Uses of Class
com.actelion.research.chem.Molecule3D

Packages that use Molecule3D

Package	Description
com.actelion.research.chem
com.actelion.research.chem.descriptor.flexophore
com.actelion.research.chem.descriptor.flexophore.calculator
com.actelion.research.chem.descriptor.flexophore.generator
com.actelion.research.chem.docking.scoring
com.actelion.research.chem.interactionstatistics
com.actelion.research.chem.io
com.actelion.research.chem.io.pdb.converter
com.actelion.research.chem.io.pdb.parser

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 subclasses
int	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)

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
protected static Molecule3D	MolDistHistViz.finalizeMolecule(Molecule3D mol)	Remove all atoms without connections.
Molecule3D	MolDistHistViz.getMolecule()	The atoms of the ff molecule contain the corresponding PPNode indices in the first field of the PPP vector.
Molecule3D	MolDistHistViz.getMoleculeRemovedUnrelatedAtoms()

Methods in com.actelion.research.chem.descriptor.flexophore with parameters of type Molecule3D

Modifier and Type	Method	Description
protected static Molecule3D	MolDistHistViz.finalizeMolecule(Molecule3D mol)	Remove all atoms without connections.
void	MolDistHistViz.set(Molecule3D ff)

Constructors in com.actelion.research.chem.descriptor.flexophore with parameters of type Molecule3D

Constructor	Description
MolDistHistViz(int nNodes, Molecule3D molecule3D)
MolDistHistVizFrag(int length, Molecule3D ff)

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> T	StructureCalculator.extractFragment(Molecule3D mol, T res, int[] atoms)	Extract the Ligand from mol and copy it into res
static <T extends Molecule3D> T	StructureCalculator.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 res

Methods 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 atoms
static java.util.List<Molecule3D>	StructureCalculator.extractLigands(Molecule3D mol)	Return all ligands with more than 5 atoms

Methods 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 ligand
static 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> T	StructureCalculator.extractFragment(Molecule3D mol, T res, int[] atoms)	Extract the Ligand from mol and copy it into res
static <T extends Molecule3D> T	StructureCalculator.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 atoms
static Molecule3D	StructureCalculator.extractLigand(Molecule3D mol)	Extract the Ligand from mol and copy it into res
static java.util.List<Molecule3D>	StructureCalculator.extractLigands(Molecule3D mol)	Return all ligands with more than 5 atoms
static 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 atoms
static long	StructureCalculator.getAtomHashkey(Molecule3D mol, int a)	Return a long representing the atom and its neighbours
static 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 in mol 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 backbone
static Coordinates[]	GeometryCalculator.getBounds(Molecule3D molecule)	Gets the Bounds of a molecule
static Coordinates[]	StructureCalculator.getBounds(Molecule3D mol)
static Coordinates	StructureCalculator.getCenter(Molecule3D mol)
static Coordinates	GeometryCalculator.getCenterGravity(Molecule3D mol)	Gets the center of Gravity of a molecule
static 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 atoms
static 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 atm
static 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 center
static 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 it
static int	StructureCalculator.markLigand(Molecule3D mol, int n)	Marks a numbered ligand
static 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 mol
static 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 Molecule
static void	StructureCalculator.translateLigand(Molecule3D mol, Coordinates v)
static void	StructureCalculator.vibrateLigand(Molecule3D mol, double radius)

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 void	CreatorMolDistHistViz.calcFragmentCenter(Molecule3D molecule3D, java.util.List<MultCoordFragIndex> liMultCoordFragIndex)	Calculates the center of the fragments and stores the coordinates in MultCoordFragIndex.
static MolDistHistViz	CreatorMolDistHistViz.create(java.util.List<MultCoordFragIndex> liMultCoordFragIndex, Molecule3D molecule3D)
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.docking.scoring

Constructors in com.actelion.research.chem.docking.scoring with parameters of type Molecule3D

Constructor	Description
ChemPLP(Molecule3D receptor, java.util.Set<java.lang.Integer> bindingSiteAtoms, MoleculeGrid grid)

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)

Uses of Molecule3D in com.actelion.research.chem.io

Methods in com.actelion.research.chem.io that return Molecule3D

Modifier and Type	Method	Description
Molecule3D	AbstractParser.load(java.io.File file)
Molecule3D	AbstractParser.load(java.lang.String fileName)
Molecule3D	AbstractParser.load(java.lang.String fileName, java.io.Reader in)

Methods in com.actelion.research.chem.io that return types with arguments of type Molecule3D

Modifier and Type	Method	Description
java.util.List<Molecule3D>	AbstractParser.loadGroup(java.lang.String fileName)
java.util.List<Molecule3D>	AbstractParser.loadGroup(java.lang.String fileName, java.io.Reader in)
abstract java.util.List<Molecule3D>	AbstractParser.loadGroup(java.lang.String fileName, java.io.Reader in, int from, int to)
java.util.List<Molecule3D>	Mol2FileParser.loadGroup(java.lang.String fileName, java.io.Reader in, int from, int to)

Methods in com.actelion.research.chem.io with parameters of type Molecule3D

Modifier and Type	Method	Description
protected static boolean	AbstractParser.is3D(Molecule3D m)
void	AbstractParser.save(Molecule3D mol, java.io.Writer writer)
void	AbstractParser.save(Molecule3D mol, java.lang.String fileName)
void	Mol2FileParser.save(Molecule3D mol, java.io.Writer writer)

Method parameters in com.actelion.research.chem.io with type arguments of type Molecule3D

Modifier and Type	Method	Description
static void	AbstractParser.convertDataToPrimitiveTypes(java.util.List<Molecule3D> res)
void	AbstractParser.save(java.util.List<Molecule3D> mols, java.io.Writer writer)	If not subclassed, save the files separately
void	AbstractParser.save(java.util.List<Molecule3D> mol, java.lang.String fileName)
void	Mol2FileParser.save(java.util.List<Molecule3D> mols, int chargeType, java.io.Writer writer)	Writes also the partial charges
void	Mol2FileParser.save(java.util.List<Molecule3D> mols, java.io.Writer writer)

Uses of Molecule3D in com.actelion.research.chem.io.pdb.converter

Methods in com.actelion.research.chem.io.pdb.converter that return Molecule3D

Modifier and Type	Method	Description
Molecule3D	AminoAcidLabeled.createResidue(java.util.Map<java.lang.String,AtomRecord> recordMap)

Uses of Molecule3D in com.actelion.research.chem.io.pdb.parser

Methods in com.actelion.research.chem.io.pdb.parser that return Molecule3D

Modifier and Type	Method	Description
Molecule3D	Residue.getMolecule()
Molecule3D	ProteinSynthesizer.retrieveProtein()

Methods in com.actelion.research.chem.io.pdb.parser that return types with arguments of type Molecule3D

Modifier and Type	Method	Description
java.util.Map<java.lang.String,java.util.List<Molecule3D>>	StructureAssembler.assemble()
java.util.Map<java.lang.String,java.util.List<Molecule3D>>	PDBCoordEntryFile.extractMols()

Methods in com.actelion.research.chem.io.pdb.parser with parameters of type Molecule3D

Modifier and Type	Method	Description
boolean	ProteinSynthesizer.addResidue(Molecule3D residue)	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