Uses of Class com.actelion.research.chem.StereoMolecule (OpenChemLib 2021.2.0 API)

Packages that use StereoMolecule
Package	Description
com.actelion.research.chem
com.actelion.research.chem.alignment3d
com.actelion.research.chem.conf
com.actelion.research.chem.contrib
com.actelion.research.chem.coords
com.actelion.research.chem.descriptor
com.actelion.research.chem.descriptor.flexophore
com.actelion.research.chem.descriptor.flexophore.generator
com.actelion.research.chem.descriptor.flexophore.redgraph
com.actelion.research.chem.descriptor.pharmacophoregraph
com.actelion.research.chem.descriptor.pharmacophoretree
com.actelion.research.chem.docking
com.actelion.research.chem.docking.scoring
com.actelion.research.chem.docking.scoring.idoscore
com.actelion.research.chem.forcefield
com.actelion.research.chem.forcefield.mmff
com.actelion.research.chem.interactionstatistics
com.actelion.research.chem.io
com.actelion.research.chem.io.pdb.converter
com.actelion.research.chem.mcs
com.actelion.research.chem.name
com.actelion.research.chem.phesa
com.actelion.research.chem.phesa.pharmacophore
com.actelion.research.chem.phesaflex
com.actelion.research.chem.prediction
com.actelion.research.chem.properties.complexity
com.actelion.research.chem.properties.fractaldimension
com.actelion.research.chem.reaction
com.actelion.research.chem.shredder
com.actelion.research.gui
com.actelion.research.gui.clipboard
com.actelion.research.gui.clipboard.external
com.actelion.research.gui.dnd
com.actelion.research.jfx.gui.chem
com.actelion.research.jfx.gui.misc
com.actelion.research.share.gui.editor
com.actelion.research.share.gui.editor.actions
com.actelion.research.share.gui.editor.chem
com.actelion.research.share.gui.editor.geom
com.actelion.research.util
org.openmolecules.chem.conf.gen
org.openmolecules.chem.conf.so

Uses of StereoMolecule in com.actelion.research.chem

Subclasses of StereoMolecule in com.actelion.research.chem
Modifier and Type	Class	Description
`class`	`Molecule3D`
`class`	`SDFileMolecule`

Fields in com.actelion.research.chem declared as StereoMolecule
Modifier and Type	Field	Description
`protected StereoMolecule`	SSSearcher.`mFragment`
`protected StereoMolecule`	SSSearcher.`mMolecule`

Methods in com.actelion.research.chem that return StereoMolecule
Modifier and Type	Method	Description
`StereoMolecule`	TautomerHelper.`createGenericTautomer()`	If no tautomers can be formed then a copy of the original molecule is returned.
`StereoMolecule`	StereoMolecule.`createMolecule(int atoms, int bonds)`
`static StereoMolecule`	ExtendedMoleculeFunctions.`getBiggestFragment(StereoMolecule mol)`
`StereoMolecule`	Canonizer.`getCanMolecule()`
`StereoMolecule`	Canonizer.`getCanMolecule(boolean includeExplicitHydrogen)`
`StereoMolecule`	StereoMolecule.`getCompactCopy()`
`StereoMolecule`	IDCodeParserWithoutCoordinateInvention.`getCompactMolecule(byte[] idcode)`	Creates and returns a molecule from the idcode with its atom and bond arrays being just as large as needed to hold the molecule.
`StereoMolecule`	IDCodeParserWithoutCoordinateInvention.`getCompactMolecule(byte[] idcode, byte[] coordinates)`	Creates and returns a molecule from the idcode with its atom and bond arrays being just as large as needed to hold the molecule.
`StereoMolecule`	IDCodeParserWithoutCoordinateInvention.`getCompactMolecule(byte[] idcode, byte[] coordinates, int idcodeStart, int coordsStart)`
