructureSearchSpecification
- setLayouted(boolean) - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
- setLi(List<T>) - Method in class com.actelion.research.chem.io.pdb.parser.ListInteger
- setLiConnect(List<int[]>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setLineWidth(double) - Method in class com.actelion.research.chem.AbstractDepictor
- setLineWidth(double) - Method in class com.actelion.research.chem.Depictor
- setLineWidth(double) - Method in class com.actelion.research.chem.Depictor2D
- setLineWidth(double) - Method in class com.actelion.research.chem.SVGDepictor
- setLineWidth(double) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- setLineWidth(double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- setLineWidth(double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- setLink(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setLinkerId(int) - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
- setLocaleFormat(Formatter.LocaleFormat) - Static method in class com.actelion.research.util.Formatter
- setMapMode(int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setMapMode(int) - Method in class com.actelion.research.gui.wmf.WMF
- setMapper(IReactionMapper) - Method in class com.actelion.research.share.gui.editor.Model
- setMappingIndex(int) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setMappingIndex(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- setMark(int, boolean) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- setMarkAll(boolean) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- setMarked(boolean) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setMarkushStructure(MarkushStructure) - Method in class com.actelion.research.gui.JDrawArea
- setMarkushStructure(MarkushStructure) - Method in class com.actelion.research.share.gui.editor.Model
- setMaster(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setMatchingInfoInQueryAndBase(SolutionCompleteGraph) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
-
Sets the color information for the visualization of the Flexophore PPPoints.
- setMatchingInfoInQueryAndBase(SolutionCompleteGraph) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- setMatchLimit(int, int) - Method in class com.actelion.research.chem.reaction.ReactionSearch
-
If the search shall be aborted once it exceed a given number of matches, then define the maximum number of matches with this method before starting the search.
- setMatchLimit(int, int) - Method in class com.actelion.research.chem.StructureSearch
-
If the search shall be aborted once it exceed a given number of matches, then define the maximum number of matches with this method before starting the search.
- setMaxAtoms(int) - Method in class com.actelion.research.chem.Molecule
-
Usually called automatically and hardly needed to be called.
- setMaxAtoms(int) - Method in class com.actelion.research.chem.Molecule3D
- setMaxBonds(int) - Method in class com.actelion.research.chem.Molecule
-
Usually called automatically and hardly needed to be called.
- setMaxConfs(int) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- setMaximumTextSize(int) - Method in class com.actelion.research.chem.Depictor
- setMaxNumSolutions(int) - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- setMaxTotalCount(int) - Method in class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- setMdltyp(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setMode(int) - Method in class com.actelion.research.share.gui.editor.Model
- setModeFlexophore(byte) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- setModeFlexophore(byte) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- setModeQuery(boolean) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- setModeQuery(boolean) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- setModRes(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setMol(StereoMolecule) - Method in class com.actelion.research.chem.shredder.Fragment
- setMol(StereoMolecule, StereoMolecule) - Method in class com.actelion.research.chem.SSSearcher
-
Defines fragment and molecule before calling isFragmentInMolecule(...) or findFragmentInMolecule(...).
- setMolecule(byte[], int[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
-
Deprecated.
- setMolecule(byte[], long[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- setMolecule(int, StereoMolecule) - Method in interface com.actelion.research.gui.CompoundCollectionModel
- setMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCode
- setMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.IDCodeWithName
- setMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.Molecule
- setMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel.Native
- setMolecule(int, StereoMolecule) - Method in class com.actelion.research.gui.DefaultCompoundCollectionModel
- setMolecule(StereoMolecule) - Method in class com.actelion.research.chem.mcs.SubStructSearchBondIndex
- setMolecule(StereoMolecule) - Method in class com.actelion.research.chem.mcs.SubStructSearchExhaustiveTreeWalker
- setMolecule(StereoMolecule) - Method in class com.actelion.research.chem.SSSearcher
-
Defines the molecule to be used in isFragmentInMolecule(...) or findFragmentInMolecule(...).
- setMolecule(StereoMolecule) - Method in class com.actelion.research.gui.JDrawArea
- setMolecule(StereoMolecule) - Method in interface com.actelion.research.jfx.gui.chem.IMoleculeView
- setMolecule(StereoMolecule) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- setMolecule(StereoMolecule) - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- setMolecule(StereoMolecule, int[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
-
Deprecated.
- setMolecule(StereoMolecule, long[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- setMolecule(String, int[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
-
Deprecated.
- setMolecule(String, long[]) - Method in class com.actelion.research.chem.SSSearcherWithIndex
- setMoleculeColor(int) - Method in class com.actelion.research.chem.Molecule
-
Currently, this method only allows to switch the default atomic number dependent atom coloring off by passing cMoleculeColorNeutral.
- setMolFile(String) - Method in class com.actelion.research.share.gui.editor.Model
- setMtrix1(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setMtrix2(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setMtrix3(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setName(String) - Method in class com.actelion.research.chem.conf.Conformer
- setName(String) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- setName(String) - Method in class com.actelion.research.chem.Molecule
- setName(String) - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- setName(String) - Method in class com.actelion.research.chem.reaction.Reaction
- setNeighbours(List<Integer>) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- setNewMolecule() - Method in class com.actelion.research.share.gui.editor.Model
- setNodesQuery(int) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
-
Only needed for the toString() method.
- setNummdl(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setNumRegressionPoints(int) - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- setObjective(IObjectiveCompleteGraph<T>) - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- setObjectiveQueryBiased(boolean) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- setObsolete(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setOccurencesArray(int[]) - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
- setOpaqueBackground(boolean) - Method in class com.actelion.research.gui.JChemistryView
- setOptimize3D(boolean) - Method in class com.actelion.research.chem.io.AbstractParser
- setOrigX1(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setOrigX2(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setOrigX3(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setOverruleColor(Color, Color) - Method in class com.actelion.research.chem.AbstractDepictor
-
If the overrule color is set, the entire molecule is drawn in the foreground color neglecting any atom color information.
- setOverruleColor(Color, Color) - Method in class com.actelion.research.chem.ExtendedDepictor
- setOverruleColor(Color, Color) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- setOverruleColors(Color, Color) - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
-
Colors to be passed to Depictor.
- setPaint(Paint) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setPaintMode() - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setPaintMode() - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setParent(TreeContainer) - Method in class com.actelion.research.gui.dock.TreeElement
- setParent(TreeContainer) - Method in class com.actelion.research.gui.dock.TreeRoot
- setParities() - Method in class com.actelion.research.chem.Canonizer
-
Creates parities based on atom indices of original molecule and stores them into the molecule.
- setParitiesValid(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Atom stereo parities and bond E/Z-parities are properties that are usually perceived from up/down-bonds and atom coordinates, respectively.
- setPartialCharge(int, double) - Method in class com.actelion.research.chem.Molecule3D
- setPasteAndDropOptions(int) - Method in class com.actelion.research.gui.JChemistryView
-
fragment status change on drop is allowed then dropping a fragment (molecule) on a molecule (fragment) inverts the status of the view's chemical object.
- setPenStyle(int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setPenWidth(int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setPixel(int, int, Color) - Method in class com.actelion.research.gui.wmf.MetaFile
- setPixel(int, int, Color) - Method in class com.actelion.research.gui.wmf.WMF
- setPolyFillMode(int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setPolyFillMode(int) - Method in class com.actelion.research.gui.wmf.WMF
- setPolyFillMode(int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setPopupProvider(PopupProvider) - Method in class com.actelion.research.gui.dock.Dockable
- setPopupProvider(PopupProvider) - Method in class com.actelion.research.gui.dock.DockableHeader
- setPopupProvider(PopupProvider) - Method in class com.actelion.research.gui.dock.HeaderMouseAdapter
- setPositionInContainer(int) - Method in class com.actelion.research.util.graph.complete.AMemorizedObject
- setPPP(int, int[]) - Method in class com.actelion.research.chem.Molecule3D
- setPreferredSize(int, int, int) - Method in class com.actelion.research.chem.Mutator
- setPreviousAlignment(StereoMolecule[]) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- setPreviousPheSAResult(double[]) - Method in class com.actelion.research.chem.phesa.DescriptorHandlerShape
- setProtAtomRecords(List<AtomRecord>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setQ0(double) - Method in class com.actelion.research.chem.phesa.Quaternion
- setQ1(double) - Method in class com.actelion.research.chem.phesa.Quaternion
- setQ2(double) - Method in class com.actelion.research.chem.phesa.Quaternion
- setQ3(double) - Method in class com.actelion.research.chem.phesa.Quaternion
- setQuery(byte[], byte[], byte[], long[], long[]) - Method in class com.actelion.research.chem.reaction.SRSearcher
- setQuery(IMolDistHist) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- setQuery(Reaction) - Method in class com.actelion.research.chem.reaction.SRSearcher
-
This defines the query reaction (or transformation).
- setQuery(Reaction, long[], long[]) - Method in class com.actelion.research.chem.reaction.SRSearcher
-
This defines the query reaction (or transformation).
- setQuery(T) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- setRandomSeed(long) - Method in class com.actelion.research.chem.coords.CoordinateInventor
- setReactant(int, StereoMolecule) - Method in class com.actelion.research.chem.reaction.Reactor
-
Defines a real world reactant.
- setReaction(byte[], byte[], byte[], long[], long[]) - Method in class com.actelion.research.chem.reaction.SRSearcher
- setReaction(Reaction) - Method in class com.actelion.research.chem.reaction.SRSearcher
- setReaction(Reaction) - Method in class com.actelion.research.gui.JDrawArea
- setReaction(Reaction) - Method in class com.actelion.research.share.gui.editor.Model
- setReaction(Reaction, long[], long[]) - Method in class com.actelion.research.chem.reaction.SRSearcher
-
This defines the query reaction (or transformation).
- setReactionMapper(IReactionMapper) - Method in class com.actelion.research.gui.JDrawArea
- setReactionMapper(IReactionMapper) - Method in class com.actelion.research.gui.JDrawDialog
- setReactionMapper(IReactionMapper) - Method in class com.actelion.research.gui.JDrawPanel
- setReactionMode(boolean) - Method in class com.actelion.research.gui.JDrawArea
- setReactionMode(boolean) - Method in class com.actelion.research.gui.JDrawToolbar
- setRearAtoms(int[][]) - Method in class com.actelion.research.chem.conf.BondRotationHelper
- setRect(float, float, float, float) - Method in class com.actelion.research.share.gui.Arrow
- setRect(float, float, float, float) - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
- setReferenceVector(Coordinates) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- setRemarks(HashMap<Integer, String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setRenderingHint(RenderingHints.Key, Object) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setRenderingHints(Map<?, ?>) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setResourcePath(String) - Static method in class com.actelion.research.chem.conf.TorsionDB
-
Use this method before initializing the TorsionDB, if you want to open the resource files from an external location in the file system rather than from the project resources.
- setResSequence(int, int) - Method in class com.actelion.research.chem.Molecule3D
- setRevdat(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setRing(boolean) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- setRMSD(int) - Method in class com.actelion.research.chem.descriptor.flexophore.ClusterNode
-
Sum of squared distances of the center to the other cluster members
- setRNDvalue(double) - Method in class com.actelion.research.util.datamodel.ByteVec
- setRNDvalue(double) - Method in class com.actelion.research.util.datamodel.IntVec
- setRNDvalue(double) - Method in class com.actelion.research.util.DoubleVec
- setRNDvalue(double, double) - Method in class com.actelion.research.util.datamodel.ByteVec
- setRNDvalue(double, double) - Method in class com.actelion.research.util.datamodel.IntVec
- setRNDvalue(double, double) - Method in class com.actelion.research.util.DoubleVec
- setRole(int) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- setROP2(int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setROP2(int) - Method in class com.actelion.research.gui.wmf.WMF
- setRotatableBonds(int[]) - Method in class com.actelion.research.chem.conf.BondRotationHelper
- setRotationCenters(int[]) - Method in class com.actelion.research.chem.conf.BondRotationHelper
- setRow(int, double) - Method in class com.actelion.research.calc.Matrix
- setRow(int, double[]) - Method in class com.actelion.research.calc.Matrix
-
Deep copy
- setRow(int, int[]) - Method in class com.actelion.research.calc.Matrix
- setRowCoordinates(String, int) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Puts the given encoded atom coordinates into the given column.
- setRowName(int, String) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- setRowStructure(StereoMolecule, int, int) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Calculates the canonical structure representation as idcode from mol and puts it into the given idcodeColumn.
- setRowStructure(String, int) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Puts the given idcode into the given column.
- setRowValue(String, int) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Puts the given value into the given column.
- setScale1(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setScale2(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setScale3(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setScaling(double) - Method in class com.actelion.research.chem.DepictorTransformation
- setScore(double) - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- setScore(double) - Method in class com.actelion.research.util.datamodel.ScorePoint
- setSelectable(boolean) - Method in class com.actelion.research.gui.CompoundCollectionPane
- setSelected(boolean) - Method in class com.actelion.research.chem.AbstractDrawingObject
- setSelected(boolean) - Method in class com.actelion.research.gui.dock.Dockable
-
This panel draws its title bar differently if it is selected, which may be used to indicate to the user that this panel has the focus, or should get more attention than other simple internal frames.
- setSelected(boolean) - Method in class com.actelion.research.gui.dock.TreeLeaf
- setSelected(boolean) - Method in class com.actelion.research.share.gui.Arrow
- setSelected(boolean) - Method in class com.actelion.research.share.gui.editor.chem.DrawingObject
- setSelected(boolean) - Method in interface com.actelion.research.share.gui.editor.chem.IDrawingObject
- setSelectedAtom(int) - Method in class com.actelion.research.share.gui.editor.Model
- setSelectedBond(int) - Method in class com.actelion.research.share.gui.editor.Model
- setSelectedDockable(Dockable) - Method in class com.actelion.research.gui.dock.TreeLeaf
- setSelectedDrawingObject(IDrawingObject) - Method in class com.actelion.research.share.gui.editor.Model
- setSelection(int) - Method in class com.actelion.research.gui.CompoundCollectionPane
-
May be overridden to act on selection changes
- setSeparatorCol(String) - Static method in class com.actelion.research.calc.Matrix
- setSeparatorRow(String) - Static method in class com.actelion.research.calc.Matrix
- setSEQADV(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setSEQRES(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setSheet(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setShiftVector(Coordinates) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- setShowValidationError(boolean) - Method in class com.actelion.research.gui.CompoundCollectionPane
-
Defines whether a large red question mark is shown in case of a structure validation error.
