Uses of Class
com.actelion.research.chem.Molecule3D
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Uses of Molecule3D in com.actelion.research.chem
Methods in com.actelion.research.chem that return Molecule3D Modifier and Type Method Description static Molecule3D
Molecule3DFunctions. removeAllAtomsWithoutNeighbours(Molecule3D ffMol)
Methods in com.actelion.research.chem with parameters of type Molecule3D Modifier and Type Method Description int
Molecule3D. addAtom(Molecule3D m, int i)
Add an atom by copying its properties from the given Molecule3D This has to be overriden by subclassesint
Molecule3D. compareTo(Molecule3D o)
int
Molecule3D. fusion(Molecule3D m2)
This method will append a Molecule3D to the end.static Molecule3D
Molecule3DFunctions. removeAllAtomsWithoutNeighbours(Molecule3D ffMol)
Constructors in com.actelion.research.chem with parameters of type Molecule3D Constructor Description Molecule3D(Molecule3D mol)
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Uses of Molecule3D in com.actelion.research.chem.descriptor.flexophore
Fields in com.actelion.research.chem.descriptor.flexophore declared as Molecule3D Modifier and Type Field Description protected Molecule3D
MolDistHistViz. molecule3D
Methods in com.actelion.research.chem.descriptor.flexophore that return Molecule3D Modifier and Type Method Description static Molecule3D
Molecule3DFunctions. add(Molecule3D mol1, Molecule3D mol2)
static Molecule3D
Molecule3DFunctions. distortCoordinates(Molecule3D molecule3D, double maxLengthDistortion)
Changes the coordinates with a random value.static Molecule3D
Molecule3DExtractor. extract(Molecule3D molecule3D, java.util.List<java.lang.Integer> liIndexAtomsFrags)
protected static Molecule3D
MolDistHistViz. finalizeMolecule(Molecule3D mol)
Remove all atoms without connections.static Molecule3D
Molecule3DFunctions. getCentered(Molecule3D ff)
static Molecule3D
Molecule3DFunctions. getCentered(Molecule3D molecule3D, java.util.List<java.lang.Integer> liAtomIndexCenter)
static Molecule3D
Molecule3DFunctions. getDeprotonated(Molecule3D molecule3D, int indexAtomReactiveCenter)
Deprotonates and decreases charge by 1.Molecule3D
MolDistHistViz. getMolecule()
The atoms of the ff molecule contain the corresponding PPNode indices in the first field of the PPP vector.Molecule3D
Molecule3DExtractor. getMolecule(int index)
Molecule3D
MolDistHistViz. getMoleculeRemovedUnrelatedAtoms()
static Molecule3D
Molecule3DFunctions. getNeutralized(Molecule3D molecule3D, int indexAtomReactiveCenter)
Protonates or deprotonates the specified atom, if necessary and possible, to neutralize a charge.static Molecule3D
Molecule3DFunctions. getProtonated(Molecule3D molecule3D, int indexAtomReactiveCenter)
Protonates and increases charge by 1.static Molecule3D
Molecule3DFunctions. randomizeAtoms(Molecule3D molecule3D)
static Molecule3D
Molecule3DFunctions. removeAllAtomsWithoutNeighbours(Molecule3D ffMol)
Methods in com.actelion.research.chem.descriptor.flexophore with parameters of type Molecule3D Modifier and Type Method Description static Molecule3D
Molecule3DFunctions. add(Molecule3D mol1, Molecule3D mol2)
static void
Molecule3DFunctions. addMissingHydrogens(Molecule3D molecule3D)
static void
Molecule3DFunctions. addRNDCoordinates(Molecule3D mol, double maxNoise)
static int
Molecule3DFunctions. calcTerminalAlkylGroupsCenter(Molecule3D mol)
Generates a center atom for each atom of a terminal alkyl group -CC, -C(C)C and -C(C)(C)C.static void
Molecule3DFunctions. calculateCoordinatesIterative(Molecule3D mol, double[][] arrDist)
static void
Molecule3DFunctions. copy(Molecule3D molSource, Molecule3D molDestination)
static Molecule3D
Molecule3DFunctions. distortCoordinates(Molecule3D molecule3D, double maxLengthDistortion)
Changes the coordinates with a random value.static Molecule3D
Molecule3DExtractor. extract(Molecule3D molecule3D, java.util.List<java.lang.Integer> liIndexAtomsFrags)
protected static Molecule3D
