Uses of Class
com.actelion.research.chem.ExtendedMolecule
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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)
Deprecated.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)
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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()
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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)
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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)
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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)
Deprecated.JAtomQueryFeatureDialog(java.awt.Dialog parent, ExtendedMolecule mol, int atom, boolean includeReactionHints)
Deprecated.JAtomQueryFeatureDialog(java.awt.Frame parent, ExtendedMolecule mol, int atom, boolean includeReactionHints)
Deprecated.JBondQueryFeatureDialog(java.awt.Dialog parent, ExtendedMolecule mol, int bond)
Deprecated.JBondQueryFeatureDialog(java.awt.Frame parent, ExtendedMolecule mol, int bond)
Deprecated. -
Uses of ExtendedMolecule in com.actelion.research.gui.editor
Constructors in com.actelion.research.gui.editor with parameters of type ExtendedMolecule Constructor Description AtomLabelDialogBuilder(GenericDialogHelper dialogHelper, ExtendedMolecule mol, int atom)
AtomQueryFeatureDialogBuilder(GenericDialogHelper dialogHelper, ExtendedMolecule mol, int atom, boolean includeReactionHints)
BondQueryFeatureDialogBuilder(GenericDialogHelper dialogHelper, ExtendedMolecule mol, int bond)
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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)
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