`StereoMolecule`	IDCodeParserWithoutCoordinateInvention.`getCompactMolecule(byte[] idcode, int idcodeStart)`
`StereoMolecule`	IDCodeParserWithoutCoordinateInvention.`getCompactMolecule(java.lang.String idcode)`	Creates and returns a molecule from the idcode with its atom and bond arrays being just as large as needed to hold the molecule.
`StereoMolecule`	IDCodeParserWithoutCoordinateInvention.`getCompactMolecule(java.lang.String idcode, java.lang.String coordinates)`	Creates and returns a molecule from the idcode with its atom and bond arrays being just as large as needed to hold the molecule.
`StereoMolecule`	MolfileParser.`getCompactMolecule(java.io.BufferedReader reader)`
`StereoMolecule`	MolfileParser.`getCompactMolecule(java.io.File file)`
`StereoMolecule`	MolfileParser.`getCompactMolecule(java.lang.String molFile)`
`static StereoMolecule`	ExtendedMoleculeFunctions.`getConverted2CarbonSkeleton(StereoMolecule m)`	Replaces all hetero-atoms, except hydrogen, with carbon.
`StereoMolecule`	MarkushStructure.`getCoreStructure(int no)`
`StereoMolecule[]`	StereoMolecule.`getFragments()`	Separates all disconnected fragments of this Molecule into individual Molecule objects.
`StereoMolecule[]`	StereoMolecule.`getFragments(int[] fragmentNo, int fragmentCount)`	Separates all disconnected fragments of this Molecule into individual molecule objects.
`static StereoMolecule`	SSSearcherWithIndex.`getKeyFragment(int no)`
`StereoMolecule`	ExtendedDepictor.`getMolecule(int i)`
`StereoMolecule`	SSSearcherWithIndex.`getMolecule()`	Returns the most recently defined molecule.
`static StereoMolecule`	ScaffoldHelper.`getMostCentralRingSystem(StereoMolecule mol)`	Creates most central ring system as new StereoMolecule from mol without touching mol.
`static StereoMolecule`	ScaffoldHelper.`getMurckoScaffold(StereoMolecule mol, boolean skeletonOnly)`	Creates Murcko scaffold as new StereoMolecule from mol without touching mol.
`StereoMolecule[]`	Mutator.`getMutatedSet(StereoMolecule mol, int mutationType, boolean regulateSize, int count)`
`StereoMolecule`	MarkushStructure.`getNextEnumeration()`	After calling validate() this method may be called until null is returned to construct one by one a new representation of the Markush structure.
`StereoMolecule`	TautomerHelper.`getNextTautomer(StereoMolecule tautomer)`
`StereoMolecule`	MarkushStructure.`getRGroup(int no)`
`static StereoMolecule`	MoleculeStandardizer.`getStandardized(java.lang.String idcode, java.lang.String coordinates, int mode)`	Under normal circumstances, one should never need to standardize a molecule from an idcode, because molecules should be standardized before generating the canonical encoding.
`StereoMolecule`	StereoIsomerEnumerator.`getStereoIsomer(int index)`	Creates and returns the molecule in a specific atom and bond parity permutation state, i.e.
`static StereoMolecule`	NamedSubstituents.`getSubstituent(java.lang.String name)`
`static StereoMolecule`	ExtendedMoleculeFunctions.`removeSubstructureFromMolecule(StereoMolecule mol, StereoMolecule frag)`
`static StereoMolecule`	ExtendedMoleculeFunctions.`removeSubstructuresFromMolecule(StereoMolecule mol, java.util.List<StereoMolecule> liFragment)`	Deletes the substructures, if found, in the molecule.
`static StereoMolecule`	ExtendedMoleculeFunctions.`removeWildcards(StereoMolecule mol)`