- setSigma(double[]) - Method in class com.actelion.research.util.SmoothingSplineInterpolator
- setSim(double) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
- setSimilarity(double) - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- setSimilarityMappingNodes(float) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setSimilarityMappingNodes(int, float) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- setSingleConformationModeQuery(boolean) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- setSingleUnknownAsRacemicParity() - Method in class com.actelion.research.chem.Canonizer
-
If the molecule contains exactly one stereo center and if that has unknown configuration, than assume that the configuration is meant to be racemic and update molecule accordingly.
- setSize(int) - Method in class com.actelion.research.chem.shredder.Fragment
- setSize(int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setSize(String) - Method in class com.actelion.research.chem.TextDrawingObject
- setSizes(double[]) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.FeatureMatch
- setSlope(double) - Method in class com.actelion.research.calc.regression.linear.simple.LinearRegression
- setSlope(double) - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- setSlopeFragments(double) - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- setSlopeR2(double) - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- setSmallerSideAtomLists(int[][]) - Method in class com.actelion.research.chem.conf.BondRotationHelper
- setSmiles(String) - Method in class com.actelion.research.share.gui.editor.Model
- setSource(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setSplineFunction(FastSpline) - Method in class com.actelion.research.chem.interactionstatistics.SplineFunction
- setSplit(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setSpotColors(Color, Color) - Static method in class com.actelion.research.gui.HeaderPaintHelper
- setSprsde(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setSSBond(List<String>) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setSSSearcher(SSSearcher) - Method in class com.actelion.research.chem.mcs.MCS
- setState(double[]) - Method in class com.actelion.research.chem.docking.LigandPose
- setState(double[]) - Method in class com.actelion.research.chem.forcefield.AbstractForceField
- setState(double[]) - Method in interface com.actelion.research.chem.optimization.Evaluable
- setState(double[]) - Method in class com.actelion.research.chem.phesa.EvaluableOverlap
- setState(double[]) - Method in class com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
- setStereoBondFromAtomParity(int) - Method in class com.actelion.research.chem.ExtendedMolecule
- setStereoBondFromBondParity(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
In case bond is a BINAP kind of chiral bond with defined parity, then the preferred neighbour single bond is converted into a stereo bond to correctly reflect its defined parity.
- setStereoBondsFromParity() - Method in class com.actelion.research.chem.ExtendedMolecule
-
This converts one single bond per parity into a stereo up/down bond to correctly reflect the given parity.
- setStereoCenters() - Method in class com.actelion.research.chem.Canonizer
- setStereoProblem(int) - Method in class com.actelion.research.chem.Molecule
-
The stereo problem flag is set by the stereo recognition (available equal/above helper level cHelperParities) if an atom has over- or under-specified stereo bonds attached, i.e.
- setStretchBltMode(int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setStretchBltMode(int) - Method in class com.actelion.research.gui.wmf.WMF
- setStroke(long) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- setStroke(long) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- setStroke(Stroke) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setStructureSize(int) - Method in class com.actelion.research.gui.CompoundCollectionPane
-
Defines the width or height of individual structure cells, depending on whether the the CompoundCollectionPane is horizontal or vertical, respectively.
- setStyle(String) - Method in class com.actelion.research.chem.TextDrawingObject
- setTerminalC(boolean) - Method in class com.actelion.research.chem.io.pdb.parser.AtomRecord
- setText(String) - Method in class com.actelion.research.chem.TextDrawingObject
- setText(String) - Method in class com.actelion.research.gui.JMessageBar
- setTextAlign(int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setTextAlign(int) - Method in class com.actelion.research.gui.wmf.WMF
- setTextCharacterExtra(int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setTextCharacterExtra(int) - Method in class com.actelion.research.gui.wmf.WMF
- setTextColor(Color) - Static method in class com.actelion.research.gui.JMessageBar
- setTextColor(Color) - Method in class com.actelion.research.gui.wmf.MetaFile
- setTextColor(Color) - Method in class com.actelion.research.gui.wmf.WMF
- setTextSize(int) - Method in class com.actelion.research.chem.AbstractDepictor
- setTextSize(int) - Method in class com.actelion.research.chem.Depictor
- setTextSize(int) - Method in class com.actelion.research.chem.Depictor2D
- setTextSize(int) - Method in class com.actelion.research.chem.SVGDepictor
- setTextSize(int) - Method in class com.actelion.research.jfx.gui.chem.JFXCanvasDepictor
- setThreadMaster(ThreadMaster) - Method in class com.actelion.research.calc.DataProcessor
- setThreadMaster(ThreadMaster) - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- setThreadMaster(ThreadMaster) - Method in class com.actelion.research.chem.descriptor.flexophore.generator.CreatorMolDistHistViz
- setThreadMaster(ThreadMaster) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
If the conformer generation must be stopped from outside, for instance because of user intervention or because of a defined timeout, the provide a ThreadMaster with this method.
- setThreadMaster(ThreadMaster) - Method in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- setThreshSimilarityHardMatch(double) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- setTitle(String) - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- setTitle(String) - Method in class com.actelion.research.gui.dock.Dockable
-
Sets a new title text of the dockable header.
- setTitle(String) - Method in class com.actelion.research.gui.dock.DockableHeader
- setToFrontInTabbedPane(String) - Method in class com.actelion.research.gui.dock.JDockingPanel
- setToRacemate() - Method in class com.actelion.research.chem.Molecule
-
This is for compatibility with old MDL stereo representation that contained a 'chiral' flag to indicate that the molecule is not a racemate.
- setTorsionAtoms(int[][]) - Method in class com.actelion.research.chem.conf.BondRotationHelper
- setTorsionIDs(String[]) - Method in class com.actelion.research.chem.conf.BondRotationHelper
- setTransform(AffineTransform) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setTransformation(DepictorTransformation) - Method in class com.actelion.research.chem.AbstractDepictor
- setTransparent(boolean) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- setUnique(int) - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- setUniqueFragmentsEstimated(int) - Method in class com.actelion.research.chem.mcs.ModelSampleFragments
- setUnknownParitiesToExplicitlyUnknown() - Method in class com.actelion.research.chem.Canonizer
-
Sets all atoms with TH-parity 'unknown' to explicitly defined 'unknown'.
- setUnknownParitiesToExplicitlyUnknown() - Method in class com.actelion.research.chem.StereoMolecule
-
Sets all atoms with TH-parity 'unknown' to explicitly defined 'unknown'.
- setupAtomAndBondFeatures(int) - Method in class com.actelion.research.chem.SSSearcher
- setUpdateMode(int) - Method in class com.actelion.research.gui.JDrawArea
- setUsed() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- setUsed(boolean) - Method in class org.openmolecules.chem.conf.so.SelfOrganizedConformer
- setUserData(Object) - Method in class com.actelion.research.chem.Molecule
- setUseSelfOrganizerIfAllFails(boolean) - Method in class org.openmolecules.chem.conf.gen.ConformerGenerator
-
If a molecule has at least one rotatable bond if all permutations of torsions collide beyond a tolerated strain, then the standard behaviour of this class is to return that clashing conformer with the lowest strain.
If passing true to this method, the ConformerGenerator will use the ConformerSelfOrganizer in these cases to generate conformers. - setValue(double) - Method in class com.actelion.research.util.Angle
- setValue(Reaction) - Method in class com.actelion.research.share.gui.editor.Model
- setValue(StereoMolecule) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- setValue(StereoMolecule) - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- setValue(StereoMolecule, boolean) - Method in class com.actelion.research.share.gui.editor.Model
- setValues(String, double, int) - Method in class com.actelion.research.chem.TextDrawingObject
- setVerbose(boolean) - Method in class com.actelion.research.calc.DataProcessor
- setVerbose(boolean) - Method in interface com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.IPPNodeSimilarity
- setVerbose(boolean) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- setVerbose(boolean) - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- setVerbose(boolean) - Method in class com.actelion.research.util.graph.complete.CompleteGraphMatcher
- setVerbose(boolean) - Method in interface com.actelion.research.util.graph.complete.IObjectiveCompleteGraph
- setVgap(int) - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Sets the Vgap attribute of the VerticalFlowLayout object
- setViewportExt(int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setViewportExt(int, int) - Method in class com.actelion.research.gui.wmf.WMF
- setVolumes(List<Double>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- setWeight(double) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- setWeights(List<Double>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- setWindowExt(int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setWindowExt(int, int) - Method in class com.actelion.research.gui.wmf.WMF
- setWindowOrg(int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- setWindowOrg(int, int) - Method in class com.actelion.research.gui.wmf.WMF
- setWMF(MetaFile, int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setX(double) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setX(int, double) - Method in class com.actelion.research.chem.conf.Conformer
- setX(String) - Method in class com.actelion.research.chem.TextDrawingObject
- setXORMode(Color) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- setXORMode(Color) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- setY(double) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setY(int, double) - Method in class com.actelion.research.chem.conf.Conformer
- setY(String) - Method in class com.actelion.research.chem.TextDrawingObject
- setZ(double) - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- setZ(int, double) - Method in class com.actelion.research.chem.conf.Conformer
- sFactory - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerStandard2DFactory
- ShadowBorder - Class in com.actelion.research.gui.dock
- ShadowBorder() - Constructor for class com.actelion.research.gui.dock.ShadowBorder
-
Creates a border with a grey 1 pixel line on left and top and a 3 pixel (scaled to Hi-dpi factor) wide shadow on right and bottom.
- ShadowBorder(int, int, int, int) - Constructor for class com.actelion.research.gui.dock.ShadowBorder
-
Creates a border with a grey 1 pixel line on left and top and a 3 pixel wide shadow on right and bottom.
- shadowSize() - Static method in class com.actelion.research.gui.dock.ShadowBorder
- shareSameFragment(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
- shear(double, double) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- shift(int[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- shift(int[], int) - Static method in class com.actelion.research.util.ArrayUtils
- SHIFTJIS_CHARSET - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- shortName - Variable in class com.actelion.research.chem.descriptor.SimilarityCalculatorInfo
- shortNameToName(String) - Static method in class com.actelion.research.chem.descriptor.DescriptorHelper
- showBusyMessage(String) - Method in class com.actelion.research.gui.JMessageBar
- showErrorMessage(String) - Method in interface com.actelion.research.calc.ProgressListener
- showErrorMessage(String) - Method in class com.actelion.research.gui.JMessageBar
- showHelpDialog() - Method in class com.actelion.research.gui.JDrawArea
- showMessage(String) - Method in class com.actelion.research.chem.io.CompoundFileHelper
- showMessage(String) - Method in class com.actelion.research.gui.FileHelper
- showText() - Method in class com.actelion.research.gui.JMessageBar
- shuffle(int[]) - Static method in class com.actelion.research.util.ArrayUtils
- shuffle(int[], Random) - Static method in class com.actelion.research.util.ArrayUtils
- shuffle(IntArray) - Static method in class com.actelion.research.util.datamodel.IntArray
- shuffle(T[]) - Static method in class com.actelion.research.util.ArrayUtils
- shuffleArray(IdentifiedObject[]) - Static method in class com.actelion.research.util.datamodel.IdentifiedObject
- Sign(double, double) - Static method in class com.actelion.research.calc.Matrix
- Silicon - Static variable in class com.actelion.research.chem.PeriodicTable
- SIMILARITY_MODE_CARBON - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- SIMILARITY_MODE_HARD_THRESH - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
-
Hard thresh means if the similarity of two atom types in a node to node comparison is below a threshold the complete node to node similarity becomes 0.
- SIMILARITY_MODE_HARD_THRESH_AVR - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- SIMILARITY_MODE_HARD_THRESH_OPTIMISTIC - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- SIMILARITY_MODE_SIMPLE - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- SIMILARITY_SCALING_SPLIT_SCORE - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- SimilarityCalculatorInfo - Class in com.actelion.research.chem.descriptor
- SimilarityCalculatorInfo(String, String) - Constructor for class com.actelion.research.chem.descriptor.SimilarityCalculatorInfo
- SIMPLE_DATE_FORMAT - Static variable in class com.actelion.research.util.ConstantsDWAR
- SimpleCanonizer - Class in com.actelion.research.chem
- SimpleCanonizer(ExtendedMolecule) - Constructor for class com.actelion.research.chem.SimpleCanonizer
- SimpleMetalTerm - Class in com.actelion.research.chem.docking.scoring.chemscore
- SimplePPGaussian - Class in com.actelion.research.chem.phesa.pharmacophore
-
Differs from the PPGaussian by lacking a directionality vector and is not associated with a molecule Can be used to represent interaction sites in protein binding sites
- SimplePPGaussian(Coordinates, IPharmacophorePoint.Functionality) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.SimplePPGaussian
- SimplePPGaussian(String) - Constructor for class com.actelion.research.chem.phesa.pharmacophore.SimplePPGaussian
- simpleUpdateCoords(Rectangle2D.Double, int) - Method in class com.actelion.research.chem.AbstractDepictor
-
Returns full transformation that moves/scales original molecule into viewRect.
- simpleValidateView(Rectangle2D.Double, int) - Method in class com.actelion.research.chem.AbstractDepictor
- simpleValidateView(Rectangle2D.Double, int) - Method in class com.actelion.research.chem.SVGDepictor
- simpleValidateView(Rectangle2D.Double, int) - Method in interface com.actelion.research.share.gui.editor.chem.IDepictor
- sin() - Method in class com.actelion.research.util.Angle
- SingularValueDecomposition - Class in com.actelion.research.calc
-
Singular Value Decomposition.
- SingularValueDecomposition(double[][], ProgressListener, ThreadMaster) - Constructor for class com.actelion.research.calc.SingularValueDecomposition
-
Construct the singular value decomposition
- SiteParser - Class in com.actelion.research.chem.io.pdb.parser
-
SiteParser Site records specify residues comprising catalytic, co-factor, anti-codon, regulatory or other essential sites or environments surrounding ligands present in the structure.
- SiteParser() - Constructor for class com.actelion.research.chem.io.pdb.parser.SiteParser
- size - Variable in class com.actelion.research.calc.statistics.median.ModelMedianDouble
- size - Variable in class com.actelion.research.calc.statistics.median.ModelMedianFloat
- size - Variable in class com.actelion.research.calc.statistics.median.ModelMedianInteger
- size - Variable in class com.actelion.research.calc.statistics.median.ModelMedianLong
- size() - Method in class com.actelion.research.chem.coords.InventorFragment
- size() - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
-
Returns the total number of atoms in this force field.
