All Classes Interface Summary Class Summary Enum Summary Exception Summary
| Class |
Description |
| AbstractDepictor |
|
| AbstractDepictor.DepictorDot |
|
| AbstractDepictor.DepictorLine |
|
| AbstractDescriptorHandlerFP<U> |
|
| AbstractDescriptorHandlerLongFP<U> |
|
| AbstractDrawingObject |
|
| AbstractExtendedDepictor<T,C> |
|
| AbstractForceField |
|
| AbstractParser |
A parser is used to load and save molecules from the filesystem.
|
| AbstractScoringEngine |
|
| AcceptorPoint |
|
| Action |
Basic Interface for all editor actions
|
| AddRingAction |
Project:
User: rufenec
Date: 2/1/13
Time: 4:03 PM
|
| AMemorizedObject |
AMemorizedObject
|
| AminoAcidLabeled |
AminoAcidLabeled
|
| AminoAcidsLabeledContainer |
AminoAcidsLabeledContainer
The txt file was generated with com.actelion.research.chem.parsers.pdb.ProcessLabeledAminoAcids
|
| Angle |
Angle table, corresponds to the MMFFANG.PAR parameters table provided in
the MMFF literature.
|
| Angle |
The angle type class provides static functions for getting angle and
stretch bend MMFF type.
|
| Angle |
This class provides various operations on angles,
while making sure that the values is always in the rangle
from -pi >= v > pi.
|
| AngleBend |
Angle bending energy term class.
|
| AngleConstraint |
|
| AromaticityResolver |
|
| AromRingPoint |
|
| ArrayUtils |
|
| ArrayUtilsCalc |
|
| Arrow |
|
| ArrowAction |
Project:
User: rufenec
Date: 5/16/13
Time: 3:46 PM
|
| Atom |
Atom table, corresponds to the MMFFPROP.PAR parameters table provided
in the MMFF literature.
|
| Atom |
The Atom type class provides static functions to perform atom typing on
atoms in a Molecule.
|
| AtomAssembler |
|
| AtomComparator |
|
| AtomFunctionAnalyzer |
|
| AtomHighlightAction |
Project:
User: rufenec
Date: 2/1/13
Time: 4:13 PM
|
| AtomicFloat |
|
| AtomicGaussian |
|
| AtomIndexLinkerId |
AtomIndexLinkerId
|
| AtomMapAction |
Project:
User: rufenec
Date: 5/22/13
Time: 4:00 PM
|
| AtomRecord |
ModelAtom
|
| AtomTypeCalculator |
|
| AtomTypeList |
|
| AtomTypeMap |
|
| AutoMapper |
Project:
User: rufenec
Date: 6/17/2014
Time: 10:04 AM
|
| AxialStereoRule |
Handles attropisomery as well as chiral allenes
|
| BadAtomTypeException |
The BadAtomTypeException is thrown when there is a bad atom type in a
molecule.
|
| BadRingAromException |
The BadRingAromException is thrown when there is a problem with the MMFF
ring aromaticity assignment.
|
| BinaryDecoder |
|
| BitArray128 |
|
| BitArray128Factory |
|
| BitUtils |
|
| Bndk |
Bndk table, corresponds to the MMFFBNDK.PAR parameters table provided
in the MMFF literature.
|
| BOMSkipper |
|
| Bond |
Bond table, corresponds to the MMFFBOND.PAR parameters table provided
in the MMFF literature.
|
| Bond |
The bond type class provides static functions for getting the MMFF bond
type (either by bond or by the atoms of a bond).
|
| BondAngleSet |
|
| BondBaseAction |
Project:
User: rufenec
Date: 1/28/13
Time: 1:07 PM
|
| BondConstraint |
|
| BondHighlightAction |
Project:
User: rufenec
Date: 1/28/13
Time: 1:07 PM
|
| BondLengthSet |
|
| BondRotationHelper |
|
| BondsCalculator |
BondsCalculator is used to recreate the bonds and / or calculate the bonds orders
based on the 3D coordinates of the atoms
|
| BondStretch |
Bond stretching energy term class.
|
| BondVector2IdCode |
|
| BurtleHasher |
http://burtleburtle.net/bob/c/lookup3.c
-------------------------------------------------------------------------------
lookup3.c, by Bob Jenkins, May 2006, Public Domain.
|
| BurtleHasherABC |
|
| ByteArray |
|
| ByteArrayComparator |
|
| ByteVec |
ByteVec:
|
| Canonizer |
|
| CanonizerBaseValue |
|
| CanonizerMesoHelper |
|
| CanonizerUtil |
|
| CanonizerUtil.IDCODE_TYPE |
|
| CanonizerUtil.StrongHasher |
64 bit hash, derived from numerical recipes
Will move this class later to dd_core.
