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

Packages that use ExtendedMolecule

Package	Description
com.actelion.research.chem
com.actelion.research.chem.descriptor.flexophore.calculator
com.actelion.research.chem.forcefield.mmff
com.actelion.research.chem.io
com.actelion.research.chem.mcs
com.actelion.research.chem.properties.complexity
com.actelion.research.gui
com.actelion.research.share.gui.editor.chem

Uses of ExtendedMolecule in com.actelion.research.chem

Subclasses of ExtendedMolecule in com.actelion.research.chem

Modifier and Type	Class	Description
class	Molecule3D
class	SDFileMolecule
class	StereoMolecule

Methods in com.actelion.research.chem that return ExtendedMolecule

Modifier and Type	Method	Description
ExtendedMolecule	ExtendedMolecule.getCompactCopy()
ExtendedMolecule	StructureTransferData.getMolecule()
static ExtendedMolecule[]	ChemistryHelper.getProducts(Reaction r)
static ExtendedMolecule[]	ChemistryHelper.getReactants(Reaction r)

Methods in com.actelion.research.chem with parameters of type ExtendedMolecule

Modifier and Type	Method	Description
void	ExtendedMolecule.addFragment(ExtendedMolecule sourceMol, int rootAtom, int[] atomMap)	This adds a fragment from sourceMol to this molecule by first copying rootAtom and then all connected atoms and bonds by traversing the graph breadth first.
static boolean	ExtendedMoleculeFunctions.containsAtLeastOneAtomicNumbersFromHashSet(ExtendedMolecule mol, java.util.HashSet<java.lang.Integer> hsAtomicNo)
static boolean	ExtendedMoleculeFunctions.containsHeteroAtom(ExtendedMolecule mol, int[] arrIndexAt)
static boolean	ExtendedMoleculeFunctions.containsSolelyAtomicNumbersFromHashSet(ExtendedMolecule mol, java.util.HashSet<java.lang.Integer> hsAtomicNo)
void	ExtendedMolecule.copyMoleculeByAtoms(ExtendedMolecule destMol, boolean[] includeAtom, boolean recognizeDelocalizedBonds, int[] atomMap)	Clears destmol and then copies a part of this Molecule into destMol, being defined by a mask of atoms to be included.
int[]	ExtendedMolecule.copyMoleculeByBonds(ExtendedMolecule destMol, boolean[] includeBond, boolean recognizeDelocalizedBonds, int[] atomMap)	Clears destmol and then copies a part of this Molecule into destMol, being defined by a mask of bonds to be included.
static boolean	ExtendedMoleculeFunctions.deleteBond(ExtendedMolecule mol, int atm1, int atm2)
java.lang.String	SmilesCreator.generateSmiles(ExtendedMolecule inMol)	public String generateSmiles (Molecule inMol) Effect on instance variable: -> increment this.mVisitedMolAtoms -> increment this.mDisconnections, if inMol consists of several isolated molecules (or atoms).
static int	ExtendedMoleculeFunctions.getBondNo(ExtendedMolecule mol, int atm1, int atm2)
static int	ExtendedMoleculeFunctions.getBondOrder(ExtendedMolecule mol, int atm1, int atm2)
static int	ExtendedMoleculeFunctions.getBondParity(ExtendedMolecule mol, int atm1, int atm2)
static int	ExtendedMoleculeFunctions.getBondType(ExtendedMolecule mol, int atm1, int atm2)
static java.awt.geom.Rectangle2D.Double	ChemistryHelper.getBoundingRect(ExtendedMolecule m)
static java.awt.geom.Rectangle2D	ChemistryHelper.getBoundingRect(ExtendedMolecule[] mols)
static Coordinates	ExtendedMolecule.getCenterGravity(ExtendedMolecule mol)
static Coordinates	ExtendedMolecule.getCenterGravity(ExtendedMolecule mol, int[] indices)
static double[][]	ExtendedMoleculeFunctions.getDistanceArray(ExtendedMolecule mol)
static int	ExtendedMoleculeFunctions.getNumAliphaticRingAtoms(ExtendedMolecule mol, int atomicNoQuery)
static int	ExtendedMoleculeFunctions.getNumAromaticAtoms(ExtendedMolecule mol)
static int	ExtendedMoleculeFunctions.getNumCarbonAtoms(ExtendedMolecule mol)
static int	ExtendedMoleculeFunctions.getNumHeavyAtoms(ExtendedMolecule mol)
static int	ExtendedMoleculeFunctions.getNumHeteroAromaticAtoms(ExtendedMolecule mol)
static int	ExtendedMoleculeFunctions.getNumHeteroAtoms(ExtendedMolecule mol)
static int	ExtendedMoleculeFunctions.getNumIsopropyl(ExtendedMolecule mol)
static int	ExtendedMoleculeFunctions.getNumQueryAtoms(ExtendedMolecule mol, int[] arrAtomicNoQuery)
int	ExtendedMolecule.getSubstituent(int coreAtom, int firstAtom, boolean[] isMemberAtom, ExtendedMolecule substituent, int[] atomMap)	Determines all atoms of the substituent attached to coreAtom and starting with firstAtom.
static int	ExtendedMoleculeFunctions.getTopologicalDistance(ExtendedMolecule mol, int at1, int at2)
static boolean	ExtendedMoleculeFunctions.isHetero(ExtendedMolecule mol, int indexAtom)
static int	ExtendedMoleculeFunctions.replaceAtoms(ExtendedMolecule[] arr, int atnoOrig, int atnoRpl)
static int	ExtendedMoleculeFunctions.replaceAtoms(ExtendedMolecule mol, int atnoOrig, int atnoRpl)