- size() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- size() - Static method in class com.actelion.research.chem.PeriodicTable
- size() - Method in interface com.actelion.research.share.gui.editor.geom.IPolygon
- size() - Method in class com.actelion.research.share.gui.Polygon
- size() - Method in class com.actelion.research.util.datamodel.ByteVec
- size() - Method in class com.actelion.research.util.datamodel.DoubleArray
- size() - Method in class com.actelion.research.util.datamodel.IntVec
- size() - Method in class com.actelion.research.util.DoubleVec
- size() - Method in class com.actelion.research.util.hash.HashSetInt
- size() - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- size() - Method in class com.actelion.research.util.SortedList
- SIZE_RATIO - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- sizeAfterLastBitSet - Variable in class com.actelion.research.chem.properties.complexity.BitArray128
- sizeBits() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- sizeBits() - Method in class com.actelion.research.util.datamodel.IntVec
- sizeBytes() - Method in class com.actelion.research.util.datamodel.IntVec
- sizeContent() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- sizeContent(boolean) - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- sizeOf(String) - Static method in class com.actelion.research.util.StringFunctions
-
https://stackoverflow.com/questions/4385623/bytes-of-a-string-in-java sizeof(string) = 8 + // object header used by the VM 8 + // 64-bit reference to char array (value) 8 + string.length() * 2 + // character array itself (object header + 16-bit chars) 4 + // offset integer 4 + // count integer 4 + // cached hash code
- sizeOf(List<String>) - Static method in class com.actelion.research.util.StringFunctions
- SizeOf - Class in com.actelion.research.util
-
13.02.2006 MvK
- SizeOf() - Constructor for class com.actelion.research.util.SizeOf
- sizePipe() - Method in class com.actelion.research.util.Pipeline
- Sketch - Class in com.actelion.research.util
-
Title: Actelion Java Library
- Sketch() - Constructor for class com.actelion.research.util.Sketch
- skip(Reader) - Static method in class com.actelion.research.io.BOMSkipper
-
Some text editors (e.g.
- skipBytes(int) - Method in class com.actelion.research.util.LittleEndianDataInputStream
- skipUntilLineMatchesRegEx(StringReadChannel, String) - Static method in class com.actelion.research.io.StringReadChannel
- skipUntilLineMatchesRegEx(StringReadChannel, String, int) - Static method in class com.actelion.research.io.StringReadChannel
- skipUntilLineMatchesRegEx(InputStream, String) - Static method in class com.actelion.research.util.IO
- SlidingWindow - Class in com.actelion.research.calc.filter
-
SlidingWindow
- SlidingWindow(double[]) - Constructor for class com.actelion.research.calc.filter.SlidingWindow
- SlidingWindowDistHist - Class in com.actelion.research.chem.descriptor.flexophore
-
SlidingWindowDistHist Created by korffmo1 on 01.03.16.
- SlidingWindowDistHist(double[]) - Constructor for class com.actelion.research.chem.descriptor.flexophore.SlidingWindowDistHist
- SmilesCreator - Class in com.actelion.research.chem
- SmilesCreator() - Constructor for class com.actelion.research.chem.SmilesCreator
- SmilesParser - Class in com.actelion.research.chem
- SmilesParser() - Constructor for class com.actelion.research.chem.SmilesParser
- SmoothingSplineInterpolator - Class in com.actelion.research.util
-
Smoothing Spline Interpolator based on the algorithm described at http://www.qmw.ac.uk/~ugte133/book/11_tsd/splines.pdf
The Smoothing Spline is used to minimize Sum(sqr((Si-yi)/sigmai)) + lambda*Sum(sqr(S''i)) If lambda=0 (default), this is equivalent to the cubic spline interpolation If lambda=Infinity, this is equivalent to the least square fitting - SmoothingSplineInterpolator() - Constructor for class com.actelion.research.util.SmoothingSplineInterpolator
- SolubilityPredictor - Class in com.actelion.research.chem.prediction
- SolubilityPredictor() - Constructor for class com.actelion.research.chem.prediction.SolubilityPredictor
- SolutionCompleteGraph - Class in com.actelion.research.util.graph.complete
-
SolutionCompleteGraph
- SolutionCompleteGraph() - Constructor for class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- solve(Matrix) - Method in class com.actelion.research.calc.LUDecomposition
-
Solve A*X = B
- SOLVENT_GROUP - Static variable in class com.actelion.research.chem.io.pdb.parser.StructureAssembler
- sort() - Method in class com.actelion.research.util.datamodel.IntArray
- SortedList<T extends java.lang.Comparable<? super T>> - Class in com.actelion.research.util
- SortedList() - Constructor for class com.actelion.research.util.SortedList
- SortedList(Comparator) - Constructor for class com.actelion.research.util.SortedList
- SortedPair - Class in com.actelion.research.chem.forcefield.mmff
-
SortedPair class is used in the Separation table.
- SortedPair(int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.SortedPair
-
Construct a new SortedPair.
- SortedStringList - Class in com.actelion.research.chem
- SortedStringList() - Constructor for class com.actelion.research.chem.SortedStringList
- sortInteractionTypes() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- SP2_AMINE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- SpecialField(String, String, String, String, String) - Constructor for class com.actelion.research.chem.io.DWARFileParser.SpecialField
- SPECIFIC - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- SplineFunction - Class in com.actelion.research.chem.interactionstatistics
-
Class used to represent a Protein Ligand Function
- SplineFunction() - Constructor for class com.actelion.research.chem.interactionstatistics.SplineFunction
- SRC_AND - Static variable in class com.actelion.research.gui.wmf.WMFGraphics
- SRC_COPY - Static variable in class com.actelion.research.gui.wmf.WMFGraphics
- SRC_PAINT - Static variable in class com.actelion.research.gui.wmf.WMFGraphics
- SRCAND - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- SRCCOPY - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- SRCERASE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- SRCINVERT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- SRCPAINT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- SRSearcher - Class in com.actelion.research.chem.reaction
-
The SRSearcher class handles reaction-sub-structure searches.
- SRSearcher() - Constructor for class com.actelion.research.chem.reaction.SRSearcher
- SSSearcher - Class in com.actelion.research.chem
- SSSearcher() - Constructor for class com.actelion.research.chem.SSSearcher
-
Instantiates a SSSearcher object for running sub-structure searches with one or more sub-structure fragments on one or more molecules.
- SSSearcher(int) - Constructor for class com.actelion.research.chem.SSSearcher
-
Instantiates a SSSearcher object for running sub-structure searches with one or more sub-structure fragments on one or more molecules.
- SSSearcherWithIndex - Class in com.actelion.research.chem
- SSSearcherWithIndex() - Constructor for class com.actelion.research.chem.SSSearcherWithIndex
- SSSearcherWithIndex(int) - Constructor for class com.actelion.research.chem.SSSearcherWithIndex
- STABILIZED - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
- standardize(StereoMolecule, int) - Static method in class com.actelion.research.chem.MoleculeStandardizer
- start() - Method in class com.actelion.research.chem.reaction.ReactionSearch
- start() - Method in class com.actelion.research.chem.StructureSearch
- start() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXDocument
- start() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXPage
- start() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXReactionStep
- START_CAPACITY - Static variable in class com.actelion.research.chem.properties.complexity.ContainerFragBondsSolutions
- startAnimation(int) - Method in class com.actelion.research.gui.hidpi.HiDPIIconButton
-
In order for a button to support an animation, it need additional images to follow after its normal appearance.
- startProgress(String, int, int) - Method in class com.actelion.research.calc.DataProcessor
- startProgress(String, int, int) - Method in interface com.actelion.research.calc.ProgressListener
- startWrite(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDXDocument
- stateChanged() - Method in interface com.actelion.research.chem.forcefield.ForceFieldChangeListener
- stateChanged(ChangeEvent) - Method in class com.actelion.research.gui.dock.TreeLeaf
- StatisticalTorsionPotential - Class in com.actelion.research.chem.conf.torsionstrain
- StatisticalTorsionTerm - Class in com.actelion.research.chem.conf.torsionstrain
-
Represents a torsion potential as a function of the angle, derived from statistical torsion distributions from the COD/CSD The dihedral angle is defined by a atom sequence of 4 atoms.
- stbn - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- Stbn - Class in com.actelion.research.chem.forcefield.mmff.table
- Stbn(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Stbn
- step() - Method in class com.actelion.research.chem.phesaflex.MetropolisMonteCarloHelper
- STEREO_ANGLE_LIMIT - Static variable in class com.actelion.research.chem.ExtendedMolecule
- StereoMolecule - Class in com.actelion.research.chem
- StereoMolecule() - Constructor for class com.actelion.research.chem.StereoMolecule
- StereoMolecule(int, int) - Constructor for class com.actelion.research.chem.StereoMolecule
- StereoMolecule(Molecule) - Constructor for class com.actelion.research.chem.StereoMolecule
- stopAnimation() - Method in class com.actelion.research.gui.hidpi.HiDPIIconButton
- stopProgress() - Method in interface com.actelion.research.calc.ProgressListener
- stopProgress(String) - Method in class com.actelion.research.calc.DataProcessor
- stopScrolling() - Method in class com.actelion.research.gui.ScrollPaneAutoScrollerWhenDragging
- storeState() - Method in class com.actelion.research.gui.JDrawArea
- StraightLineRule - Class in org.openmolecules.chem.conf.so
- StraightLineRule(int[]) - Constructor for class org.openmolecules.chem.conf.so.StraightLineRule
- StrainTerm - Class in com.actelion.research.chem.docking.scoring.idoscore
-
knowledge-based term for the internal strain of a ligand, composed of the pair-potentials (only atoms further away than 3 bonds from each other)
- StrainTerm(StereoMolecule) - Constructor for class com.actelion.research.chem.docking.scoring.idoscore.StrainTerm
- STRATEGY_ADAPTIVE_RANDOM - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- STRATEGY_LIKELY_RANDOM - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- STRATEGY_LIKELY_SYSTEMATIC - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- STRATEGY_PURE_RANDOM - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- STRETCH_ANDSCANS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- STRETCH_DELETESCANS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- STRETCH_ORSCANS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- StretchBend - Class in com.actelion.research.chem.forcefield.mmff
-
Stretch bending energy term class.
- StretchBend(Tables, MMFFMolecule, int, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.StretchBend
-
Constructs a new stretch bend object.
- stretchBlt(int, int, int, int, int, int, int, int, int, int[], int, int) - Method in class com.actelion.research.gui.wmf.MetaFile
- stretchBlt(int, int, int, int, int, int, int, int, int, int[], int, int) - Method in class com.actelion.research.gui.wmf.WMF
- String2DoubleArray - Class in com.actelion.research.util.convert
- String2DoubleArray() - Constructor for class com.actelion.research.util.convert.String2DoubleArray
- StringFunctions - Class in com.actelion.research.util
- StringFunctions() - Constructor for class com.actelion.research.util.StringFunctions
- StringReadChannel - Class in com.actelion.research.io
-
StringReadChannel 2007 MvK: Start implementation 25.06.2009 MvK: implementation changed 12.02.2014 MvK: added charset encoding to handle Umlaute.
- StringReadChannel(ReadableByteChannel) - Constructor for class com.actelion.research.io.StringReadChannel
- stringToColor(String) - Static method in class com.actelion.research.gui.hidpi.ColorUtils
- stripIsotopInfo() - Method in class com.actelion.research.chem.Molecule
-
Removes all isotop information, i.e.
- stripSmallFragments() - Method in class com.actelion.research.chem.ExtendedMolecule
-
Removes all unconnected fragments except for the largest one.
- stripSmallFragments(boolean) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Removes all unconnected fragments except for the largest one.
- stripStereoInformation() - Method in class com.actelion.research.chem.StereoMolecule
-
Removes defined and implicit stereo information from the molecule.
- up/down-bonds are converted to double bonds
- stereo centers are flagged to be unknown
- double bonds with implicit stereo configurations are converted into cross bonds
- all atom and bond ESR assignments are removed
- parity and CIP helper state is set to invalid, such that stereo calculation is redone, if needed. - strokeLine(double, double, double, double) - Method in class com.actelion.research.jfx.gui.GraphicsContextImpl
- strokeLine(double, double, double, double) - Method in interface com.actelion.research.share.gui.editor.geom.IDrawContext
- StrokeLineCap<T> - Interface in com.actelion.research.share.gui.editor.geom
-
Project: User: rufenec Date: 11/24/2014 Time: 4:20 PM
- StrokeLineJoin - Interface in com.actelion.research.share.gui.editor.geom
-
Project: User: rufenec Date: 11/24/2014 Time: 4:20 PM
- StrongHasher() - Constructor for class com.actelion.research.chem.CanonizerUtil.StrongHasher
- StructureAssembler - Class in com.actelion.research.chem.io.pdb.parser
- StructureAssembler(List<int[]>, List<AtomRecord>, List<AtomRecord>) - Constructor for class com.actelion.research.chem.io.pdb.parser.StructureAssembler
- StructureCalculator - Class in com.actelion.research.chem.descriptor.flexophore.calculator
-
Utility function based on the molecule's connections (groups, rings,...)
- StructureCalculator() - Constructor for class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- structureChanged() - Method in class com.actelion.research.gui.JStructureView
-
Should only be called if JStructureView's internal Molecule is changed from outside as: theStructureView.getMolecule().setFragment(false); The caller is responsible to update displayMol also, if it is different from the molecule.
- structureChanged(StereoMolecule) - Method in class com.actelion.research.gui.CompoundCollectionPane
- structureChanged(StereoMolecule) - Method in class com.actelion.research.gui.JStructureView
-
Updates the molecule used for display, drag & drop and clipboard transfer.
- structureChanged(StereoMolecule) - Method in interface com.actelion.research.gui.StructureListener
- structureChanged(StereoMolecule, StereoMolecule) - Method in class com.actelion.research.gui.JStructureView
-
Updates both molecules used for display and for drag & drop/clipboard transfer.
- StructureInfo - Class in com.actelion.research.chem
- StructureInfo() - Constructor for class com.actelion.research.chem.StructureInfo
- StructureInfo(String, String, String, float, String) - Constructor for class com.actelion.research.chem.StructureInfo
- StructureListener - Interface in com.actelion.research.gui
- StructureNameResolver - Class in com.actelion.research.chem.name
-
Created by thomas on 7/13/17.
- StructureNameResolver() - Constructor for class com.actelion.research.chem.name.StructureNameResolver
- StructureSearch - Class in com.actelion.research.chem
- StructureSearch(StructureSearchSpecification, StructureSearchDataSource, StructureSearchController, ProgressController, DescriptorHandlerFactory) - Constructor for class com.actelion.research.chem.StructureSearch
-
This contructs a new structure search, which upon calling start() runs a multithreaded structure search on the structure rows provided by dataSource.