MolDistHistViz. finalizeMolecule(Molecule3D mol)
Remove all atoms without connections.static int[]
Molecule3DFunctions. findTerminalMethylAtCarb(Molecule3D mol)
static void
Molecule3DFunctions. flagCarbon(Molecule3D mol)
static void
Molecule3DFunctions. flagSubstructure(Molecule3D molecule3D, java.lang.String idCodeQ1, int[] arrIndexAts2Flag)
static void
Molecule3DFunctions. flagUnflaggedWithFlagCenter(Molecule3D mol)
static void
Molecule3DFunctions. formatAtomDescriptionsForViewer(Molecule3D mol)
static void
Molecule3DFunctions. formatAtomDescriptionsForViewer(Molecule3D mol, boolean showIndex)
static java.util.List<java.lang.Integer>
Molecule3DFunctions. getAcidicProtons(Molecule3D mol)
Protons attached to an O.static double[][]
Molecule3DFunctions. getAdjacencyMatrix(Molecule3D mol)
static Molecule3D
Molecule3DFunctions. getCentered(Molecule3D ff)
static Molecule3D
Molecule3DFunctions. getCentered(Molecule3D molecule3D, java.util.List<java.lang.Integer> liAtomIndexCenter)
static Coordinates
Molecule3DFunctions. getCenterGravity(Molecule3D mol)
static Coordinates
Molecule3DFunctions. getCenterGravity(Molecule3D mol, int[] indices)
static int[][]
Molecule3DFunctions. getConnectionTable(Molecule3D mol)
static java.util.List<java.lang.Integer>
Molecule3DFunctions. getDeprotonableAtoms(Molecule3D mol)
Donor atoms.static Molecule3D
Molecule3DFunctions. getDeprotonated(Molecule3D molecule3D, int indexAtomReactiveCenter)
Deprotonates and decreases charge by 1.static double[][]
Molecule3DFunctions. getDistanceArray(Molecule3D mol)
static double
Molecule3DFunctions. getDistanceFromCoord(Molecule3D mol, int atom1, int atom2)
static java.util.List<java.util.List<java.lang.Integer>>
Molecule3DFunctions. getLayersFromBroadFirstSearch(Molecule3D molecule3D, int indexAtomStart)
Returns the atom indices as layers of the start atom.static java.util.List<java.lang.Integer>
Molecule3DFunctions. getLongestChain(Molecule3D ff)
static java.util.List<java.lang.Integer>
Molecule3DFunctions. getLongestChain(Molecule3D molecule3D, int indexAtomStart)
static Molecule3D
Molecule3DFunctions. getNeutralized(Molecule3D molecule3D, int indexAtomReactiveCenter)
Protonates or deprotonates the specified atom, if necessary and possible, to neutralize a charge.static int[]
Molecule3DFunctions. getPath(Molecule3D ff, int indexAt1, int indexAt2)
static java.util.List<java.lang.Integer>
Molecule3DFunctions. getProtonableAtoms(Molecule3D mol)
static Molecule3D
Molecule3DFunctions. getProtonated(Molecule3D molecule3D, int indexAtomReactiveCenter)
Protonates and increases charge by 1.static double
Molecule3DFunctions. getStericHindrance(Molecule3D molecule3D, java.util.List<java.lang.Integer> liIndexAtoms)
Calculates a value for the steric hindrance of the atoms from liIndexAtoms to all other atoms.static int[][]
Molecule3DFunctions. getTopologicalDistanceMatrix(Molecule3D mol)
static javax.swing.tree.DefaultMutableTreeNode
Molecule3DFunctions. getTreeFromBroadFirstSearch(Molecule3D molecule3D, int indexAtomStart)
User object in DefaultMutableTreeNode is the index of the atom.static javax.swing.tree.DefaultMutableTreeNode
Molecule3DFunctions. getTreeFromComplete(Molecule3D molecule3D, int indexAtomStart)
Get all possible paths.static boolean
Molecule3DFunctions. has2DCoordinates(Molecule3D mol)
static boolean
Molecule3DFunctions. has3DCoordinates(Molecule3D mol)
static boolean
Molecule3DFunctions. hasChargedAtom(Molecule3D ff)
static boolean
Molecule3DFunctions. isAliphaticAtom(Molecule3D mol, int atm)
static boolean
Molecule3DFunctions. isConnectedAtoms(Molecule3D ff, java.util.List<java.lang.Integer> liIndexAtoms, int atm2)
static boolean
Molecule3DFunctions. isParametrized(Molecule3D mol)
static boolean
Molecule3DFunctions. isProtonableNitrogen(Molecule3D mol, int indexAtom)
static boolean
Molecule3DFunctions. isPyramedal(Molecule3D molecule3D)
static boolean
Molecule3DFunctions. isTripleBond(Molecule3D molecule3D)
