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

Packages that use Molecule

Package	Description
com.actelion.research.chem
com.actelion.research.chem.descriptor.flexophore.calculator
com.actelion.research.chem.forcefield.mmff
com.actelion.research.chem.io.pdb.converter
com.actelion.research.util

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.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)