- StructureSearchController - Interface in com.actelion.research.chem
- StructureSearchDataSource - Interface in com.actelion.research.chem
- StructureSearchSpecification - Class in com.actelion.research.chem
- StructureSearchSpecification(int, byte[][], Object[], String, float) - Constructor for class com.actelion.research.chem.StructureSearchSpecification
-
Creates a complete specification for a substructure or similarity search with one or more query fragments or molecules.
- StructureTransferData - Class in com.actelion.research.chem
- StructureTransferData() - Constructor for class com.actelion.research.chem.StructureTransferData
- StructureTransferData(ExtendedMolecule, StructureInfo) - Constructor for class com.actelion.research.chem.StructureTransferData
- sub(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- sub(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Subtracts that vector from this vector by component.
- sub(ByteVec) - Method in class com.actelion.research.util.datamodel.ByteVec
-
Substraction
- sub(IntVec) - Method in class com.actelion.research.util.datamodel.IntVec
-
Substraction
- sub(DoubleVec) - Method in class com.actelion.research.util.DoubleVec
-
Substraction
- subC(Coordinates) - Method in class com.actelion.research.chem.Coordinates
- SubFlexophoreGenerator - Class in com.actelion.research.chem.descriptor.flexophore.generator
-
SubFlexophoreGenerator
- SubFlexophoreGenerator(int, int, int) - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator
- SubFlexophoreGenerator.ViolatedConditionsCount - Class in com.actelion.research.chem.descriptor.flexophore.generator
- SubGraphExtractor - Class in com.actelion.research.chem.descriptor.flexophore.redgraph
-
SubGraphExtractor Creates substructures by fragmentation and summarizes them.
- SubGraphExtractor() - Constructor for class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphExtractor
- SubGraphIndices - Class in com.actelion.research.chem.descriptor.flexophore.redgraph
-
SubGraphIndices A class to handle indices in a molecular graph.
- SubGraphIndices() - Constructor for class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- SubStructSearchBondIndex - Class in com.actelion.research.chem.mcs
- SubStructSearchBondIndex() - Constructor for class com.actelion.research.chem.mcs.SubStructSearchBondIndex
- SubStructSearchExhaustiveTreeWalker - Class in com.actelion.research.chem.mcs
- SubStructSearchExhaustiveTreeWalker() - Constructor for class com.actelion.research.chem.mcs.SubStructSearchExhaustiveTreeWalker
- subtract(double) - Method in class com.actelion.research.calc.Matrix
- subtract(double) - Method in class com.actelion.research.util.Angle
- subtract(Matrix) - Method in class com.actelion.research.calc.Matrix
- subtract(Angle) - Method in class com.actelion.research.util.Angle
- subtractByteWise(IntVec, IntVec) - Static method in class com.actelion.research.util.datamodel.IntVec
- subtractFromCols(Matrix) - Method in class com.actelion.research.calc.Matrix
- suggestBondType(int, int) - Method in class com.actelion.research.chem.Molecule
-
Suggests either cBondTypeSingle or cBondTypeMetalLigand whatever seems more appropriate for a new bond between the two atoms.
- suggestNewX2AndY2(int) - Method in class com.actelion.research.share.gui.editor.actions.DrawAction
- SULFONAMIDE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- SULFONATE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- SULFONE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- SULFOXIDE - com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- Sulfur - Static variable in class com.actelion.research.chem.PeriodicTable
- sum() - Method in class com.actelion.research.util.datamodel.DoubleArray
- sum(byte[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- sum(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- sum(double[]) - Static method in class com.actelion.research.util.ArrayUtils
- sum(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- sum(int[]) - Static method in class com.actelion.research.util.ArrayUtils
- sum(long[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- summarizeAlkaneCluster(MolDistHistViz, int) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
-
Summarizes alkane cluster.
- SummaryFragments - Class in com.actelion.research.chem.properties.complexity
- SummaryFragments(ResultFragmentsStatistic) - Constructor for class com.actelion.research.chem.properties.complexity.SummaryFragments
- supportsImplicitHydrogen(int) - Method in class com.actelion.research.chem.ExtendedMolecule
-
Whether an atom may be considered to carry implicit hydrogen atoms depends on the atomicNo of that atom.
- SVGDepictor - Class in com.actelion.research.chem
- SVGDepictor(StereoMolecule, int, String) - Constructor for class com.actelion.research.chem.SVGDepictor
- SVGDepictor(StereoMolecule, String) - Constructor for class com.actelion.research.chem.SVGDepictor
- swapAtoms(int, int) - Method in class com.actelion.research.chem.Molecule
-
Swaps two atoms' indexes/locations in the atom table.
- swapAtoms(int, int) - Method in class com.actelion.research.chem.Molecule3D
- swapBonds(int, int) - Method in class com.actelion.research.chem.Molecule
-
Swaps two bonds' indexes/locations in the atom table.
- swapNodes(int, int) - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- SWISS - com.actelion.research.util.Formatter.LocaleFormat
- switchBit(int) - Method in class com.actelion.research.util.datamodel.IntVec
- symbol(int) - Static method in class com.actelion.research.chem.PeriodicTable
- SYMBOL_CHARSET - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- SYMMETRY_C1C1_OR_C1D1 - Static variable in class com.actelion.research.chem.conf.TorsionDetail
- SYMMETRY_C1D2 - Static variable in class com.actelion.research.chem.conf.TorsionDetail
- SYMMETRY_D1D1 - Static variable in class com.actelion.research.chem.conf.TorsionDetail
- SYMMETRY_D1D2_OR_D2D2 - Static variable in class com.actelion.research.chem.conf.TorsionDetail
- SymmetryCalculator - Class in com.actelion.research.chem.properties.complexity
- SymmetryCalculator() - Constructor for class com.actelion.research.chem.properties.complexity.SymmetryCalculator
- SymmetryCorrectedRMSDCalculator - Class in com.actelion.research.chem.conf
-
employing RMSD calculation using a HungarianAlgorithm for the atom assignment to correct for overestimated RMSD values obtained by conventional methods for molecules with symmetric substructures based on: dx.doi.org/10.1021/ci400534h
- SymmetryCorrectedRMSDCalculator(Conformer, Conformer) - Constructor for class com.actelion.research.chem.conf.SymmetryCorrectedRMSDCalculator
- systemExec(String[]) - Static method in class com.actelion.research.util.Platform
-
Wrapper for Runtime.exec() that allows different handling by platform This method fixes forking issues in Windows when starting Mercury (by default new processes do not seem to be forked correctly)
T
- TA_BASELINE - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- TA_BOTTOM - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- TA_CENTER - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- TA_LEFT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- TA_NOUPDATECP - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- TA_RIGHT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- TA_TOP - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- TA_UPDATECP - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- TAB_STRING - Static variable in interface com.actelion.research.chem.io.CompoundTableConstants
- table - Variable in class com.actelion.research.chem.forcefield.mmff.Separation
- table - Variable in class com.actelion.research.chem.forcefield.mmff.table.Def
- table(String) - Static method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
-
Returns a table given a table name.
- TableModelString - Class in com.actelion.research.util.datamodel.table
-
TableModelText Data model for an only text containing table
- TableModelString() - Constructor for class com.actelion.research.util.datamodel.table.TableModelString
- TableModelString(int, int) - Constructor for class com.actelion.research.util.datamodel.table.TableModelString
- TableModelString(List<String>, List<String>) - Constructor for class com.actelion.research.util.datamodel.table.TableModelString
- Tables - Class in com.actelion.research.chem.forcefield.mmff
-
A collection of tables with the official parameters of the MMFF94/MMFF94s force field variants.
- Tables(String, String, String, String, String, String, String, String, String, String, String, String, String, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.Tables
-
Construct a new Tables object.
- TAG_AAS_ABBR1 - Static variable in class com.actelion.research.chem.io.pdb.converter.ConstantsAminoAcidsLabeled
- TAG_AAS_NAME - Static variable in class com.actelion.research.chem.io.pdb.converter.ConstantsAminoAcidsLabeled
- TAG_ACTNO - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_ANISOU - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_ATOM - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_ATOMS - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_AUTHOR - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_BONDS - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_BONDS_AT_MAX_FRAGS_CALC - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- TAG_CAVEAT - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_CISPEP - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_COMPLEXITY - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
- TAG_COMPND - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_CONECT - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_CONFORMERSET - Static variable in class com.actelion.research.util.ConstantsDWAR
-
Contains the idcode and the 3d coordinates.
- TAG_COOR - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_COOR2 - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_COOR3D - Static variable in class com.actelion.research.util.ConstantsDWAR
-
Can be one or multiple sets of 3D coordinates.
- TAG_CRYST1 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_DBREF - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_DBREF1_DBREF2 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_END - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_ENDMDL - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_EXPDTA - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_FORMUL - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_FRACTAL_DIM - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- TAG_FREQUENCY - Static variable in class com.actelion.research.chem.shredder.Fragment
- TAG_FREQUENCY_ONE_PER_MOLECULE - Static variable in class com.actelion.research.chem.shredder.Fragment
- TAG_HEADER - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_HELIX - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_HET - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_HETATM - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_HETNAM - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_HETSYN - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_ID - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- TAG_ID_QUERY - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_IDCODE - Static variable in class com.actelion.research.util.ConstantsDWAR
-
Deprecated.
- TAG_IDCODE2 - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_JRNL - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_KEYWDS - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_LIGAND_EFFICIENCY - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_LINK - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_MASTER - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_MAX_NUM_UNIQUE_FRAGMENTS_CALC - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- TAG_MAXIMUM_SLOPE - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
- TAG_MDLTYP - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_MESSAGE - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- TAG_MODEL - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_ModelExhaustiveStatistics - Static variable in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- TAG_MODRES - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_MTRIX1 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_MTRIX2 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_MTRIX3 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_MultipleNonOverlapSolution - Static variable in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- TAG_MW - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_NAME - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_NAMES - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_NUM_BONDS_AT_MAXIMUM_FREQ - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
- TAG_NUM_BONDS_AT_MAXIMUM_SLOPE - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
- TAG_NUMMDL - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_OBSOLTE - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_ORIGX1 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_ORIGX2 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_ORIGX3 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_QUERY_IDENTIFIER - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_RATIO_NON_SYMMETRIC_ATOMS - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
- TAG_RATIO_USED_BONDS_UP_TO_MAX_FREQ - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
- TAG_REACTION_CODE - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_REACTION_COORD - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_REACTION_DRAW_OBJ - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_REACTION_MAPPING - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_RECORD_NO - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_RELATIVE_FREQUNCY - Static variable in class com.actelion.research.chem.shredder.Fragment
- TAG_REMARK - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_REMARK_N - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_REMARK0 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_REMARK1 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_REMARK2 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_REMARK3 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_ResultFragmentsStatistic - Static variable in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- TAG_REVDAT - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SCALE1 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SCALE2 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SCALE3 - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SEQADV - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SEQRES - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SHEET - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SIMILARITY - Static variable in class com.actelion.research.chem.descriptor.DescriptorHelper
- TAG_SITE - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SIZE - Static variable in class com.actelion.research.chem.shredder.Fragment
- TAG_SMILES - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- TAG_SOURCE - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SOURCE - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_SPLIT - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SPRSDE - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_SSBOND - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_STRUCTURE_EXCLUDE - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_STRUCTURE_INCLUDE - Static variable in class com.actelion.research.util.ConstantsDWAR
- TAG_SUM_UNIQUE_FRAGMENTS_CALC - Static variable in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- TAG_SUM_UNIQUE_FRAGMENTS_UNTIL_MAX - Static variable in class com.actelion.research.chem.properties.complexity.SummaryFragments
- TAG_TER - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_TITLE - Static variable in class com.actelion.research.chem.io.pdb.parser.PDBFileParser
- TAG_VIZ_INFO_ENCODED - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- tan() - Method in class com.actelion.research.util.Angle
- TANIMOTO - Static variable in class com.actelion.research.util.datamodel.ByteVec
- TANIMOTO - Static variable in class com.actelion.research.util.DoubleVec
- TANIMOTO_INV - Static variable in class com.actelion.research.util.datamodel.ByteVec
- TANIMOTO_INV - Static variable in class com.actelion.research.util.DoubleVec
- TAUTOMER - com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
- TautomerHelper - Class in com.actelion.research.chem
- TautomerHelper(StereoMolecule) - Constructor for class com.actelion.research.chem.TautomerHelper
- test() - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- test(StereoMolecule) - Static method in class com.actelion.research.chem.contrib.DiastereotopicAtomID
- test01() - Static method in class com.actelion.research.util.datamodel.ByteVec
- testChiralDia - Class in com.actelion.research.chem.contrib
- testChiralDia() - Constructor for class com.actelion.research.chem.contrib.testChiralDia
- testDiaID - Class in com.actelion.research.chem.contrib
- testDiaID() - Constructor for class com.actelion.research.chem.contrib.testDiaID
- testFolder(String, String, String, Sdf.OnMolecule) - Static method in class com.actelion.research.chem.forcefield.mmff.Sdf
-
Tests an entire pair of folders, one containing SDF files and the other containing reference files.
- testHoses - Class in com.actelion.research.chem.contrib
- testHoses() - Constructor for class com.actelion.research.chem.contrib.testHoses
- testS1() - Static method in class com.actelion.research.util.datamodel.ByteVec
- testTakeda1() - Static method in class com.actelion.research.util.datamodel.ByteVec
- TetrahedralStereoRule - Class in org.openmolecules.chem.conf.so
- TetrahedralStereoRule(StereoMolecule, int[]) - Constructor for class org.openmolecules.chem.conf.so.TetrahedralStereoRule
- TextClipboardHandler - Class in com.actelion.research.gui.clipboard
- TextDrawingObject - Class in com.actelion.research.chem
- TextDrawingObject() - Constructor for class com.actelion.research.chem.TextDrawingObject
- TextDrawingObject(String) - Constructor for class com.actelion.research.chem.TextDrawingObject
- TextDrawingObject(String, double, double) - Constructor for class com.actelion.research.chem.TextDrawingObject
- TextDrawingObject(String, double, double, double, int) - Constructor for class com.actelion.research.chem.TextDrawingObject
- textOut(int, int, String) - Method in class com.actelion.research.gui.wmf.MetaFile
- textOut(int, int, String) - Method in class com.actelion.research.gui.wmf.WMF
- theta(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
-
Returns 'theta0' the equilibrium angle for a given index in the table.