|
| CDXConstants |
|
| ChangeAtomAction |
Project:
User: rufenec
Date: 2/1/13
Time: 4:13 PM
|
| ChangeAtomPropertiesAction |
Project:
User: rufenec
Date: 2/1/13
Time: 4:13 PM
|
| ChangeChargeAction |
Project:
User: rufenec
Date: 2/1/13
Time: 4:13 PM
|
| Charge |
|
| Charge |
The charge class provides static functions for calculating formal and
partial charges on a molecule.
|
| ChargePoint |
|
| ChemDrawCDX |
|
| ChemistryDataFormats |
|
| ChemistryFlavors |
|
| ChemistryHelper |
|
| ChemPLP |
Implementation of ChemPLP scoring function as described in: doi: 10.1021/ci800298z
THIS SCORING FUNCTION REQUIRES EXPLICIT HYDROGENS TO BE PRESENT!
|
| ClassificationData |
|
| CleanAction |
Project:
User: rufenec
Date: 1/28/13
Time: 10:09 AM
|
| ClearAction |
Project:
User: rufenec
Date: 1/24/13
Time: 5:09 PM
|
| ClipboardHandler |
Title: Actelion Library
|
| ClipboardHelper |
Created by baerr on 7/28/14.
|
| CLogPPredictor |
|
| ClusterNode |
|
| ColorHelper |
|
| ColorUtils |
Defines a color with some utility methods.
|
| CombinationGenerator |
CombinationGenerator
|
| CommandAction |
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
|
| CommandLineParser |
CommandLineParser
Simple command line parser.
|
| CommonSubGraphHelper |
|
| CompleteGraphMatcher<T extends ICompleteGraph> |
CompleteGraphMatcher
|
| CompoundCollectionListener |
|
| CompoundCollectionModel<T> |
|
| CompoundCollectionPane<T> |
|
| CompoundFileFilter |
A convenience implementation of FileFilter that filters out
all files except for those type extensions that it knows about.
|
| CompoundFileHelper |
|
| CompoundFileParser |
|
| CompoundTableConstants |
|
| ConformationRule |
|
| ConformationSelfOrganizer |
|
| Conformer |
|
| ConformerGenerator |
This class generates 3D-conformers of a given molecule using the following strategy:
All rotatable, non-ring bonds are determined.
|
| ConformerSet |
|
| ConformerSetGenerator |
|
| Constants |
The Constants class holds numerical constants that are reused in
multiple classes.
|
| ConstantsAminoAcidsLabeled |
ConstantsAminoAcidsLabeled
|
| ConstantsDWAR |
ConstantsDWAR
|
| ConstantsFlexophore |
|
| ConstantsFlexophoreGenerator |
|
| ConstantsFlexophoreHardPPPoints |
|
| ConstantsHistogram |
ConstantsHistogram
|
| ContainerBitArray |
|
| ContainerFragBondsSolutions |
|
| ContainerListWithIntVec |
|
| ContainerMemory<S extends AMemorizedObject> |
ContainerMemory
|
| CoordinateInventor |
|
| Coordinates |
Class to encapsulate 3D coordinates
|
| CopyAction |
Project:
User: rufenec
Date: 5/16/13
Time: 3:31 PM
|
| CorrelationCalculator |
|
| CovRad |
CovRad table, used in the bond stretch empirical calculations of 'kb'
and 'r0'.
|
| CreatorMolDistHistViz |
CreatorMolDistHistViz
|
| Csv |
Basic CSV parser.
|
| CursorHelper |
|
| CutAction |
Project:
User: rufenec
Date: 5/16/13
Time: 3:43 PM
|
| DataProcessor |
|
| DateAnalysis |
|
| Def |
Equivalence table, corresponds to MMFFDEF.PAR parameters table provided
in the MMFF literature.
|
| DefaultCompoundCollectionModel<T> |
|
| DefaultCompoundCollectionModel.IDCode |
This version of the DefaultCompoundCollectionModel collects
molecules as IDCodes.
|
| DefaultCompoundCollectionModel.IDCodeWithName |
This version of the DefaultCompoundCollectionModel collects
molecules as String[2] with idcodes & idcoords (index 0) and molecule name (index 1).
|
| DefaultCompoundCollectionModel.Molecule |
This version of the DefaultCompoundCollectionModel collects molecules as StereoMolecules.
|
| DefaultCompoundCollectionModel.Native |
This version of the DefaultCompoundCollectionModel collects
IDCodes and StereoMolecules without conversion into their native type.
