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 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)
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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 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)
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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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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 separatelyvoid
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 chargesvoid
Mol2FileParser. save(java.util.List<Molecule3D> mols, java.io.Writer writer)
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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)
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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
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