- theta(MMFFMolecule, int, int, int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Angle
-
Returns 'theta0' the ideal angle given a molecule and three connected atoms which form an angle.
- theta0 - Variable in class com.actelion.research.chem.forcefield.mmff.AngleBend
- theta0 - Variable in class com.actelion.research.chem.forcefield.mmff.StretchBend
- thinSize() - Static method in class com.actelion.research.gui.dock.ShadowBorder
- ThreadMaster - Interface in com.actelion.research.calc
- threadMustDie() - Method in class com.actelion.research.calc.DataProcessor
- threadMustDie() - Method in interface com.actelion.research.calc.ThreadMaster
- THRESH_HISTOGRAM_SIMILARITY - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- THRESH_HISTOGRAM_SIMILARITY - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- THRESH_SIMILARITY_COMPARISON_NODE - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- THRESH_SIMILARITY_HARD_MATCH - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
-
Similarity value distribution of the interaction table (April 2020).
- TIE_BREAK_FREE_VALENCE_ATOMS - Static variable in class com.actelion.research.chem.Canonizer
- TINY - Static variable in class com.actelion.research.calc.Matrix
- TINY_FACTOR - Static variable in class com.actelion.research.calc.histogram.ConstantsHistogram
- TINY04 - Static variable in class com.actelion.research.calc.Matrix
- TINY08 - Static variable in class com.actelion.research.calc.Matrix
- TINY16 - Static variable in class com.actelion.research.calc.Matrix
- to(Vector3) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Returns a vector that points from this vector to that vector.
- toArray() - Method in class com.actelion.research.calc.Matrix
- toArray() - Method in class com.actelion.research.chem.SortedStringList
- toArray() - Method in class com.actelion.research.chem.UniqueStringList
- toArray() - Method in class com.actelion.research.util.datamodel.ByteVec
- toArray() - Method in class com.actelion.research.util.datamodel.IntVec
- toArray() - Method in class com.actelion.research.util.DoubleVec
- toArray(List<String>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toArray(T[]) - Method in class com.actelion.research.util.SortedList
- toArray(T[]) - Method in class com.actelion.research.util.UniqueList
- toArrayStrStr(List<List<String>>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toBinaryString() - Method in class com.actelion.research.util.datamodel.ByteVec
- toBinaryStringDense() - Method in class com.actelion.research.util.datamodel.ByteVec
- toByteArray(double[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
- toByteArray(int) - Static method in class com.actelion.research.util.datamodel.ByteVec
- toByteArray(int[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
- toByteArray(long) - Static method in class com.actelion.research.util.datamodel.ByteVec
- toBytes(String, int) - Static method in class com.actelion.research.util.BinaryDecoder
-
Convenience method to directly decode a String-encoded byte array.
- toDegrees() - Method in class com.actelion.research.util.Angle
- toDoubleArray(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toDoubleArray(List<Double>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toDoubleBitWise() - Method in class com.actelion.research.util.datamodel.IntVec
- toIntArray(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toIntArray(Collection<Integer>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
-
Converts a List of Integer to an int[]
- toIntArray(List<Integer>) - Static method in class com.actelion.research.util.ArrayUtils
-
Converts a List of Integer to an int[]
- toIntByteWise() - Method in class com.actelion.research.util.datamodel.IntVec
- toInts(String, int) - Static method in class com.actelion.research.util.BinaryDecoder
-
Convenience method to directly decode a String-encoded int array.
- toList() - Method in class com.actelion.research.util.datamodel.IntArray
- toList() - Method in class com.actelion.research.util.hash.HashSetInt
- toList(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toList(int[]) - Static method in class com.actelion.research.util.ArrayUtils
- toList(int[]) - Static method in class com.actelion.research.util.datamodel.IntArray
- toList(int[], List<Integer>) - Static method in class com.actelion.research.util.ArrayUtils
- toList(String[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toList(T[]) - Static method in class com.actelion.research.util.ArrayUtils
- TOLX - Static variable in class com.actelion.research.chem.forcefield.AbstractForceField
- toMolecule() - Method in class com.actelion.research.chem.conf.Conformer
-
Copies this Conformer's atom coordinates to the associated molecule.
- toMolecule(StereoMolecule) - Method in class com.actelion.research.chem.conf.Conformer
-
Copies this Conformer's atom coordinates to the given molecule.
- TOOL_CHAINCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_CTEXTCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_CURSOR_BASE - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_DELETECURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_FISTCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_HANDCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_HANDPLUSCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_LASSOCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_LASSOPLUSCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_POINTERCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_SELECTRECTCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_SELECTRECTPLUSCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- TOOL_ZOOMCURSOR - Static variable in interface com.actelion.research.share.gui.editor.geom.ICursor
- ToolbarSelectionChange - Interface in com.actelion.research.share.gui.editor.actions
-
Created by rufenec on 5/3/16.
- toolChanged(int) - Method in class com.actelion.research.gui.JDrawArea
- TOP - Static variable in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Field
- toRow() - Method in class com.actelion.research.calc.Matrix
- torsion - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- Torsion - Class in com.actelion.research.chem.forcefield.mmff.table
- Torsion - Class in com.actelion.research.chem.forcefield.mmff.type
-
The torsion type class provides a static function for getting the torsion type of a torsion angle.
- Torsion() - Constructor for class com.actelion.research.chem.forcefield.mmff.type.Torsion
- Torsion(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.Torsion
- TORSION_GREEN - Static variable in class com.actelion.research.chem.conf.TorsionDB
- TORSION_NOT_FOUND - Static variable in class com.actelion.research.chem.conf.TorsionDB
- TORSION_RED - Static variable in class com.actelion.research.chem.conf.TorsionDB
- TORSION_YELLOW - Static variable in class com.actelion.research.chem.conf.TorsionDB
- Torsion.Kb - Class in com.actelion.research.chem.forcefield.mmff.table
- TorsionAngle - Class in com.actelion.research.chem.forcefield.mmff
-
Torsional Angle energy term class.
- TorsionAngle(Tables, MMFFMolecule, int, int, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.TorsionAngle
-
Construct a new torsion angle energy term.
- TorsionConstraint - Class in com.actelion.research.chem.potentialenergy
- TorsionConstraint(Conformer, int[], double, double) - Constructor for class com.actelion.research.chem.potentialenergy.TorsionConstraint
-
Term that forces a torsion angle with a harmonic potential to a range of acceptable values (range given by the width)
- TorsionDB - Class in com.actelion.research.chem.conf
- TorsionDescriptor - Class in com.actelion.research.chem.conf
- TorsionDescriptor(float[], float[]) - Constructor for class com.actelion.research.chem.conf.TorsionDescriptor
- TorsionDescriptorHelper - Class in com.actelion.research.chem.conf
- TorsionDescriptorHelper(StereoMolecule) - Constructor for class com.actelion.research.chem.conf.TorsionDescriptorHelper
- TorsionDescriptorHelper(StereoMolecule, int[]) - Constructor for class com.actelion.research.chem.conf.TorsionDescriptorHelper
- TorsionDetail - Class in com.actelion.research.chem.conf
- TorsionDetail() - Constructor for class com.actelion.research.chem.conf.TorsionDetail
-
This creates an empty torsion classification detail, which multiply can be used to classify the environment of a rotatable bond.
- TorsionPrediction - Class in com.actelion.research.chem.conf
- TorsionPrediction(StereoMolecule, int[]) - Constructor for class com.actelion.research.chem.conf.TorsionPrediction
- TorsionRelevanceHelper - Class in com.actelion.research.chem.conf
- TorsionRelevanceHelper() - Constructor for class com.actelion.research.chem.conf.TorsionRelevanceHelper
- TorsionRule - Class in org.openmolecules.chem.conf.so
- TorsionRule(short[], short[], short[][], int[], int[], int) - Constructor for class org.openmolecules.chem.conf.so.TorsionRule
- TorsionSet - Class in org.openmolecules.chem.conf.gen
- TorsionSet(int[], int[], int[], int[], double) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSet
-
Creates a new conformer description from torsion and conformer indexes.
- TorsionSet(TorsionSet) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSet
-
Deep-Copy constructor not including collision intensities
- TorsionSetEliminationRule - Class in org.openmolecules.chem.conf.gen
- TorsionSetEliminationRule(long[], long[], double) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSetEliminationRule
- TorsionSetStrategy - Class in org.openmolecules.chem.conf.gen
-
Knowing all rotatable bonds of an underlying molecule and knowing those rigid fragments that are connected by them, the TorsionSetStrategy provides a mechanism to deliver valid and unique torsion sets, each effectively defining an individual conformer.
- TorsionSetStrategy(RotatableBond[], RigidFragment[]) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSetStrategy
- TorsionSetStrategyAdaptiveRandom - Class in org.openmolecules.chem.conf.gen
- TorsionSetStrategyAdaptiveRandom(RotatableBond[], RigidFragment[], boolean, boolean, long) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSetStrategyAdaptiveRandom
-
This torsion set strategy produces random sets of torsion indices until a torsion set collides.
- TorsionSetStrategyLikelySystematic - Class in org.openmolecules.chem.conf.gen
-
TorsionSetStrategy that systematically creates all possible TorsionSets in batches while keeping a focus on the likelyhood of individual torsions.
- TorsionSetStrategyLikelySystematic(RotatableBond[], RigidFragment[]) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSetStrategyLikelySystematic
- TorsionSetStrategyRandom - Class in org.openmolecules.chem.conf.gen
- TorsionSetStrategyRandom(RotatableBond[], RigidFragment[], boolean, long) - Constructor for class org.openmolecules.chem.conf.gen.TorsionSetStrategyRandom
-
This simple TorsionSetStrategy produces random sets of torsion indexes in a loop.
- toShortString(long, int) - Static method in class com.actelion.research.util.DoubleFormat
-
Converts the value with the given exponent into a short string representation using the scientific notation if it is more compact.
- toSortedArray() - Method in class com.actelion.research.chem.UniqueStringList
- toSortedArray(T[]) - Method in class com.actelion.research.util.UniqueList
- toSortedString(List<String>) - Static method in class com.actelion.research.util.StringFunctions
- toString() - Method in class com.actelion.research.calc.histogram.Histogram
-
First row: bins, upper border.
- toString() - Method in class com.actelion.research.calc.Matrix
- toString() - Method in class com.actelion.research.calc.statistics.median.ModelMedianDouble
- toString() - Method in class com.actelion.research.calc.statistics.median.ModelMedianFloat
- toString() - Method in class com.actelion.research.calc.statistics.median.ModelMedianInteger
- toString() - Method in class com.actelion.research.calc.statistics.median.ModelMedianLong
- toString() - Method in class com.actelion.research.chem.AbstractDrawingObject
- toString() - Method in class com.actelion.research.chem.conf.ConformerSet
- toString() - Method in class com.actelion.research.chem.conf.TorsionDescriptor
- toString() - Method in class com.actelion.research.chem.Coordinates
- toString() - Method in class com.actelion.research.chem.DepictorTransformation
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.AtomIndexLinkerId
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.IndexCoordinates
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeVizTriangle
- toString() - Method in class com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
- toString() - Method in class com.actelion.research.chem.DrawingObjectList
- toString() - Method in class com.actelion.research.chem.Element
- toString() - Method in class com.actelion.research.chem.forcefield.mmff.SortedPair
- toString() - Method in class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
- toString() - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Returns a string form of this vector.
- toString() - Method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
- toString() - Method in class com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable.InteractionDescriptor
- toString() - Method in class com.actelion.research.chem.io.pdb.converter.AminoAcidLabeled
- toString() - Method in class com.actelion.research.chem.io.pdb.parser.PDBCoordEntryFile
- toString() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- toString() - Method in class com.actelion.research.chem.mcs.ModelSampleFragments
- toString() - Method in class com.actelion.research.chem.Molecule3D
- toString() - Method in class com.actelion.research.chem.Mutation
- toString() - Method in class com.actelion.research.chem.PeriodicTable
- toString() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- toString() - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- toString() - Method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- toString() - Method in class com.actelion.research.chem.properties.complexity.MultipleNonOverlapSolution
- toString() - Method in class com.actelion.research.chem.properties.complexity.ResultFragmentsStatistic
- toString() - Method in class com.actelion.research.chem.properties.complexity.ResultObjective
- toString() - Method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- toString() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- toString() - Method in class com.actelion.research.chem.SDFileMolecule
- toString() - Method in class com.actelion.research.chem.StructureSearchSpecification
- toString() - Method in class com.actelion.research.chem.SVGDepictor
- toString() - Method in class com.actelion.research.gui.dnd.MoleculeTransferable
- toString() - Method in class com.actelion.research.gui.dnd.ReactionTransferable
- toString() - Method in class com.actelion.research.gui.dnd.SDFileMoleculeTransferable
- toString() - Method in class com.actelion.research.gui.VerticalFlowLayout
-
Description of the Method
- toString() - Method in class com.actelion.research.util.Angle
- toString() - Method in class com.actelion.research.util.CommandLineParser
- toString() - Method in class com.actelion.research.util.datamodel.ByteVec
-
Converts a byte into its decimal.
- toString() - Method in class com.actelion.research.util.datamodel.DoubleArray
- toString() - Method in class com.actelion.research.util.datamodel.IdentifiedObject
- toString() - Method in class com.actelion.research.util.datamodel.IntArray
- toString() - Method in class com.actelion.research.util.datamodel.IntegerDouble
- toString() - Method in class com.actelion.research.util.datamodel.IntVec
- toString() - Method in class com.actelion.research.util.datamodel.ScorePoint
- toString() - Method in class com.actelion.research.util.datamodel.table.TableModelString
- toString() - Method in class com.actelion.research.util.DoubleVec
- toString() - Method in class com.actelion.research.util.ErrorHashMap
- toString() - Method in class com.actelion.research.util.graph.complete.SolutionCompleteGraph
- toString() - Method in class org.openmolecules.chem.conf.gen.TorsionSet
- toString() - Method in class org.openmolecules.chem.conf.so.AxialStereoRule
- toString() - Method in class org.openmolecules.chem.conf.so.ConformationRule
- toString() - Method in class org.openmolecules.chem.conf.so.DistanceRule
- toString() - Method in class org.openmolecules.chem.conf.so.PlaneRule
- toString() - Method in class org.openmolecules.chem.conf.so.StraightLineRule
- toString() - Method in class org.openmolecules.chem.conf.so.TetrahedralStereoRule
- toString() - Method in class org.openmolecules.chem.conf.so.TorsionRule
- toString(boolean[]) - Static method in class com.actelion.research.util.StringFunctions
- toString(byte[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(byte[]) - Static method in class com.actelion.research.util.ArrayUtils
- toString(byte[]) - Static method in class com.actelion.research.util.datamodel.ByteVec
- toString(byte[]) - Static method in class com.actelion.research.util.StringFunctions
- toString(byte[], String) - Static method in class com.actelion.research.util.datamodel.ByteVec
- toString(double) - Static method in class com.actelion.research.util.DoubleFormat
-
Converts a double value into a String representation in scientific format rounded to 5 significant digits, e.g.