|
| Delegator<T> |
|
| DeleteAction |
Project:
User: rufenec
Date: 3/26/13
Time: 4:15 PM
|
| Depictor |
|
| Depictor2D |
|
| DepictorTransformation |
|
| DescriptorConstants |
|
| DescriptorEncoder |
DescriptorEncoder encodes int[] based descriptors
into byte arrays that may be used to instantiate Strings
|
| DescriptorHandler<T,U> |
DescriptorHandler is the base Interface for any molecular descriptor
handling StereoMolecules or Reactions
|
| DescriptorHandlerFactory |
|
| DescriptorHandlerFFP512 |
|
| DescriptorHandlerFlexophore |
DescriptorHandlerFlexophore
|
| DescriptorHandlerFunctionalGroups |
|
| DescriptorHandlerHashedCFp |
|
| DescriptorHandlerHashedPharmSphere |
|
| DescriptorHandlerLongCFP |
|
| DescriptorHandlerLongFFP512 |
|
| DescriptorHandlerLongPFP512 |
|
| DescriptorHandlerPFP512 |
|
| DescriptorHandlerPharmPath |
|
| DescriptorHandlerPTree |
|
| DescriptorHandlerReactionFP |
|
| DescriptorHandlerShape |
|
| DescriptorHandlerShapeOneConf |
|
| DescriptorHandlerSkeletonSpheres |
|
| DescriptorHandlerStandard2DFactory |
|
| DescriptorHandlerStandardFactory |
|
| DescriptorHelper |
|
| DescriptorInfo |
|
| Dfsb |
|
| DialogResult |
Return values from Dialog calls
|
| DiastereoIDTest |
|
| DiastereotopicAtomID |
|
| DistanceRule |
|
| DistHist |
|
| DistHistEncoder |
|
| DistHistHelper |
DistHistHelper
|
| DistHistHelper.RangeStatistics |
|
| DiversitySelector |
|
| Dockable |
A lightweight component derived from JPanel that features certain subcomponents
that make it look similar to a frame or internal frame.
|
| DockableHeader |
|
| DockingEngine |
|
| DockingEngine.DockingResult |
|
| DockingEngine.ScoringFunction |
|
| DockingEngine.StartPosition |
|
| DockingFailedException |
|
| DockingUtils |
|
| DonorPoint |
|
| DoubleArray |
DoubleArray
26 Jun 2010 MvK: Start implementation
|
| DoubleFormat |
|
| DoubleVec |
|
| DownBondAction |
Project:
User: rufenec
Date: 1/28/13
Time: 1:51 PM
|
| DragGlassPane |
Project:
User: rufenec
Date: 2/21/14
Time: 6:14 PM
|
| DrawAction |
Basic class which handles all actions which interact with the drawing surface
|
| DrawAreaEvent |
|
| DrawAreaListener |
|
| DrawConfig |
User: rufenec
Creation Date: 8/24/2016
|
| DrawingObject |
Project:
User: rufenec
Date: 5/16/13
Time: 12:31 PM
|
| DrawingObjectFactory |
|
| DrawingObjectList |
|
| DruglikenessPredictor |
|
| DrugScoreCalculator |
Created by rufenec on 26/10/15.
|
| DWARFileCreator |
|
| DWARFileParser |
|
| Electrostatic |
Nonbonded electrostatic energy term class.
|
| Element |
|
| EmpiricalLigandStrain |
|
| EncodeFunctions |
February 2018
Author: J.
|
| EncoderFloatingPointNumbers |
|
| EncoderIntegerNumbers |
Encodes integer numbers into a string.
|
| EnergyTerm |
Interface class for energy terms.
|
| ErrorHashMap |
ErrorHashMap
2005 MvK: Start implementation
|
| Evaluable |
|
| EvaluableFlexibleOverlap |
|
| EvaluableOverlap |
|
| ExceptionConformationGenerationFailed |
|
| ExhaustiveFragmentGeneratorAtoms |
|
| ExhaustiveFragmentGeneratorBonds |
|
| ExhaustiveFragmentGeneratorParallizer |
|
| ExhaustiveFragmentsStatistics |
|
| ExhaustiveMCSGeneratorParallel |
|
| ExitVectorPoint |
|
| ExtendedDepictor |
|
| ExtendedMolecule |
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.
|
| ExtendedMoleculeFunctions |
ExtendedMoleculeFunctions
|
| FactorySolution |
FactorySolution
|
| FastSpline |
Represents a polynomial spline function.
