Uses of Class
com.actelion.research.chem.Molecule
-
-
Uses of Molecule in com.actelion.research.chem
Subclasses of Molecule in com.actelion.research.chem Modifier and Type Class Description class
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.class
Molecule3D
class
SDFileMolecule
class
StereoMolecule
Fields in com.actelion.research.chem declared as Molecule Modifier and Type Field Description protected Molecule
AtomComparator. mol_
Methods in com.actelion.research.chem with parameters of type Molecule Modifier and Type Method Description int[]
Molecule. addMolecule(Molecule mol)
Copies all atoms and bonds of mol to the end of this Molecule's atom and bond tables.int[]
Molecule. addMolecule(Molecule mol, int atoms, int bonds)
Copies first atoms and first bonds of mol to the end of this Molecule's atom and bond tables.int[]
Molecule. addSubstituent(Molecule substituent, int connectionAtom)
Adds and connects the substituent molecule to the connectionAtom of this molecule.int[]
Molecule. addSubstituent(Molecule substituent, int connectionAtom, boolean encodeRingClosuresInMapNo)
Adds and connects the substituent molecule to the connectionAtom of this molecule.void
DepictorTransformation. applyTo(Molecule m)
int
Molecule. copyAtom(Molecule destMol, int sourceAtom, int esrGroupOffsetAND, int esrGroupOffsetOR)
Creates a new atom in destMol and copies all source atom properties including atom list, custom label, flags, and mapNo to it.int
Molecule3D. copyAtom(Molecule destMol, int sourceAtom, int esrGroupOffsetAND, int esrGroupOffsetOR)
int
Molecule. copyBond(Molecule destMol, int sourceBond, int esrGroupOffsetAND, int esrGroupOffsetOR, int[] atomMap, boolean useBondTypeDelocalized)
int
Molecule. copyBond(Molecule destMol, int sourceBond, int esrGroupOffsetAND, int esrGroupOffsetOR, int destAtom1, int destAtom2, boolean useBondTypeDelocalized)
void
Molecule. copyMolecule(Molecule destMol)
Copies this molecule including parity settings, if valid.void
Molecule. copyMoleculeProperties(Molecule destMol)
Copies name,isFragment,chirality and validity of parity & CIP flags.void
StereoMolecule. copyMoleculeProperties(Molecule destMol)
Copies name, isFragment, chirality.static java.lang.String
ExtendedMoleculeFunctions. getColorRecord(Molecule mol, java.util.Collection<java.lang.Integer> liIndexAtom, int cAtomColor)
static java.lang.String
ExtendedMoleculeFunctions. getColorVal2String(Molecule mol, int indexAtom)
static void
ChemistryHelper. transformMolecule(Molecule m, double offsetx, double offsety, double scale)
static void
ChemistryHelper. transformMolecules(Molecule[] mols, double offsetx, double offsety, double scale)
Constructors in com.actelion.research.chem with parameters of type Molecule Constructor Description ExtendedMolecule(Molecule mol)
SDFileMolecule(Molecule m)
StereoMolecule(Molecule mol)
-
Uses of Molecule in com.actelion.research.chem.descriptor.flexophore.calculator
Methods in com.actelion.research.chem.descriptor.flexophore.calculator with parameters of type Molecule Modifier and Type Method Description static double
GeometryCalculator. getAngle(Molecule mol, int a1, int a2, int a3)
static Coordinates
GeometryCalculator. getCoordinates(Molecule mol, int atm)
-
Uses of Molecule in com.actelion.research.chem.forcefield.mmff
Subclasses of Molecule in com.actelion.research.chem.forcefield.mmff Modifier and Type Class Description class
MMFFMolecule
MMFF molecule is a wrapper class for the ExtendedMolecule. -
Uses of Molecule in com.actelion.research.chem.io.pdb.converter
Methods in com.actelion.research.chem.io.pdb.converter with parameters of type Molecule Modifier and Type Method Description java.util.Set<java.lang.Integer>
MoleculeGrid. getNeighbours(Molecule mol, int atom, double maxDist)
java.util.Set<java.lang.Integer>
MoleculeGrid. getNeighbours(Molecule mol, int atom, double maxDist, boolean enforceDist)
-
Uses of Molecule in com.actelion.research.util
Methods in com.actelion.research.util with parameters of type Molecule Modifier and Type Method Description static byte[]
Sketch. createSketchFromMol(Molecule m)
static boolean
Sketch. writeMolSketchFile(Molecule mol, java.io.OutputStream os)
static boolean
Sketch. writeMolSketchFile(Molecule mol, java.lang.String filename)
-