- toString(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(double[]) - Static method in class com.actelion.research.util.ArrayUtils
- toString(double[]) - Static method in class com.actelion.research.util.StringFunctions
- toString(double[][]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(double[][], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(double[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(double[], DecimalFormat) - Static method in class com.actelion.research.util.ArrayUtils
- toString(double[], NumberFormat) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(double[], NumberFormat) - Static method in class com.actelion.research.util.StringFunctions
- toString(double, int) - Static method in class com.actelion.research.util.DoubleFormat
-
Converts a double value into a String representation in scientific format rounded to a definable number of digits, e.g.
- toString(double, int, boolean) - Static method in class com.actelion.research.util.DoubleFormat
-
Converts a double value into a String representation in scientific format rounded to a definable number of digits, e.g.
- toString(float[]) - Static method in class com.actelion.research.util.ArrayUtils
- toString(float[], int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(float[], NumberFormat) - Static method in class com.actelion.research.util.StringFunctions
- toString(int) - Method in class com.actelion.research.calc.Matrix
- toString(int) - Method in class com.actelion.research.util.datamodel.ByteVec
- toString(int) - Method in class com.actelion.research.util.datamodel.IntVec
- toString(int) - Method in class com.actelion.research.util.DoubleVec
- toString(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(int[]) - Static method in class com.actelion.research.util.ArrayUtils
- toString(int[][]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(int[][], String) - Static method in class com.actelion.research.util.StringFunctions
- toString(int[], String) - Static method in class com.actelion.research.util.StringFunctions
- toString(int, int, int) - Method in class com.actelion.research.calc.Matrix
- toString(long) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- toString(long, int) - Static method in class com.actelion.research.chem.AtomTypeCalculator
- toString(ResultFragmentsStatistic) - Static method in class com.actelion.research.chem.properties.complexity.ModelExhaustiveStatistics
- toString(Exception) - Static method in class com.actelion.research.util.StringFunctions
- toString(Object[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(Object[]) - Static method in class com.actelion.research.util.ArrayUtils
- toString(String) - Method in class com.actelion.research.util.datamodel.IntArray
- toString(String[], String) - Static method in class com.actelion.research.util.StringFunctions
- toString(Collection<Integer>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toString(Collection<String>, String) - Static method in class com.actelion.research.util.StringFunctions
- toString(List<ModelMedianDouble>) - Static method in class com.actelion.research.calc.statistics.median.ModelMedianDouble
- toString(List<ModelMedianFloat>) - Static method in class com.actelion.research.calc.statistics.median.ModelMedianFloat
- toString(List<Double>, NumberFormat) - Static method in class com.actelion.research.util.StringFunctions
- toString(List<String>) - Static method in class com.actelion.research.util.StringFunctions
- toStringArray() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
-
The array part of the object.
- toStringArray(List<Integer>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringArray(List<String>) - Static method in class com.actelion.research.util.ArrayUtils
- toStringBinary() - Method in class com.actelion.research.calc.Matrix
- toStringBinary() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- toStringBinary() - Method in class com.actelion.research.util.datamodel.IntVec
- toStringBinary(int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringBinary(int) - Static method in class com.actelion.research.util.datamodel.IntVec
- toStringBinary(int) - Static method in class com.actelion.research.util.StringFunctions
- toStringBinary(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringBinary(int, boolean) - Static method in class com.actelion.research.util.datamodel.IntVec
- toStringBinary(long) - Static method in class com.actelion.research.util.StringFunctions
- toStringBinaryDense() - Method in class com.actelion.research.util.datamodel.IntVec
- toStringBytes() - Method in class com.actelion.research.util.datamodel.IntVec
- toStringFileNameCompatible(double) - Static method in class com.actelion.research.util.StringFunctions
- toStringFormatted(int[][]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringFormatted(int[], int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringForValueTable() - Method in class com.actelion.research.chem.Element
- toStringHeader() - Static method in class com.actelion.research.chem.properties.fractaldimension.ResultFracDimCalc
- toStringHex() - Method in class com.actelion.research.util.datamodel.IntVec
- toStringHex(String) - Static method in class com.actelion.research.util.StringFunctions
- toStringHists() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- toStringHistsIndexed() - Method in class com.actelion.research.chem.descriptor.flexophore.DistHist
- toStringInevitable() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- toStringInt(List<Integer>) - Static method in class com.actelion.research.util.StringFunctions
- toStringInt(List<Integer>, String) - Static method in class com.actelion.research.util.StringFunctions
- toStringIntArrays(List<int[]>) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringInteger(List<Integer>, String) - Static method in class com.actelion.research.util.StringFunctions
- toStringIntegerList(List<Integer>, int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
-
Writes a list into a string with line terminators.
- toStringInteractionTypes() - Method in class com.actelion.research.chem.descriptor.flexophore.entity.FlexophorePoint
- toStringLaTex() - Method in class com.actelion.research.util.datamodel.table.TableModelString
-
\begin{table}[] \begin{tabular}{lllllllll} & 0.20 & 0.30 & 0.40 & 0.50 & 0.60 & 0.70 & 0.80 & 0.90 \\ Gaussian process regression & 1.3550 & 1.3059 & 1.3818 & 1.4046 & 1.5150 & 1.4804 & 1.4579 & 1.6223 \\ KNN regression & 1.6776 & 1.7294 & 1.8899 & 2.1573 & 2.3484 & 2.6003 & 2.6931 & 2.8232 \\ Median & 1.6730 & 1.7421 & 1.9217 & 2.3378 & 2.7606 & 3.2241 & 3.6768 & 4.5243 \\ PLS & 1.4264 & 1.2870 & 1.2131 & 1.2989 & 1.3866 & 1.3830 & 1.4414 & 1.1730 \\ PLS Power & 1.4886 & 1.3616 & 1.4954 & 1.7442 & 2.2339 & 2.3904 & 2.1669 & 2.6130 \\ Random Forest regression & 1.6746 & 1.6848 & 1.8421 & 2.0106 & 2.2479 & 2.3896 & 2.5420 & 2.6523 \\ SVM regression & 1.5580 & 1.4634 & 1.5879 & 1.6687 & 1.8423 & 1.9769 & 1.8803 & 1.9618 \end{tabular} \end{table}
- toStringLong() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- toStringLong(List<Long>, String) - Static method in class com.actelion.research.util.StringFunctions
- toStringLongHardPPPoint() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNode
- toStringLongList(List<Long>, int) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringNoBrackets(Collection<Integer>, String) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringNodes() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- toStringNoDigits(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringParameter() - Method in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- toStringParameter() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- toStringParameter() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.PPNodeSimilarity
- toStringPPPoints(int) - Static method in class com.actelion.research.chem.descriptor.flexophore.ConstantsFlexophoreHardPPPoints
- toStringPure(double[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringPure(int[]) - Static method in class com.actelion.research.calc.ArrayUtilsCalc
- toStringRecentSimilarityResults() - Method in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- toStringRow(int, int) - Method in class com.actelion.research.calc.Matrix
- toStringRowNumber(int, String) - Method in class com.actelion.research.calc.Matrix
- toStringShort() - Method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistViz
- toStringShort() - Method in class com.actelion.research.chem.descriptor.flexophore.PPNodeViz
- toStringShortMessage() - Method in class com.actelion.research.util.ErrorHashMap
- toStringSpaceDelimited() - Method in class com.actelion.research.chem.Coordinates
- toStringString() - Method in class com.actelion.research.util.datamodel.ByteVec
-
Converts the bytes into chars.
- toStringTabNL(String[][]) - Static method in class com.actelion.research.util.StringFunctions
-
Elements are separated by tabs and rows are separated by newline.
- toStringValues(IntegerDouble[], NumberFormat) - Static method in class com.actelion.research.util.datamodel.IntegerDouble
- toStringValues(List<IntegerDouble>, NumberFormat) - Static method in class com.actelion.research.util.datamodel.IntegerDouble
- toStringVizInfoEncoded(MolDistHistViz) - Static method in class com.actelion.research.chem.descriptor.flexophore.MolDistHistVizEncoder
-
Encodes the structure information, that it can be written to an DWAR file.
- toStringWithColTags(List<String>, DecimalFormat, String) - Method in class com.actelion.research.calc.Matrix
- toStringWithRowTags(List<String>, DecimalFormat, String) - Method in class com.actelion.research.calc.Matrix
- TOTAL_CAPACITY - Static variable in class com.actelion.research.chem.mcs.ExhaustiveFragmentGeneratorParallizer
- TOTAL_CAPACITY - Static variable in class com.actelion.research.chem.properties.complexity.ExhaustiveFragmentsStatistics
- TOTAL_CAPACITY - Static variable in class com.actelion.research.chem.properties.complexity.MolecularComplexityCalculator
- TOTAL_CAPACITY - Static variable in class com.actelion.research.chem.properties.fractaldimension.FractalDimensionMoleculeMain
- ToxicityPredictor - Class in com.actelion.research.chem.prediction
- ToxicityPredictor() - Constructor for class com.actelion.research.chem.prediction.ToxicityPredictor
- transform(AffineTransform) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- transformMolecule(Molecule, double, double, double) - Static method in class com.actelion.research.chem.ChemistryHelper
- transformMolecules(Molecule[], double, double, double) - Static method in class com.actelion.research.chem.ChemistryHelper
- transformReaction(Reaction, double, double, double) - Static method in class com.actelion.research.chem.ChemistryHelper
- transformX(double) - Method in class com.actelion.research.chem.DepictorTransformation
- transformY(double) - Method in class com.actelion.research.chem.DepictorTransformation
- translate(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
- translate(double, double) - Method in class com.actelion.research.chem.coords.InventorFragment
- translate(double, double) - Method in class com.actelion.research.chem.reaction.ReactionArrow
- translate(double, double) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- translate(double, double, double) - Method in class com.actelion.research.chem.conf.Conformer
-
Translate this conformer's coordinates by adding the dx,dy,dz shifts to all atom coordinates.
- translate(double, double, double) - Method in class com.actelion.research.chem.Molecule
-
Translate this molecule's 3D-coordinates by adding the dx,dy,dz shifts to all atom coordinates.
- translate(int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics
- translate(int, int) - Method in class com.actelion.research.gui.wmf.WMFGraphics2D
- translate(Molecule3D, Coordinates) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator
-
Translate a Molecule
- translate(StereoMolecule, Coordinates) - Static method in class com.actelion.research.chem.io.pdb.converter.GeometryCalculator
-
Translate a Molecule
- translateCoords(double, double) - Method in class com.actelion.research.chem.Molecule
- translateFontName(String) - Method in class com.actelion.research.gui.wmf.MetaFile
- translateFontName(String) - Method in class com.actelion.research.gui.wmf.WMF
- translateInit(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
- translateLigand(Molecule3D, Coordinates) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- translateMol(StereoMolecule, double[]) - Static method in class com.actelion.research.chem.phesa.PheSAAlignment
- translateRef(Coordinates) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- translateTHParity(int, int[]) - Method in class com.actelion.research.chem.StereoMolecule
-
This method translates the parity of a stereo center, if its neighbour atoms are assigned new atom indexes, or are assigned to a matching fragment or molecule with different atom indexes.
- translateToCOM(Coordinates) - Method in class com.actelion.research.chem.phesa.MolecularVolume
- TRANSPARENT - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- TRANSPARENT - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
- transpose(double[][]) - Static method in class com.actelion.research.chem.descriptor.pharmacophoretree.HungarianAlgorithm
- TreeContainer - Class in com.actelion.research.gui.dock
- TreeContainer() - Constructor for class com.actelion.research.gui.dock.TreeContainer
- TreeElement - Class in com.actelion.research.gui.dock
- TreeElement() - Constructor for class com.actelion.research.gui.dock.TreeElement
- TreeFork - Class in com.actelion.research.gui.dock
- TreeFork(TreeLeaf, TreeLeaf, int, double) - Constructor for class com.actelion.research.gui.dock.TreeFork
-
Constructor to create a fork element that is inserted between the specified parent and its former oldLeaf to carry newLeaf at the specified position.
- TreeLeaf - Class in com.actelion.research.gui.dock
- TreeLeaf(Dockable, JDockingPanel, boolean) - Constructor for class com.actelion.research.gui.dock.TreeLeaf
-
Constructor to create a leaf element with a visible component on the screen.
- TreeMatcher - Class in com.actelion.research.chem.descriptor.pharmacophoretree
-
Finds the optimal matching of nodes between two PharmacophoreTrees employing a dynamic programing scheme termed as "match-search" algorithm in the original publication (DOI:10.1023/a:1008068904628).
- TreeMatcher(PharmacophoreTree, PharmacophoreTree) - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher
- TreeMatcher.FeatureMatch - Class in com.actelion.research.chem.descriptor.pharmacophoretree
-
TODO: don't add null-matches!
- TreeMatcher.TreeMatching - Class in com.actelion.research.chem.descriptor.pharmacophoretree
- TreeMatching() - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.TreeMatcher.TreeMatching
- TreeRoot - Class in com.actelion.research.gui.dock
- TreeRoot(JComponent, TreeElement) - Constructor for class com.actelion.research.gui.dock.TreeRoot
-
Constructor to create a root element to which the first leaf should be connected.
- TreeUtils - Class in com.actelion.research.chem.descriptor.pharmacophoretree
- TreeUtils() - Constructor for class com.actelion.research.chem.descriptor.pharmacophoretree.TreeUtils
- treeWalkBFS(int, int, List<Integer>, List<Integer>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTree
-
Walks a subtree of the PharmacophoreTree in breadth-first manner starting from a deleted edge and a designated head node.
- Triangle - Class in com.actelion.research.calc.geometry
-
Triangle Created by korffmo1 on 04.06.17.