Constructors in com.actelion.research.chem with parameters of type ExtendedMolecule

Constructor	Description
AromaticityResolver(ExtendedMolecule mol)	Creates a new AromaticityResolver for molecule mol.
CanonizerMesoHelper(ExtendedMolecule mol, int[] canRankWithoutStereo, boolean[] isStereoCenter, byte[] thParity, byte[] ezParity, byte[] thESRType, byte[] thESRGroup, byte[] ezESRType, byte[] ezESRGroup, boolean[] thParityRoundIsOdd, boolean[] ezParityRoundIsOdd, boolean[] esrTypeNeedsNormalization)
MolecularFormula(ExtendedMolecule mol)
MolfileCreator(ExtendedMolecule mol)	This creates a new molfile version 2 from the given molecule.
MolfileCreator(ExtendedMolecule mol, boolean allowScaling)	This creates a new molfile version 2 from the given molecule.
MolfileCreator(ExtendedMolecule mol, boolean allowScaling, double scalingFactor, java.lang.StringBuilder builder)	This creates a new molfile version 2 from the given molecule.
MolfileCreator(ExtendedMolecule mol, boolean allowScaling, java.lang.StringBuilder builder)	This creates a new molfile version 2 from the given molecule.
RingCollection(ExtendedMolecule mol, int mode)	Generates the complete set of small rings, which don't contain metal atoms and have up to 7 members. If mode includes LARGE_RINGS, then it determines for every atom and bond the size of the smallest ring, which they are a member of. If mode includes AROMATICITY then every small ring is checked, whether it is aromatic.
RingCollection(ExtendedMolecule mol, int mode, int maxSmallRingSize)	Generates the complete set of small rings, which don't contain metal atoms and have up to 7 members. If mode includes LARGE_RINGS, then it determines for every atom and bond the size of the smallest ring, which they are a member of. If mode includes AROMATICITY then every small ring is checked, whether it is aromatic.
SimpleCanonizer(ExtendedMolecule mol)
StructureTransferData(ExtendedMolecule mol, StructureInfo si)

Uses of ExtendedMolecule in com.actelion.research.chem.descriptor.flexophore.calculator

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

Modifier and Type	Method	Description
static int[]	StructureCalculator.getHDonorsAcceptors(ExtendedMolecule m)	Returns a array of 2 elements [number of donors, number of acceptors]

Uses of ExtendedMolecule in com.actelion.research.chem.forcefield.mmff

Subclasses of ExtendedMolecule in com.actelion.research.chem.forcefield.mmff

Modifier and Type	Class	Description
class	MMFFMolecule	MMFF molecule is a wrapper class for the ExtendedMolecule.

Constructors in com.actelion.research.chem.forcefield.mmff with parameters of type ExtendedMolecule

Constructor	Description
Vector3(ExtendedMolecule mol, int atom)	Constructs a new vector from the x, y, z coordinates of an atom in a molecule.
Vector3(ExtendedMolecule mol, int atom1, int atom2)	Constructs a vector that represents the line travelling from the position of atom1 to the position of atom2.

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

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

Modifier and Type	Method	Description
java.util.ArrayList<ExtendedMolecule>	NativeMDLReactionReader.getCatalysts()
java.util.ArrayList<ExtendedMolecule>	NativeMDLReactionReader.getSolvents()

Uses of ExtendedMolecule in com.actelion.research.chem.mcs

Methods in com.actelion.research.chem.mcs with parameters of type ExtendedMolecule

Modifier and Type	Method	Description
void	ExhaustiveFragmentGeneratorAtoms.set(ExtendedMolecule mol, int nMaximumFragmentSize)
void	ExhaustiveFragmentGeneratorBonds.set(ExtendedMolecule mol, int nMaximumNumberBonds)

Uses of ExtendedMolecule in com.actelion.research.chem.properties.complexity

Methods in com.actelion.research.chem.properties.complexity with parameters of type ExtendedMolecule

Modifier and Type	Method	Description
void	UniqueFragmentEstimator.set(ExtendedMolecule mol, int nMaximumNumberBonds)

Uses of ExtendedMolecule in com.actelion.research.gui

Constructors in com.actelion.research.gui with parameters of type ExtendedMolecule

Constructor	Description
JAtomLabelDialog(java.awt.Frame owner, ExtendedMolecule mol, int atom)
JAtomQueryFeatureDialog(java.awt.Dialog parent, ExtendedMolecule mol, int atom, boolean includeReactionHints)
JAtomQueryFeatureDialog(java.awt.Frame parent, ExtendedMolecule mol, int atom, boolean includeReactionHints)
JBondQueryFeatureDialog(java.awt.Dialog parent, ExtendedMolecule mol, int bond)
JBondQueryFeatureDialog(java.awt.Frame parent, ExtendedMolecule mol, int bond)

Uses of ExtendedMolecule in com.actelion.research.share.gui.editor.chem

Methods in com.actelion.research.share.gui.editor.chem that return ExtendedMolecule

Modifier and Type	Method	Description
ExtendedMolecule	AbstractExtendedDepictor.getMolecule(int i)