|
| FastSpline.Polynome |
|
| FeatureCalculator |
calculates features for all atoms in a molecule:
H-bond acceptors/donors, negatively/positively ionizable, aromatic, lipophilic
|
| FileHelper |
|
| FingerPrintGenerator |
Generator of a path-based Fingerprint
Not thread safe!
|
| FingerPrintGeneratorPharmGraph |
Generator of a path-based Fingerprint
Not thread safe!
|
| FlexibleShapeAlignment |
Performs flexible Alignment of two Molecules that are prealigned.
|
| FlexophoreCreateFunctions |
FlexophoreCreateFunctions
|
| FlexophorePoint |
FlexophorePoint
|
| ForceField |
|
| ForceFieldChangeListener |
|
| ForceFieldMMFF94 |
|
| Formatter |
|
| Formatter.LocaleFormat |
|
| FormulaParser |
FormulaParser
|
| FractalDimensionMolecule |
FractalDimensionMolecule
|
| FractalDimensionMoleculeMain |
FractalDimensionMoleculeMain
|
| Fragment |
Fragment
Jan 18, 2013 MvK Start implementation
|
| Fragment3D |
|
| FragmentAssociation |
Created by thomas on 9/23/16.
|
| FragmentDefinedByBondsHasher |
|
| FragmentDefinedByBondsIdCode |
|
| Fragmenter3D |
|
| FunctionalGroupClassifier |
|
| Gaussian3D |
|
| GeometryCalculator |
Utility class to perform 3D geometry calculations on molecules
|
| GeometryCalculator |
Utility class to perform 3D geometry calculations on molecules
|
| GeomFactory |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:15 PM
|
| GhostPreview |
|
| Graph |
|
| GraphicsContextImpl |
Project:
User: rufenec
Date: 11/24/2014
Time: 6:24 PM
|
| HashSetInt |
HashSetInt
|
| HBTerm |
|
| HeaderMouseAdapter |
|
| HeaderPaintHelper |
|
| HerschbachLaurie |
Table for Herschbach-Laurie version of Badger's rule.
|
| HetNameParser |
HetNameParser
|
| HetSynonymParser |
HetSynonymParser
|
| HiDPIHelper |
|
| HiDPIIcon |
Created by thomas on 07/12/15.
|
| HiDPIIconButton |
Created by sandert on 04/12/15.
|
| HiDPIToggleButton |
Created by thomas on 07/12/15.
|
| HiDPIUtil |
|
| Histogram |
Histogram
|
| HistogramMatchCalculator |
HistogramMatchCalculator
|
| HoseCodeCreator |
|
| HungarianAlgorithm |
|
| HydrogenHandler |
|
| IArrow |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:28 PM
|
| IAtomPropertiesDialog |
Project:
User: rufenec
Date: 11/24/2014
Time: 5:03 PM
|
| IAtomQueryFeaturesDialog |
Project:
User: rufenec
Date: 11/24/2014
Time: 4:53 PM
|
| IBitArray |
|
| IBitArrayFactory<T extends IBitArray> |
|
| IBondQueryFeaturesDialog |
Project:
User: rufenec
Date: 11/24/2014
Time: 4:57 PM
|
| IChangeListener |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:25 PM
|
| IClipboardHandler |
|
| IColor |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:21 PM
|
| ICompleteGraph |
ICompleteGraph
|
| ICursor |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:21 PM
|
| IDCodeCoord |
IDCodeCoord
Apr 12, 2012 MvK: Start implementation
|
| IDCodeParser |
|
| IDCodeParserWithoutCoordinateInvention |
Typically you should use IDCodeParser instead of this class.
|
| IdentifiedObject<T> |
IdentifiedObject
Nov 2, 2011 MvK: Start implementation
|
| IDepictor<T> |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:26 PM
|
| IDescriptorHandlerFlexophore |
|
| IDialog |
|
| IdoScore |
|
| IDrawContext<T> |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:22 PM
|
| IDrawingObject |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:28 PM
|
| IFactory<S extends AMemorizedObject> |
IFactory
|
| IIdentifiedObject<T> |
IIdentifiedObject
Nov 4, 2011 MvK: Start implementation
|
| IKeyCode |
Project:
User: rufenec
Date: 11/24/2014
Time: 4:17 PM
|
| IKeyEvent |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:20 PM
|
| ImageClipboardHandler |
|
| ImageClipboardHandler.ImageSelection |
|
| ImageProvider<T> |
Created by rufenec on 08/05/15.