- Triangle() - Constructor for class com.actelion.research.calc.geometry.Triangle
- TRUE - com.actelion.research.chem.forcefield.mmff.RingBoolean
- tryAutoMapReaction() - Method in class com.actelion.research.share.gui.editor.Model
- TWO_PI - Variable in class com.actelion.research.util.Angle
- type - Variable in class com.actelion.research.chem.descriptor.DescriptorInfo
- type - Variable in class com.actelion.research.chem.io.DWARFileParser.SpecialField
- TYPE_BACKBONE_NO_STEREO - Static variable in class com.actelion.research.chem.StructureSearchSpecification
- TYPE_BRAVAIS_PEARSON - Static variable in class com.actelion.research.calc.CorrelationCalculator
- TYPE_CODE - Static variable in class com.actelion.research.calc.CorrelationCalculator
- TYPE_EXACT_NO_STEREO - Static variable in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- TYPE_EXACT_NO_STEREO - Static variable in class com.actelion.research.chem.StructureSearchSpecification
- TYPE_EXACT_STRICT - Static variable in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- TYPE_EXACT_STRICT - Static variable in class com.actelion.research.chem.StructureSearchSpecification
- TYPE_HILITE_ATOM_CHANGED - Static variable in class com.actelion.research.gui.DrawAreaEvent
- TYPE_HILITE_BOND_CHANGED - Static variable in class com.actelion.research.gui.DrawAreaEvent
- TYPE_LONG_NAME - Static variable in class com.actelion.research.calc.CorrelationCalculator
- TYPE_MARKUSH - Static variable in class com.actelion.research.chem.ExtendedDepictor
- TYPE_MOLECULE_CHANGED - Static variable in class com.actelion.research.gui.DrawAreaEvent
- TYPE_MOLECULES - Static variable in class com.actelion.research.chem.ExtendedDepictor
- TYPE_NAME - Static variable in class com.actelion.research.calc.CorrelationCalculator
- TYPE_NO_REACTION - Static variable in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- TYPE_NO_STRUCTURE - Static variable in class com.actelion.research.chem.StructureSearchSpecification
- TYPE_NONE - Static variable in class com.actelion.research.calc.CorrelationCalculator
- TYPE_REACTION - Static variable in class com.actelion.research.chem.ExtendedDepictor
- TYPE_RETRON - Static variable in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- TYPE_SELECTION_CHANGED - Static variable in class com.actelion.research.gui.DrawAreaEvent
- TYPE_SIMILARITY - Static variable in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- TYPE_SIMILARITY - Static variable in class com.actelion.research.chem.StructureSearchSpecification
- TYPE_SPEARMAN - Static variable in class com.actelion.research.calc.CorrelationCalculator
- TYPE_STRING - Static variable in class com.actelion.research.chem.reaction.ReactionArrow
- TYPE_STRING - Static variable in class com.actelion.research.chem.TextDrawingObject
- TYPE_SUBREACTION - Static variable in class com.actelion.research.chem.reaction.ReactionSearchSpecification
- TYPE_SUBSTRUCTURE - Static variable in class com.actelion.research.chem.StructureSearchSpecification
- TYPE_TAUTOMER - Static variable in class com.actelion.research.chem.StructureSearchSpecification
- TYPE_TAUTOMER_NO_STEREO - Static variable in class com.actelion.research.chem.StructureSearchSpecification
U
- UndoAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 3/26/13 Time: 4:39 PM
- UndoAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.UndoAction
- undock(String) - Method in class com.actelion.research.gui.dock.JDockingPanel
- undock(String, boolean) - Method in class com.actelion.research.gui.dock.JDockingPanel
- undockAll() - Method in class com.actelion.research.gui.dock.JDockingPanel
- undoStep() - Method in class com.actelion.research.chem.phesaflex.MetropolisMonteCarloHelper
- UniqueFragmentEstimator - Class in com.actelion.research.chem.properties.complexity
- UniqueFragmentEstimator() - Constructor for class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
- UniqueFragmentEstimator(int) - Constructor for class com.actelion.research.chem.properties.complexity.UniqueFragmentEstimator
- UniqueList<T extends java.lang.Comparable<? super T>> - Class in com.actelion.research.util
- UniqueList() - Constructor for class com.actelion.research.util.UniqueList
- UniqueList(Comparator) - Constructor for class com.actelion.research.util.UniqueList
- UniqueStringList - Class in com.actelion.research.chem
- UniqueStringList() - Constructor for class com.actelion.research.chem.UniqueStringList
- unit() - Method in class com.actelion.research.chem.Coordinates
- unitC() - Method in class com.actelion.research.chem.Coordinates
- UNKNOWN - Static variable in class com.actelion.research.share.gui.editor.actions.DrawAction
- UnknownParityAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 3/26/13 Time: 4:33 PM
- UnknownParityAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.UnknownParityAction
- UnparametrizedAtomTypeException - Exception in com.actelion.research.chem.descriptor.flexophore
- UnparametrizedAtomTypeException() - Constructor for exception com.actelion.research.chem.descriptor.flexophore.UnparametrizedAtomTypeException
- UnparametrizedAtomTypeException(String) - Constructor for exception com.actelion.research.chem.descriptor.flexophore.UnparametrizedAtomTypeException
- unsetBit(int) - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- unsetBit(int) - Method in class com.actelion.research.util.datamodel.IntVec
-
Don't forget to set the hash code!
- unsetBit(int[], int) - Static method in class com.actelion.research.util.BitUtils
- UpBondAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 1/28/13 Time: 1:49 PM
- UpBondAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.UpBondAction
- update(boolean) - Method in class com.actelion.research.gui.dock.DockableHeader
- update(Conformer) - Method in class com.actelion.research.chem.phesa.MolecularVolume
- update(StereoMolecule) - Method in class com.actelion.research.chem.phesa.MolecularVolume
- update(Graphics) - Method in class com.actelion.research.gui.JDrawToolbar
- UPDATE_CHECK_COORDS - Static variable in class com.actelion.research.gui.JDrawArea
- UPDATE_CHECK_VIEW - Static variable in class com.actelion.research.gui.JDrawArea
- UPDATE_INVENT_COORDS - Static variable in class com.actelion.research.gui.JDrawArea
- UPDATE_NONE - Static variable in class com.actelion.research.gui.JDrawArea
- UPDATE_REDRAW - Static variable in class com.actelion.research.gui.JDrawArea
- UPDATE_SCALE_COORDS - Static variable in class com.actelion.research.gui.JDrawArea
- UPDATE_SCALE_COORDS_USE_FRAGMENTS - Static variable in class com.actelion.research.gui.JDrawArea
- updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.MolecularVolume
- updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
- updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
- updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
- updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
- updateAtomIndeces(int[]) - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
- updateAtomIndeces(int[]) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
- updateChildElement(Component, TreeElement) - Method in class com.actelion.research.gui.dock.TreeContainer
- updateChildElement(Component, TreeElement) - Method in class com.actelion.research.gui.dock.TreeFork
- updateChildElement(Component, TreeElement) - Method in class com.actelion.research.gui.dock.TreeRoot
- updateCOM() - Method in class com.actelion.research.chem.phesa.MolecularVolume
- updateCoordinates(Conformer) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- updateCoordinates(Conformer) - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
- updateCoordinates(Conformer) - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
- updateCoordinates(Conformer) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- updateCoordinates(Conformer) - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
- updateCoordinates(Conformer) - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
- updateCoordinates(Conformer) - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
- updateCoordinates(Conformer) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
- updateCoordinates(Conformer) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- updateCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.phesa.Gaussian3D
- updateCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint
- updateCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.phesa.pharmacophore.AromRingPoint
- updateCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.phesa.pharmacophore.ChargePoint
- updateCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.phesa.pharmacophore.DonorPoint
- updateCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.phesa.pharmacophore.ExitVectorPoint
- updateCoordinates(StereoMolecule) - Method in interface com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint
- updateCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.phesa.pharmacophore.PPGaussian
- updateCoordinates(StereoMolecule) - Method in class com.actelion.research.chem.phesa.VolumeGaussian
- updateCoords(IDrawContext<T>, Rectangle2D.Double, int) - Method in interface com.actelion.research.share.gui.editor.chem.IDepictor
- updateCoords(Graphics, Rectangle2D.Double, int) - Method in class com.actelion.research.chem.AbstractDepictor
-
Returns full transformation that moves/scales original molecule into viewRect.
- updateCoords(Object, Rectangle2D.Double, int) - Method in class com.actelion.research.chem.ExtendedDepictor
- updateCoords(T, Rectangle2D.Double, int) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- updateGradient() - Method in interface com.actelion.research.chem.forcefield.ForceField
-
updates the gradient of the ForceField and returns the gradient scale
- updateGradient() - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
-
Minimise the current molecule using default parameter values for the number of iterations, energy tolerance and gradient tolerance.
- updateGrid(StereoMolecule) - Method in class com.actelion.research.chem.io.pdb.converter.MoleculeGrid
- updateProgress(int) - Method in class com.actelion.research.calc.DataProcessor
- updateProgress(int) - Method in interface com.actelion.research.calc.ProgressListener
- updateProgress(int, String) - Method in interface com.actelion.research.calc.ProgressListener
- updateRenderer(JComponent, String) - Static method in class com.actelion.research.gui.hidpi.ScaledHTML
- updateState() - Method in class com.actelion.research.chem.docking.LigandPose
- updateState() - Method in class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
- updateState() - Method in class com.actelion.research.chem.docking.scoring.ChemPLP
- updateState() - Method in class com.actelion.research.chem.docking.scoring.IdoScore
- updateUI() - Method in class com.actelion.research.gui.dock.Dockable
-
Updates the UI.
- updateUI() - Method in class com.actelion.research.gui.dock.DockableHeader
- updateUI() - Method in class com.actelion.research.gui.hidpi.HiDPIIconButton
- updateUI() - Method in class com.actelion.research.gui.hidpi.HiDPIToggleButton
- updateWeights(Map<Integer, List<Integer>>) - Method in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- upperQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianDouble
- upperQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianFloat
- upperQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianInteger
- upperQuartile - Variable in class com.actelion.research.calc.statistics.median.ModelMedianLong
- usedMemory() - Static method in class com.actelion.research.util.SizeOf
- usedMemoryMB() - Static method in class com.actelion.research.util.SizeOf
V
- v1 - Variable in class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
- v1 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- v2 - Variable in class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
- v2 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- v3 - Variable in class com.actelion.research.chem.forcefield.mmff.table.Torsion.Kb
- v3 - Variable in class com.actelion.research.chem.forcefield.mmff.TorsionAngle
- val(int) - Method in class com.actelion.research.chem.forcefield.mmff.table.Atom
-
Returns the VAL type of an atom given its MMFF type.
- valid(Tables, MMFFMolecule, int, int, int) - Static method in class com.actelion.research.chem.forcefield.mmff.StretchBend
-
Checks if a Stretch Bend is valid
- validate() - Method in class com.actelion.research.chem.ExtendedMolecule
- validate() - Method in class com.actelion.research.chem.MarkushStructure
-
Check the validity of a defined Markush structure.
- validate() - Method in class com.actelion.research.chem.reaction.ReactionSearchSpecification
-
Checks, whether this specification is correctly defining a search.
- validate() - Method in class com.actelion.research.chem.StereoMolecule
- validate() - Method in class com.actelion.research.chem.StructureSearchSpecification
-
Checks, whether this specification is correctly defining a search.
- validateBondType(int, int) - Method in class com.actelion.research.chem.ExtendedMolecule
- validateBondType(int, int) - Method in class com.actelion.research.chem.Molecule
- validateMapping() - Method in class com.actelion.research.chem.reaction.Reaction
-
Removes mapping numbers that are only used on one side of the reaction.
- validateMemberIndex(int, int) - Method in class com.actelion.research.chem.RingCollection
-
Adds or subtracts the ring size from index to move it into the valid range from 0 to ringSize-1.
- validateView(Object, Rectangle2D.Double, int) - Method in class com.actelion.research.chem.AbstractDepictor
-
A depictor maintains a DepictorTransformation object, which defines translation and scaling of molecule coordinates into the viewRect.
- validateView(Object, Rectangle2D.Double, int) - Method in class com.actelion.research.chem.ExtendedDepictor
- validateView(T, Rectangle2D.Double, int) - Method in class com.actelion.research.share.gui.editor.chem.AbstractExtendedDepictor
- VALIDATION_ERROR_AMBIGUOUS_CONFIGURATION - Static variable in class com.actelion.research.chem.StereoMolecule
- VALIDATION_ERROR_ESR_CENTER_UNKNOWN - Static variable in class com.actelion.research.chem.StereoMolecule
- VALIDATION_ERROR_OVER_UNDER_SPECIFIED - Static variable in class com.actelion.research.chem.StereoMolecule
- VALIDATION_ERRORS_STEREO - Static variable in class com.actelion.research.chem.StereoMolecule
- value(double) - Method in class com.actelion.research.util.FastSpline.Polynome
- value(double) - Method in class com.actelion.research.util.FastSpline
-
Compute the value for the function.
- valueInvalidated() - Method in interface com.actelion.research.share.gui.editor.listeners.IValidationListener
- valueInvalidated() - Method in class com.actelion.research.share.gui.editor.Model
- valueOf(String) - Static method in enum com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.docking.DockingEngine.ScoringFunction
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.docking.DockingEngine.StartPosition
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.forcefield.mmff.RingBoolean
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.forcefield.mmff.Separation.Relation
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomFlagCount
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyShift
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.io.pdb.converter.AminoAcidsLabeledContainer
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint.Functionality
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.chem.phesa.PheSAAlignment.axis
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.share.gui.DialogResult
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum com.actelion.research.util.Formatter.LocaleFormat
-
Returns the enum constant of this type with the specified name.
- valueProperty() - Method in class com.actelion.research.jfx.gui.chem.MoleculeView
- valueProperty() - Method in class com.actelion.research.jfx.gui.chem.MoleculeViewSkin
- values() - Static method in enum com.actelion.research.chem.CanonizerUtil.IDCODE_TYPE
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.docking.DockingEngine.ScoringFunction
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.docking.DockingEngine.StartPosition
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.forcefield.mmff.RingBoolean
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.forcefield.mmff.Separation.Relation
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomFlagCount
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyMask
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.AtomPropertyShift
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator.FunctionalGroup
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.io.pdb.converter.AminoAcidsLabeledContainer
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint.Functionality
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.chem.phesa.PheSAAlignment.axis
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.share.gui.DialogResult
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum com.actelion.research.util.Formatter.LocaleFormat
-
Returns an array containing the constants of this enum type, in the order they are declared.
- VanDerWaals - Class in com.actelion.research.chem.forcefield.mmff.table
- VanDerWaals - Class in com.actelion.research.chem.forcefield.mmff
-
Nonbonded van der Waals energy term class.