static Molecule3D
Molecule3DFunctions. randomizeAtoms(Molecule3D molecule3D)
static Molecule3D
Molecule3DFunctions. removeAllAtomsWithoutNeighbours(Molecule3D ffMol)
static void
Molecule3DFunctions. removeAtoms(Molecule3D mol, java.util.List<java.lang.Integer> liIndices2Delete)
static void
Molecule3DFunctions. removeAtomsIfCarbon(Molecule3D mol, java.util.List<java.lang.Integer> liIndices2Delete)
static void
Molecule3DFunctions. removeCarbon(Molecule3D mol)
Removes all Carbon atoms, except the FLAG_CENTER_ATOM is set.static void
Molecule3DFunctions. removeElectronPairs(Molecule3D mol)
static void
Molecule3DFunctions. removeElement(Molecule3D mol, int atomicNo)
static void
Molecule3DFunctions. removeFlaggedAtoms(Molecule3D mol)
static void
Molecule3DFunctions. removeHydrogensAndElectronPairs(Molecule3D mol)
static void
Molecule3DFunctions. removeNonAromaticC(Molecule3D mol)
static void
Molecule3DFunctions. replaceAtoms(Molecule3D ffMol, java.lang.String idcode2Replace, java.lang.String idcodeNewSubstructure, int[][] arrMapAtoms)
09.03.2020 For what is that good?void
MolDistHistViz. set(Molecule3D ff)
static java.lang.String
Molecule3DFunctions. toString(Molecule3D mol)
static void
Molecule3DFunctions. writeCharge2Label(Molecule3D molecule3D)
Constructors in com.actelion.research.chem.descriptor.flexophore with parameters of type Molecule3D Constructor Description MolDistHistViz(int nNodes, Molecule3D ff)
MolDistHistVizFrag(int length, Molecule3D ff)
Molecule3DExtractor(Molecule3D molecule3D)
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Uses of Molecule3D in com.actelion.research.chem.descriptor.flexophore.calculator
Methods in com.actelion.research.chem.descriptor.flexophore.calculator with type parameters of type Molecule3D Modifier and Type Method Description static <T extends Molecule3D>
TStructureCalculator. extractFragment(Molecule3D mol, T res, int[] atoms)
Extract the Ligand from mol and copy it into resstatic <T extends Molecule3D>
TStructureCalculator. extractFragment(Molecule3D mol, T res, java.util.List<java.lang.Integer> atoms)
Methods in com.actelion.research.chem.descriptor.flexophore.calculator that return Molecule3D Modifier and Type Method Description static Molecule3D
StructureCalculator. crop(Molecule3D mol, Coordinates center, double radius)
static Molecule3D
StructureCalculator. cropLigand(Molecule3D mol, double radius)
static Molecule3D
StructureCalculator. extractLigand(Molecule3D mol)
Extract the Ligand from mol and copy it into resMethods in com.actelion.research.chem.descriptor.flexophore.calculator that return types with arguments of type Molecule3D Modifier and Type Method Description static java.util.List<Molecule3D>
StructureCalculator. extractFragments(Molecule3D mol)
Return all connex components with more than 5 atomsstatic java.util.List<Molecule3D>
StructureCalculator. extractLigands(Molecule3D mol)
Return all ligands with more than 5 atomsMethods in com.actelion.research.chem.descriptor.flexophore.calculator with parameters of type Molecule3D Modifier and Type Method Description static boolean
StructureCalculator. addHydrogens(Molecule3D mol)
Add the missing hydrogens for the ligandstatic boolean
StructureCalculator. addHydrogens(Molecule3D mol, boolean alsoRigidAtoms)
Adds the missing hydrogens (no optimization)static boolean
StructureCalculator. addHydrogensAroundLigand(Molecule3D mol, double radius)
static int
StructureCalculator. connected(Molecule3D mol, int a, int atomicNo, int bondOrder)
Returns the rotatable bonds (sorted).static void
StructureCalculator. copyAtoms(Molecule3D mol, Molecule3D res, java.util.List<java.lang.Integer> atomsToBeAdded)
static Molecule3D
StructureCalculator. crop(Molecule3D mol, Coordinates center, double radius)
static Molecule3D
StructureCalculator. cropLigand(Molecule3D mol, double radius)
static boolean
StructureCalculator. deleteHydrogens(Molecule3D mol)
static int