|
| IMolDistHist |
|
| IMoleculeView |
|
| IMouseEvent |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:19 PM
|
| IncrementTable |
|
| IndexCoordinates |
|
| IndexHash |
|
| InputObjectFracDimCalc |
InputObjectFracDimCalc
|
| IntArray |
|
| IntArrayComparator |
|
| IntegerDouble |
IntegerDouble
Oct 24, 2011 MvK: Start implementation
|
| InteractionAtomTypeCalculator |
|
| InteractionAtomTypeCalculator.AtomFlagCount |
|
| InteractionAtomTypeCalculator.AtomPropertyMask |
|
| InteractionAtomTypeCalculator.AtomPropertyShift |
|
| InteractionAtomTypeCalculator.FunctionalGroup |
|
| InteractionDistanceStatistics |
|
| InteractionSimilarityTable |
distance gives the distance of the point of highest potential.
|
| InteractionSimilarityTable.InteractionDescriptor |
|
| InteractionTerm |
ProteinLigandTerm is used to represent the energy between 2 atoms.
|
| InteractionTypeMap |
|
| IntQueue |
Implementation for a FIFO of int.
|
| IntQueue |
Implementation for a FIFO of int.
|
| IntVec |
|
| INumericalDataColumn |
|
| InventorAngle |
Created by thomas on 9/23/16.
|
| InventorChain |
Created by thomas on 9/23/16.
|
| InventorCharge |
Created by thomas on 9/28/16.
|
| InventorDefaultTemplateList |
|
| InventorFragment |
|
| InventorTemplate |
|
| IO |
IO
2003 MvK: Start implementation
|
| IObjectiveCompleteGraph<T extends ICompleteGraph> |
IObjectiveCompleteGraph
|
| IonizableGroupDetector |
|
| IonizableGroupDetector2D |
|
| IPharmacophorePoint |
|
| IPharmacophorePoint.Functionality |
|
| IPipeline<T> |
IPipeline
Interface to connect several Runable in a pipeline
Mar 27, 2012 MvK: Start implementation
Oct 9 2012 MvK: wereAllDataFetched() added.
|
| IPolygon |
Project:
User: rufenec
Date: 11/24/2014
Time: 4:45 PM
|
| IPPNode |
|
| IPPNodeSimilarity |
IPPNodeSimilarity
|
| IReactionArrow |
Project:
User: rufenec
Date: 11/24/2014
Time: 5:49 PM
|
| IReactionMapper |
|
| IRectangle2D |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:17 PM
|
| ISimilarityCalculator<T> |
|
| ISimilarityHandlerFactory |
|
| IsomericSmilesCreator |
|
| IsotopeHelper |
|
| IStructureNameResolver |
Created by thomas on 7/13/17.
|
| IValidationListener |
Project:
User: rufenec
Date: 11/24/2014
Time: 3:27 PM
|
| JAtomLabelDialog |
|
| JAtomQueryFeatureDialog |
|
| JBondQueryFeatureDialog |
|
| JBrowseButtons |
|
| JChemistryView |
|
| JDockingPanel |
|
| JDrawArea |
|
| JDrawDialog |
|
| JDrawPanel |
|
| JDrawToolbar |
|
| JEditableChemistryView |
|
| JEditableStructureView |
|
| JFileChooserOverwrite |
|
| JFXCanvasDepictor |
Project:
User: rufenec
Date: 10/12/11
Time: 6:00 PM
|
| JMessageBar |
|
| JStructureView |
|
| JTextDrawingObjectDialog |
|
| KabschAlignment |
described in: DOI 10.1002/jcc.20110 "Using Quaternions to Calculate RMSD"
|
| LigandPose |
|
| LinearRegression |
LinearRegression
2009 MvK: Start implementation
|
| Linker |
Linker
|
| ListInteger<T> |
ListInteger
|
| ListWithIntVec |
|
| ListWithIntVecIdCode |
|
| LittleEndianDataInputStream |
|
| LittleEndianDataOutputStream |
|
| Logarithm |
Logarithm
Mar 14, 2013 MvK Start implementation
|
| LookAndFeelHelper |
|
| LUDecomposition |
LU Decomposition.
|
| MarkushStructure |
|
| MatchFlexophoreNodesMain |
|
| MathHelper |
|
| Matrix |
|
| MatrixBasedHistogram |
MatrixBasedHistogram
|
| MCS |
|
| MCSFast |
|
| MCSFunctions |
|
| MCSReactionMapper |
|
| MDHIndexTables |
|
| MedianStatisticFunctions |
MedianStatisticFunctions
Aug 5, 2011 MvK: Start implementation
|
| MetaFile |
|
| MetalTerm |
|
| MetropolisMonteCarloHelper |
|
| MinimumSpanningTree |
MinimumSpanningTree
Kruskal's algorithm
|
| MMFFMolecule |
MMFF molecule is a wrapper class for the ExtendedMolecule.