- VanDerWaals(Tables, MMFFMolecule, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.VanDerWaals
-
Construct a new van der Waals energy term.
- VanDerWaals(Tables, String) - Constructor for class com.actelion.research.chem.forcefield.mmff.table.VanDerWaals
- VARIABLE_PITCH - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- VDW_RADIUS - Static variable in interface com.actelion.research.chem.conf.VDWRadii
-
VDW Radii indexed by atomic numbers, taken from DOI: 10.1039/c3dt50599e Santiago Alvarez: A cartography of the van der Waals territories Published on 01 May 2013 on http://pubs.rsc.org | doi:10.1039/C3DT50599E (in a few cases no value was given (marked ??), where we use estimated values)
- VDW_TOLERANCE_HYDROGEN - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- VDW_TOLERANCE_OTHER - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- VDWRadii - Interface in com.actelion.research.chem.conf
- vdws - Variable in class com.actelion.research.chem.forcefield.mmff.Tables
- Vector3 - Class in com.actelion.research.chem.forcefield.mmff
-
The Vector3 class provides common vector operations used throughout the MMFF codebase.
- Vector3() - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
-
Constructs a new vector with default coordinates.
- Vector3(double[], int) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
-
Constructs a new vector from three consecutive doubles in a positions array.
- Vector3(double[], int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
-
Constructs a new vector starting at atom1 position and ending at atom2 position.
- Vector3(double, double, double) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
-
Constructs a new vector with given x, y and z coordinates.
- Vector3(ExtendedMolecule, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
-
Constructs a new vector from the x, y, z coordinates of an atom in a molecule.
- Vector3(ExtendedMolecule, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
-
Constructs a vector that represents the line travelling from the position of atom1 to the position of atom2.
- Vector3(MMFFMolecule, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
-
Constructs a new vector from the x, y, z coordinates of an atom in a molecule.
- Vector3(MMFFMolecule, int, int) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
-
Constructs a vector that represents the line travelling from the position of atom1 to the position of atom2.
- Vector3(Vector3) - Constructor for class com.actelion.research.chem.forcefield.mmff.Vector3
-
Copy constructor, copies the x,y,z coordinates from another vector.
- VectorSimilarity - Class in com.actelion.research.calc
- VectorSimilarity() - Constructor for class com.actelion.research.calc.VectorSimilarity
- VERBOSE - Static variable in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- VERBOSE - Static variable in class com.actelion.research.chem.descriptor.flexophore.MolDistHist
- VERBOSE - Static variable in class com.actelion.research.chem.properties.complexity.ObjectiveExhaustiveStatistics
- version - Variable in class com.actelion.research.chem.descriptor.DescriptorInfo
- version - Variable in class com.actelion.research.chem.io.DWARFileParser.SpecialField
- VERSION - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFFP512
- VERSION - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512
- VERSION - Static variable in class com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered
- VERSION_INTERACTION_TABLES - Static variable in class com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
- VerticalFlowLayout - Class in com.actelion.research.gui
-
A vertical flow layout is similar to a flow layuot but it layouts the components vertically instead of horizontally.
- VerticalFlowLayout() - Constructor for class com.actelion.research.gui.VerticalFlowLayout
-
Constructor for the VerticalFlowLayout object
- VerticalFlowLayout(int, int) - Constructor for class com.actelion.research.gui.VerticalFlowLayout
-
Constructor for the VerticalFlowLayout object
- VerticalFlowLayout(int, int, int, int, boolean) - Constructor for class com.actelion.research.gui.VerticalFlowLayout
-
Constructor for the VerticalFlowLayout object
- vibrateLigand(Molecule3D, double) - Static method in class com.actelion.research.chem.descriptor.flexophore.calculator.StructureCalculator
- ViolatedConditionsCount() - Constructor for class com.actelion.research.chem.descriptor.flexophore.generator.SubFlexophoreGenerator.ViolatedConditionsCount
- visibilityChanged(Dockable, boolean) - Method in class com.actelion.research.gui.dock.JDockingPanel
-
This is called when a Dockable's visibility changes, i.e.
- when a new Dockable is docked
- when a new Dockable is undocked
- when the user drags & docks a Dockable
- when the user actively switches tabs in a tabbed pane
It may be overridden in order to react on a visibility change due to the user selecting a different tab of dragging & docking a Dockable. - volume - Variable in class com.actelion.research.chem.phesa.Gaussian3D
- VolumeGaussian - Class in com.actelion.research.chem.phesa
- VolumeGaussian(int, int, Coordinates, Coordinates, int) - Constructor for class com.actelion.research.chem.phesa.VolumeGaussian
- VolumeGaussian(VolumeGaussian) - Constructor for class com.actelion.research.chem.phesa.VolumeGaussian
W
- weakCompareAndSet(float, float) - Method in class com.actelion.research.util.concurrent.AtomicFloat
- weight - Variable in class com.actelion.research.chem.phesa.Gaussian3D
- well_depth - Variable in class com.actelion.research.chem.forcefield.mmff.VanDerWaals
- wereAllDataFetched() - Method in interface com.actelion.research.util.IPipeline
-
Has to be true when all data were fetched.
- wereAllDataFetched() - Method in class com.actelion.research.util.Pipeline
-
Returns true if all data in was set and the queue is empty.
- WHITE - Static variable in interface com.actelion.research.share.gui.editor.geom.IColor
- WHITENESS - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- WINDING - Static variable in interface com.actelion.research.gui.wmf.WMFConstants
- WMF - Class in com.actelion.research.gui.wmf
- WMF() - Constructor for class com.actelion.research.gui.wmf.WMF
- WMFConstants - Interface in com.actelion.research.gui.wmf
- WMFGraphics - Class in com.actelion.research.gui.wmf
- WMFGraphics(MetaFile, int, int, Color, Color) - Constructor for class com.actelion.research.gui.wmf.WMFGraphics
- WMFGraphics2D - Class in com.actelion.research.gui.wmf
- WMFGraphics2D(WMF, int, int, Color, Color) - Constructor for class com.actelion.research.gui.wmf.WMFGraphics2D
- write(byte[]) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- write(byte[], int, int) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- write(double[], int) - Method in class com.actelion.research.chem.forcefield.mmff.Vector3
-
Writes the contents of this vector to the specified positions in a positions array.
- write(int) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPAtomCharge
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPAtomCIP
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPAtomEnhGroup
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPAtomEnhStereoType
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPAtomIsotope
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPAtomRadical
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondAttach
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondDisplay
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPBondType
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPElement
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPPoint2D
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPProducts
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPReactants
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPShowAtomStereo
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPShowBondStereo
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPShowEnhAtomStereo
- write(DataOutput) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX.CDPText
- write(DataOutput, ChemDrawCDX.CDXNode) - Method in class com.actelion.research.gui.clipboard.external.ChemDrawCDX
- write(File) - Method in class com.actelion.research.calc.Matrix
- write(File, boolean, int) - Method in class com.actelion.research.calc.Matrix
- write(File, double[]) - Static method in class com.actelion.research.util.IO
- write(File, int[]) - Static method in class com.actelion.research.util.IO
- write(File, String) - Method in class com.actelion.research.util.datamodel.table.TableModelString
- write(File, String) - Static method in class com.actelion.research.util.IO
- write(File, String, boolean) - Static method in class com.actelion.research.util.IO
- write(File, DecimalFormat, boolean) - Method in class com.actelion.research.calc.Matrix
- write(File, List<String>) - Static method in class com.actelion.research.util.IO
-
Writes each string in a separate line
- write(OutputStream) - Method in class com.actelion.research.calc.Matrix
- write(OutputStream, NumberFormat) - Method in class com.actelion.research.calc.Matrix
- write(String) - Method in class com.actelion.research.calc.Matrix
- write(String) - Method in class com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics
- write(String, boolean) - Method in class com.actelion.research.calc.Matrix
- write(String, boolean, int) - Method in class com.actelion.research.calc.Matrix
- write(String, boolean, int, int) - Method in class com.actelion.research.calc.Matrix
- write(String, String) - Static method in class com.actelion.research.util.IO
- write(String, String, boolean) - Static method in class com.actelion.research.util.IO
- WRITE_DW_FILE - Static variable in class org.openmolecules.chem.conf.so.ConformationSelfOrganizer
- WRITE_DW_FRAGMENT_FILE - Static variable in class org.openmolecules.chem.conf.gen.ConformerGenerator
- write2Channel(FileChannel, String) - Method in class com.actelion.research.util.IO
- write2String() - Method in class com.actelion.research.chem.mcs.ListWithIntVec
- write2String() - Method in class com.actelion.research.chem.properties.complexity.BitArray128
- write2String() - Method in class com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode
- write2String() - Method in interface com.actelion.research.chem.properties.complexity.IBitArray
- write2String() - Method in class com.actelion.research.chem.properties.complexity.ListWithIntVecIdCode
- write2String() - Method in class com.actelion.research.util.datamodel.IntArray
- write2String() - Method in class com.actelion.research.util.datamodel.IntVec
- writeAsLineBase64Encoded() - Method in class com.actelion.research.calc.Matrix
- writeBitmap(int[], int, int) - Method in class com.actelion.research.gui.wmf.WMF
- writeBitStringDense(File, List<IntVec>) - Static method in class com.actelion.research.util.datamodel.IntVec
- writeBoolean(boolean) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeByte(int) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeBytes(String) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeChar(int) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeChars(String) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeColor(Color) - Method in class com.actelion.research.gui.wmf.WMF
- writeContent(StereoMolecule) - Static method in class com.actelion.research.jfx.gui.misc.ClipboardHelper
- writeContent(StereoMolecule, ClipboardContent) - Static method in class com.actelion.research.jfx.gui.misc.ClipboardHelper
- writeCTAB(StereoMolecule, double) - Static method in class com.actelion.research.chem.MolfileV3Creator
- writeCurrentRow() - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Call this once per row after setting individual cell content with the respective setRowXXXX() methods.
- writeDouble(double) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeEnd() - Method in class com.actelion.research.chem.io.DWARFileCreator
- writeFloat(float) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeHeader(int) - Method in class com.actelion.research.chem.io.DWARFileCreator
-
Call this after defining columns and specifying column properties
- writeHistogram(String, Matrix, boolean, int, int) - Static method in class com.actelion.research.calc.histogram.MatrixBasedHistogram
- writeInt(int) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeInteger(int) - Method in class com.actelion.research.gui.wmf.WMF
- writeIntegerList(File, List<Integer>) - Static method in class com.actelion.research.util.IO
- writeL(Writer, String, int) - Static method in class com.actelion.research.chem.io.AbstractParser
- writeLong(long) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeMolfile(Writer) - Method in class com.actelion.research.chem.MolfileCreator
- writeMolfile(Writer) - Method in class com.actelion.research.chem.MolfileV3Creator
- writeMolSketchFile(Molecule, OutputStream) - Static method in class com.actelion.research.util.Sketch
- writeMolSketchFile(Molecule, String) - Static method in class com.actelion.research.util.Sketch
- writeR(Writer, String, int) - Static method in class com.actelion.research.chem.io.AbstractParser
- writeReactionSketchFile(Reaction, OutputStream) - Static method in class com.actelion.research.util.Sketch
- writeReactionSketchFile(Reaction, String) - Static method in class com.actelion.research.util.Sketch
- writeRecordHeader(int, int) - Method in class com.actelion.research.gui.wmf.WMF
- writeRXNfile(Writer) - Method in class com.actelion.research.chem.io.RXNFileCreator
- writeRXNfile(Writer) - Method in class com.actelion.research.chem.io.RXNFileV3Creator
- writeSerialized(File) - Method in class com.actelion.research.calc.Matrix
- writeShort(int) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeTabDelimitedTable(String) - Method in class org.openmolecules.chem.conf.gen.RigidFragmentCache
-
Writes a TAB delimited text file that can be opened for debug or other purposes by DataWarrior containing idcode, idcoords, multiple conformer likelihoods
- writeTextFile(String, int) - Method in class com.actelion.research.chem.AtomTypeList
-
Writes this AtomTypeList into a TAB-delimited text file in human readable form.
- writeTypeFile(String) - Method in class com.actelion.research.chem.AtomTypeList
- writeUTF(String) - Method in class com.actelion.research.util.LittleEndianDataOutputStream
- writeWMF(OutputStream) - Method in class com.actelion.research.gui.wmf.WMF
- writeWord(int) - Method in class com.actelion.research.gui.wmf.WMF
X
- x - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorDot
- x - Variable in class com.actelion.research.chem.Coordinates
- x - Variable in class com.actelion.research.chem.forcefield.mmff.Vector3
- x - Variable in class com.actelion.research.util.datamodel.PointDouble
- X - com.actelion.research.chem.phesa.PheSAAlignment.axis
- x1 - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorLine
- x2 - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorLine
Y
- y - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorDot
- y - Variable in class com.actelion.research.chem.Coordinates
- y - Variable in class com.actelion.research.chem.forcefield.mmff.Vector3
- y - Variable in class com.actelion.research.util.datamodel.PointDouble
- Y - com.actelion.research.chem.phesa.PheSAAlignment.axis
- y1 - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorLine
- y2 - Variable in class com.actelion.research.chem.AbstractDepictor.DepictorLine
Z
- z - Variable in class com.actelion.research.chem.Coordinates
- z - Variable in class com.actelion.research.chem.forcefield.mmff.Vector3
- Z - com.actelion.research.chem.phesa.PheSAAlignment.axis
- ZERO_NODE - Static variable in class com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreNode
- zeroGradient() - Method in class com.actelion.research.chem.forcefield.AbstractForceField
- zeroGradient() - Method in interface com.actelion.research.chem.forcefield.ForceField
-
zeroes out gradient for fixed atoms
- zeroGradient() - Method in class com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94
- zoomAndRotate(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
- zoomAndRotate(double, double) - Method in class com.actelion.research.chem.TextDrawingObject
- zoomAndRotate(double, double, boolean) - Method in class com.actelion.research.chem.Molecule
- zoomAndRotateInit(double, double) - Method in class com.actelion.research.chem.AbstractDrawingObject
- zoomAndRotateInit(double, double) - Method in class com.actelion.research.chem.Molecule
- zoomAndRotateInit(double, double) - Method in class com.actelion.research.chem.TextDrawingObject
- ZoomRotateAction - Class in com.actelion.research.share.gui.editor.actions
-
Project: User: rufenec Date: 4/28/2014 Time: 12:39 PM
- ZoomRotateAction(Model) - Constructor for class com.actelion.research.share.gui.editor.actions.ZoomRotateAction
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