StructureCalculator. dfs(Molecule3D lig, int start, java.util.Set<java.lang.Integer> seen)
static int
StructureCalculator. dfs(Molecule3D lig, int start, java.util.Set<java.lang.Integer> seen, int depth, boolean takeRingsAsWhole)
static <T extends Molecule3D>
TStructureCalculator. extractFragment(Molecule3D mol, T res, int[] atoms)
Extract the Ligand from mol and copy it into resstatic <T extends Molecule3D>
TStructureCalculator. extractFragment(Molecule3D mol, T res, java.util.List<java.lang.Integer> atoms)
static java.util.List<Molecule3D>
StructureCalculator. extractFragments(Molecule3D mol)
Return all connex components with more than 5 atomsstatic Molecule3D
StructureCalculator. extractLigand(Molecule3D mol)
Extract the Ligand from mol and copy it into resstatic java.util.List<Molecule3D>
StructureCalculator. extractLigands(Molecule3D mol)
Return all ligands with more than 5 atomsstatic void
StructureCalculator. flagBackbone(Molecule3D mol)
Return a List of int[] representing all the atom-atom pairs having an intermolecular interactions (distance close to sum of VDW)static double
GeometryCalculator. getAngle(Molecule3D mol, int a1, int a2, int a3)
Gets the Angle between 3 atomsstatic long
StructureCalculator. getAtomHashkey(Molecule3D mol, int a)
Return a long representing the atom and its neighboursstatic int[]
StructureCalculator. getAtomsOnPath(Molecule3D mol, int a1, int a2)
Finds on all atoms going on a path from a1 to a2.static int[]
StructureCalculator. getAtomToGroups(Molecule3D mol)
static int[]
StructureCalculator. getAtomToGroups(Molecule3D mol, java.util.List<java.lang.Integer> seeds)
For each molecule inmol
one group is created.static java.util.List<java.lang.Integer>
StructureCalculator. getBackbone(Molecule3D lig, int a)
static boolean[]
StructureCalculator. getBackbones(Molecule3D molecule)
static boolean[]
StructureCalculator. getBackbones(Molecule3D molecule, int minChain)
Gets the backbonestatic Coordinates[]
GeometryCalculator. getBounds(Molecule3D molecule)
Gets the Bounds of a moleculestatic Coordinates[]
StructureCalculator. getBounds(Molecule3D mol)
static Coordinates
StructureCalculator. getCenter(Molecule3D mol)
static Coordinates
GeometryCalculator. getCenterGravity(Molecule3D mol)
Gets the center of Gravity of a moleculestatic java.util.List<java.util.List<java.lang.Integer>>
StructureCalculator. getConnexComponents(Molecule3D mol)
Returns a List of all Connex Components of the graph (List of List of Integer)static double
GeometryCalculator. getDihedral(Molecule3D mol, int a1, int a2, int a3, int a4)
Gets the Dihedral Angle between 4 atomsstatic double[][]
StructureCalculator. getDistanceMatrix(Molecule3D m1, Molecule3D m2)
static int
StructureCalculator. getExplicitHydrogens(Molecule3D mol, int atm)
static java.util.List<int[]>
StructureCalculator. getFragmentMatches(Molecule3D fragment, Molecule3D mol)
Find all fragment occurences in mol (only the movable atoms are considered).static int
StructureCalculator. getImplicitHydrogens(Molecule3D mol, int atm)
Return the number of implicit hydrogens, ie.static java.util.List<int[]>
StructureCalculator. getInterMolecularInteractions(Molecule3D mol)
Return a List of int[] representing all the atom-atom pairs having an intermolecular interactions (distance close to sum of VDW)static Coordinates[]
StructureCalculator. getLigandBounds(Molecule3D mol)
static Coordinates
StructureCalculator. getLigandCenter(Molecule3D mol)
static double
StructureCalculator. getLigandRMSD(Molecule3D mol1, Molecule3D mol2)
Gets the root mean square deviation between 2 positions.static java.util.List<java.lang.Integer>
StructureCalculator. getLongestChain(Molecule3D mol, int atm)
Return the longest molecular chain starting at atmstatic int
StructureCalculator. getMaxFreeValence(Molecule3D mol, int atm)
static int
StructureCalculator. getMolecularPathCount(Molecule3D mol, int length)
Returns the number of paths of the given length (gives an idea of the number of branches)static int[][]