|
| Model |
Project:
User: rufenec
Date: 1/24/13
Time: 5:02 PM
|
| Model.AtomHighlightCallback |
|
| Model.BondHighlightCallback |
|
| ModelExhaustiveStatistics |
|
| ModelMedianDouble |
|
| ModelMedianFloat |
|
| ModelMedianInteger |
ModelMedianInteger
Feb 9, 2012 MvK: Start implementation
|
| ModelMedianLong |
ModelMedianInteger
Feb 14, 2017 MvK: Start implementation
|
| ModelParser |
ModelParser
|
| ModelSampleFragments |
|
| ModelSolutionSimilarity |
|
| Mol2FileParser |
|
| MolDistHist |
|
| MolDistHistEncoder |
|
| MolDistHistViz |
Class for Flexophore visualization and atom tracking.
|
| MolDistHistVizEncoder |
|
| MolDistHistVizFrag |
|
| MolecularComplexityCalculator |
|
| MolecularFormula |
|
| MolecularVolume |
|
| Molecule |
|
| Molecule3D |
|
| Molecule3DFunctions |
|
| MoleculeAutoMapper |
|
| MoleculeDataFormats |
Deprecated. |
| MoleculeDragAdapter |
|
| MoleculeDropAdapter |
|
| MoleculeFilter |
|
| MoleculeGrid |
Class used to speed up the calculation of neighbours by creating a grid.
|
| MoleculeNeutralizer |
|
| MoleculeStandardizer |
MoleculeStandardizer
|
| MoleculeTransferable |
|
| MoleculeView |
Project:
User: rufenec
Date: 10/12/11
Time: 4:03 PM
|
| MoleculeViewSkin |
Project:
User: rufenec
Date: 10/12/11
Time: 4:10 PM
|
| MolfileCreator |
|
| MolfileParser |
|
| MolfileV3Creator |
This class generates an MDL molfile version 3.0 from a StereoMolecule
as described by MDL in 'CTFile Formats June 2005'.
|
| MultCoordFragIndex |
|
| MultipleNonOverlapSolution |
|
| Mutation |
|
| MutationBiasProvider |
|
| Mutator |
|
| NamedSubstituents |
|
| NativeClipboardAccessor |
|
| NewBondAction |
Project:
User: rufenec
Date: 1/28/13
Time: 1:28 PM
|
| NewChainAction |
Project:
User: rufenec
Date: 3/26/13
Time: 3:42 PM
|
| ObjectiveBlurFlexophoreHardMatchUncovered |
ObjectiveBlurFlexophoreHardMatchUncovered
The weighting of the coverage is hard.
|
| ObjectiveExhaustiveStatistics |
|
| ODEFileParser |
|
| OptimizerLBFGS |
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
|
| OutOfPlane |
Out of plane energy term class.
|
| OutOfPlane |
|
| ParameterizedStringList |
|
| PasteAction |
Project:
User: rufenec
Date: 5/16/13
Time: 3:39 PM
|
| PDBCoordEntryFile |
PDBCoordEntryFile
|
| PDBFileParser |
PDBFileParser
|
| PeriodicTable |
|
| PeriodicTable |
|
| PharmacophoreCalculator |
|
| PharmacophoreNode |
A PharmacophoreNode represents a node in a PharmacophoreTree.
|
| PharmacophorePointFactory |
|
| PharmacophoreTree |
A PharmacophoreTree closely follows the concepts of FeatureTrees as described by Rarey and Dixon
(DOI:10.1023/a:1008068904628).
|
| PharmacophoreTree.BiGramInt |
container of an undirected edge
|
| PharmacophoreTreeGenerator |
Generates a PharmacophoreTree from a StereoMolecule.
|
| PharmGraphGenerator |
|
| PheSAAlignment |
|
| PheSAAlignment.axis |
|
| PheSAAlignment.PheSAResult |
|
| PheSAAlignmentOptimizer |
|
| PheSABindingHypothesis |
|
| PheSAMolecule |
|
| Pipeline<T> |
Pipeline
Enables concurrent access to a queue.
|
| PlaneRule |
|
| Platform |
Requires JRE 1.6
|
| PLPTerm |
piecewise linear potential (PLP) as described in doi:10.1021/ci800298z
parameters from model 3 (M3)
|
| PointDouble |
|
| PointUtils |
|
| PolarSurfaceAreaPredictor |
This class predicts the topological polar surface area (TPSA) of a molecule as a sum of
contributions of its polar atom-types.