StructureCalculator. getNumberOfAtomsBetweenBonds(Molecule3D mol, int maxAtoms, int[][] dist)
Computes a matrix of distances between all the bonds in the graph.static int[][]
StructureCalculator. getNumberOfBondsBetweenAtoms(Molecule3D mol, int maxBonds, int[][] dist)
Computes a matrix of distances between all the atoms in the graph.static int[]
StructureCalculator. getOverlap(Molecule3D m1, Molecule3D m2)
static java.util.List<java.lang.Integer>[]
StructureCalculator. getRings(Molecule3D mol, java.util.List<int[]> allRings)
static java.util.List<java.lang.Integer>[]
StructureCalculator. getRingsAccurate(Molecule3D mol, java.util.List<int[]> allRings)
Find the smallest covering set of rings for the Molecule.static java.util.List<java.lang.Integer>[]
StructureCalculator. getRingsFast(Molecule3D mol, java.util.List<int[]> allRings)
Find the list of rings for the Molecule.static int
StructureCalculator. getStructureCenter(Molecule3D lig, int[] rotatables, int[][] dists)
static int
StructureCalculator. getStructureCenter(Molecule3D lig, int a, int[] rotatables, int[][] dists)
The Structure Center Atom is defined as the atom with the biggest no of rotatables bonds and the closest to the centerstatic int
StructureCalculator. getValence(Molecule3D mol, int atm)
static void
StructureCalculator. insertLigand(Molecule3D mol, Molecule3D lig, Coordinates center)
static boolean
StructureCalculator. isAcceptor(Molecule3D m, int a)
static boolean
StructureCalculator. isDonor(Molecule3D m, int a)
static int
StructureCalculator. makeProteinFlexible(Molecule3D mol, Coordinates center, double radius, boolean keepBackboneRigid)
static void
StructureCalculator. makeProteinRigid(Molecule3D mol)
static boolean
StructureCalculator. markLigand(Molecule3D mol)
Find the most likely ligand (in term of size, rings, polar atoms) and mark itstatic int
StructureCalculator. markLigand(Molecule3D mol, int n)
Marks a numbered ligandstatic void
StructureCalculator. markLigands(Molecule3D mol)
Find the most likely ligands (in term of size)static void
StructureCalculator. removeLigand(Molecule3D mol)
static boolean
StructureCalculator. removeLonePairs(Molecule3D mol)
static void
StructureCalculator. removeWater(Molecule3D mol)
static void
StructureCalculator. removeWater(Molecule3D mol, boolean removeAlsoImportant)
static void
StructureCalculator. removeWaterSalts(Molecule3D mol)
static void
StructureCalculator. replaceLigand(Molecule3D mol, Molecule3D lig)
static void
StructureCalculator. replaceLigand(Molecule3D mol, Molecule3D lig, Coordinates center)
Replaces the preoptimized ligand in molstatic void
StructureCalculator. rotateBond(Molecule3D mol, int a2, int a3, double angle)
Make sure the parity of mol match the one from ref, otherwise fix it.static void
StructureCalculator. rotateLigand(Molecule3D mol, double angle, Coordinates normal, Coordinates center)
static void
GeometryCalculator. translate(Molecule3D molecule, Coordinates c)
Translate a Moleculestatic void
StructureCalculator. translateLigand(Molecule3D mol, Coordinates v)
static void
StructureCalculator. vibrateLigand(Molecule3D mol, double radius)
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Uses of Molecule3D in com.actelion.research.chem.descriptor.flexophore.generator
Methods in com.actelion.research.chem.descriptor.flexophore.generator with parameters of type Molecule3D Modifier and Type Method Description static boolean
CreatorMolDistHistViz. generateConformerAndSetCoordinates(ConformerGenerator conformerGenerator, int nAtoms, Molecule3D molInPlace)
08.03.2017 Method set to public for debugging purposes. -
Uses of Molecule3D in com.actelion.research.chem.interactionstatistics
Methods in com.actelion.research.chem.interactionstatistics with parameters of type Molecule3D Modifier and Type Method Description static void
InteractionAtomTypeCalculator. setInteractionTypes(Molecule3D mol)
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