|
| Polygon |
|
| PopupProvider |
|
| PositionConstraint |
|
| PotentialEnergyTerm |
|
| PPGaussian |
|
| PPNode |
|
| PPNodeRGroup |
PPNodeStructure
|
| PPNodeSimilarity |
PPNodeSimilarity
|
| PPNodeViz |
Pharmacophore node with information about corresponding atoms in the molecule used for construction.
|
| PPNodeVizTriangle |
|
| PPTriangle |
|
| PPTriangleCreator |
|
| PPTriangleMatcher |
|
| PPTriangleMatcher.AlignmentResult |
|
| ProgressController |
|
| ProgressListener |
|
| PropertyCalculator |
|
| ProteinSynthesizer |
|
| Quaternion |
|
| QuickMathCalculator |
|
| RDFileParser |
Quick and dirty RD-File parser that reads non-hierarchical RD-Files.
|
| Reaction |
|
| ReactionArrow |
|
| ReactionDragAdapter |
|
| ReactionDropAdapter |
|
| ReactionEncoder |
|
| ReactionSearch |
|
| ReactionSearchDataSource |
|
| ReactionSearchSpecification |
|
| ReactionTransferable |
|
| Reactor |
|
| RemarkParser |
RemarkParser
|
| REPTerm |
repulsive term, see PLPTerm for reference
|
| Residue |
ModelGroupAtoms
handles a group of atoms, e.g.
|
| ResultFracDimCalc |
ResultFracDimCalc
|
| ResultFragmentsStatistic |
|
| ResultObjective |
|
| RigidFragment |
|
| RigidFragmentCache |
This class implements a thread-save, concurrent cache of rigid fragments' 3D-atom-coordinates.
|
| RigidFragmentCache.CacheEntry |
|
| RigidFragmentProvider |
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.
|
| RingBoolean |
|
| RingCollection |
|
| RotatableBond |
A RotatableBond knows the two rigid fragments within a molecule
that are connected by this bond.
|
| RunBondVector2IdCode |
|
| RXNFileCreator |
|
| RXNFileParser |
|
| RXNFileV3Creator |
|
| ScaffoldHelper |
|
| ScaledEditorKit |
|
| ScaledHTML |
|
| ScaledStyleSheet |
|
| ScorePoint |
|
| ScrollPaneAutoScrollerWhenDragging |
|
| Sdf |
The Sdf class provides helper functions for dealing with the SDF file
format.
|
| Sdf.OnMolecule |
|
| SDFileMolecule |
|
| SDFileMoleculeDropAdapter |
|
| SDFileMoleculeTransferable |
|
| SDFileParser |
|
| Search |
The search class provides binary searching on arrays.
|
| Searchable |
Interface that must be implemented for array objects that can be
searched by the binary search function.
|
| SelectionAction |
Project:
User: rufenec
Date: 1/24/13
Time: 5:57 PM
|
| Selector<T> |
Created with IntelliJ IDEA.
|
| SelfOrganizedConformer |
|
| Separation |
The Separation class is an efficient storage of an adjacency matrix
representing how many degrees of separation there are between any two
atoms.
|
| Separation.Relation |
Relation class shows the relationship between two atoms A1 and A2.
|
| ShadowBorder |
|
| SimilarityCalculatorInfo |
|
| SimpleCanonizer |
|
| SimpleMetalTerm |
|
| SimplePPGaussian |
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
|
| SingularValueDecomposition |
Singular Value Decomposition.
|
| SiteParser |
SiteParser
Site records specify residues comprising catalytic, co-factor, anti-codon, regulatory or other
essential sites or environments surrounding ligands present in the structure.
|
| SizeOf |
13.02.2006 MvK
|
| Sketch |
Title: Actelion Java Library
|
| SlidingWindow |
SlidingWindow
|
| SlidingWindowDistHist |
SlidingWindowDistHist
Created by korffmo1 on 01.03.16.
|
| SmilesCreator |
|
| SmilesParser |
|
| SmoothingSplineInterpolator |
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
|
| SolubilityPredictor |
|
| SolutionCompleteGraph |
SolutionCompleteGraph
|
| SortedList<T extends java.lang.Comparable<? super T>> |
|
| SortedPair |
SortedPair class is used in the Separation table.
|
| SortedStringList |
|
| SplineFunction |
Class used to represent a Protein Ligand Function
|
| SRSearcher |
The SRSearcher class handles reaction-sub-structure searches.
|
| SSSearcher |
|
| SSSearcherWithIndex |
|
| StatisticalTorsionPotential |
|
| StatisticalTorsionTerm |
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 |
|
| StereoMolecule |
|
| StraightLineRule |
|
| StrainTerm |
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)
|
| StretchBend |
Stretch bending energy term class.
|
| String2DoubleArray |
|
| StringFunctions |
|
| StringReadChannel |
StringReadChannel
2007 MvK: Start implementation
25.06.2009 MvK: implementation changed
12.02.2014 MvK: added charset encoding to handle Umlaute.
|
| StrokeLineCap<T> |
Project:
User: rufenec
Date: 11/24/2014
Time: 4:20 PM
|
| StrokeLineJoin |
Project:
User: rufenec
Date: 11/24/2014
Time: 4:20 PM
|
| StructureAssembler |
|
| StructureCalculator |
Utility function based on the molecule's connections (groups, rings,...)
|
| StructureInfo |
|
| StructureListener |
|
| StructureNameResolver |
Created by thomas on 7/13/17.
|
| StructureSearch |
|
| StructureSearchController |
|
| StructureSearchDataSource |
|
| StructureSearchSpecification |
|
| StructureTransferData |
|
| SubFlexophoreGenerator |
SubFlexophoreGenerator
|
| SubFlexophoreGenerator.ViolatedConditionsCount |
|
| SubGraphExtractor |
SubGraphExtractor
Creates substructures by fragmentation and summarizes them.
|
| SubGraphIndices |
SubGraphIndices
A class to handle indices in a molecular graph.
|
| SubStructSearchBondIndex |
|
| SubStructSearchExhaustiveTreeWalker |
|
| SummaryFragments |
|
| SVGDepictor |
|
| SymmetryCalculator |
|
| SymmetryCorrectedRMSDCalculator |
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
|
| TableModelString |
TableModelText
Data model for an only text containing table
|
| Tables |
A collection of tables with the official parameters of the
MMFF94/MMFF94s force field variants.
|
| TautomerHelper |
|
| testChiralDia |
|
| testDiaID |
|
| testHoses |
|
| TetrahedralStereoRule |
|
| TextClipboardHandler |
| TextDrawingObject |
|
| ThreadMaster |
|
| ToolbarSelectionChange |
Created by rufenec on 5/3/16.
|
| Torsion |
|
| Torsion |
The torsion type class provides a static function for getting the
torsion type of a torsion angle.
|
| TorsionAngle |
Torsional Angle energy term class.
|
| TorsionConstraint |
|
| TorsionDB |
|
| TorsionDescriptor |
|
| TorsionDescriptorHelper |
|
| TorsionDetail |
|
| TorsionPrediction |
|
| TorsionRelevanceHelper |
|
| TorsionRule |
|
| TorsionSet |
|
| TorsionSetEliminationRule |
|
| TorsionSetStrategy |
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.
|
| TorsionSetStrategyAdaptiveRandom |
|
| TorsionSetStrategyLikelySystematic |
TorsionSetStrategy that systematically creates all possible TorsionSets in
batches while keeping a focus on the likelyhood of individual torsions.
|
| TorsionSetStrategyRandom |
|
| ToxicityPredictor |
|
| TreeContainer |
|
| TreeElement |
|
| TreeFork |
|
| TreeLeaf |
|
| TreeMatcher |
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.FeatureMatch |
TODO: don't add null-matches!
|
| TreeMatcher.TreeMatching |
|
| TreeRoot |
|
| TreeUtils |
|
| Triangle |
Triangle
Created by korffmo1 on 04.06.17.
|
| UndoAction |
Project:
User: rufenec
Date: 3/26/13
Time: 4:39 PM
|
| UniqueFragmentEstimator |
|
| UniqueList<T extends java.lang.Comparable<? super T>> |
|
| UniqueStringList |
|
| UnknownParityAction |
Project:
User: rufenec
Date: 3/26/13
Time: 4:33 PM
|
| UnparametrizedAtomTypeException |
|
| UpBondAction |
Project:
User: rufenec
Date: 1/28/13
Time: 1:49 PM
|
| VanDerWaals |
|
| VanDerWaals |
Nonbonded van der Waals energy term class.
|
| VDWRadii |
|
| Vector3 |
The Vector3 class provides common vector operations used throughout the
MMFF codebase.
|
| VectorSimilarity |
|
| VerticalFlowLayout |
A vertical flow layout is similar to a flow layuot but it layouts the
components vertically instead of horizontally.
|
| VolumeGaussian |
|
| WMF |
|
| WMFConstants |
|
| WMFGraphics |
|
| WMFGraphics2D |
|
| ZoomRotateAction |
Project:
User: rufenec
Date: 4/28/2014
Time: 12:39 PM
|