Methods in com.actelion.research.chem that return types with arguments of type StereoMolecule
Modifier and Type	Method	Description
`static java.util.Comparator<StereoMolecule>`	ExtendedMoleculeFunctions.`getComparatorAtomsBonds()`
`static java.util.LinkedList<StereoMolecule>`	ExtendedMoleculeFunctions.`removeSubStructures(java.util.List<StereoMolecule> liInput)`	Removes all molecules that are a substructure of one of the molecules in the input list.

Methods in com.actelion.research.chem with parameters of type StereoMolecule
Modifier and Type	Method	Description
`void`	MarkushStructure.`addCore(StereoMolecule core)`
`void`	MarkushStructure.`addRGroup(StereoMolecule substituents)`	This adds a substituent list representing one R-group as multiple fragments within one StereoMolecule.
`static void`	ExtendedMoleculeFunctions.`analyzeMolecule(StereoMolecule mol)`
`static boolean`	ExtendedMoleculeFunctions.`atomAtomSubStrucMatch(StereoMolecule molecule, int at, StereoMolecule fragment)`
`static boolean`	ExtendedMoleculeFunctions.`checkBiggestFragmentForUnwanted(StereoMolecule mol, java.util.List<java.lang.Integer> liAtomicNo)`
`int[]`	SSSearcherWithIndex.`createIndex(StereoMolecule mol)`
`long[]`	SSSearcherWithIndex.`createLongIndex(StereoMolecule mol)`
`static void`	ScaffoldHelper.`createMostCentralRingSystem(StereoMolecule mol)`	Modifies mol in-place to represent the most central ring system of the original mol.
`static void`	ScaffoldHelper.`createMurckoScaffold(StereoMolecule mol, boolean skeletonOnly)`	Modifies mol in-place to represent the Murcko scaffold from the original mol.
`static int[]`	ExtendedMoleculeFunctions.`extractAromaticRing(StereoMolecule mol, int[] arrIndexAt)`
`static boolean[]`	ScaffoldHelper.`findMostCentralRingSystem(StereoMolecule mol)`	This method flags all atoms that are a member of that ring system in mol, which is most central within this molecule graph.
`static boolean[]`	ScaffoldHelper.`findMurckoScaffold(StereoMolecule mol)`	This method flags all atoms that are a member of the Murcko fragment of mol.
`java.util.ArrayList<Mutation>`	Mutator.`generateMutationList(StereoMolecule mol, int mutationType, boolean regulateSize)`	Creates a list of possible mutations and their probabilities
`static long`	AtomTypeCalculator.`getAtomType(StereoMolecule mol, int atom)`
`static long`	AtomTypeCalculator.`getAtomType(StereoMolecule mol, int atom, int mode)`
`static long`	CanonizerUtil.`getBackboneHash(StereoMolecule m, boolean largestFragmentOnly)`
`double`	MutationBiasProvider.`getBiasFactor(StereoMolecule mutatedMolecule)`
`static StereoMolecule`	ExtendedMoleculeFunctions.`getBiggestFragment(StereoMolecule mol)`
`static java.lang.String`	ExtendedMoleculeFunctions.`getColorVectorSubstructure(StereoMolecule mol, StereoMolecule frag, int atomColor)`	Returns the colors vector for the substructure in mol.
`static StereoMolecule`	ExtendedMoleculeFunctions.`getConverted2CarbonSkeleton(StereoMolecule m)`	Replaces all hetero-atoms, except hydrogen, with carbon.
`static long`	CanonizerUtil.`getHash(StereoMolecule m, CanonizerUtil.IDCODE_TYPE type, boolean largestFragmentOnly)`
`static java.lang.String`	CanonizerUtil.`getIDCode(StereoMolecule mol, CanonizerUtil.IDCODE_TYPE type, boolean largestFragmentOnly)`	Generates an IDCODE for a defined and simplified state of a given molecule.
`static StereoMolecule`	ScaffoldHelper.`getMostCentralRingSystem(StereoMolecule mol)`	Creates most central ring system as new StereoMolecule from mol without touching mol.
`static StereoMolecule`	ScaffoldHelper.`getMurckoScaffold(StereoMolecule mol, boolean skeletonOnly)`	Creates Murcko scaffold as new StereoMolecule from mol without touching mol.
`StereoMolecule[]`	Mutator.`getMutatedSet(StereoMolecule mol, int mutationType, boolean regulateSize, int count)`
`java.lang.String[]`	NastyFunctionDetector.`getNastyFunctionList(StereoMolecule mol, long[] index)`
`java.lang.String`	NastyFunctionDetector.`getNastyFunctionString(StereoMolecule mol, long[] index)`
`static int`	AtomFunctionAnalyzer.`getNegativeNeighbourCount(StereoMolecule mol, int atom)`
`StereoMolecule`	TautomerHelper.`getNextTautomer(StereoMolecule tautomer)`
`static long`	CanonizerUtil.`getNoStereoHash(StereoMolecule m, boolean largestFragmentOnly)`
`static long`	CanonizerUtil.`getNoStereoTautomerHash(StereoMolecule m, boolean largestFragmentOnly)`
`static int`	ExtendedMoleculeFunctions.`getNumAcidicOxygen(StereoMolecule mol)`
`static int`	ExtendedMoleculeFunctions.`getNumAlcoholicOxygen(StereoMolecule mol)`
`static int`	ExtendedMoleculeFunctions.`getNumAmide(StereoMolecule mol)`
`static int`	ExtendedMoleculeFunctions.`getNumArylAmine(StereoMolecule mol)`
`static int`	ExtendedMoleculeFunctions.`getNumBasicNitrogen(StereoMolecule mol)`
`static int[][]`	ExtendedMoleculeFunctions.`getNumberOfBondsBetweenAtoms(StereoMolecule mol, int maxBonds, int[][] dist)`	From Joel Freyss developed for the FFMolecule Computes a matrix of distances between all the atoms in the graph.
`static int`	ExtendedMoleculeFunctions.`getNumCarboxy(StereoMolecule mol)`
`static int`	ExtendedMoleculeFunctions.`getNumCyanoGroups(StereoMolecule mol)`	Counts cyano and iso-cyano
`static int`	ExtendedMoleculeFunctions.`getNumNitroGroupN(StereoMolecule mol)`
`static int`	ExtendedMoleculeFunctions.`getNumSubstructure(StereoMolecule mol, java.lang.String idcodeFragment)`
`static int`	ExtendedMoleculeFunctions.`getNumSulfOxyGroups(StereoMolecule mol)`
`static int`	ExtendedMoleculeFunctions.`getNumThioEther(StereoMolecule mol)`
`static int`	ExtendedMoleculeFunctions.`getNumWildcards(StereoMolecule mol)`
`static float`	ExtendedMoleculeFunctions.`getSimilarity(StereoMolecule m1, StereoMolecule m2, DescriptorHandler dh)`
`static long`	CanonizerUtil.`getTautomerHash(StereoMolecule m, boolean largestFragmentOnly)`
`static int[][]`	ExtendedMoleculeFunctions.`getTopologicalDistanceMatrix(StereoMolecule mol)`
`static boolean`	AtomFunctionAnalyzer.`hasUnbalancedAtomCharge(StereoMolecule mol, int atom)`
`protected void`	IDCodeParser.`inventCoordinates(StereoMolecule mol)`
`protected void`	IDCodeParserWithoutCoordinateInvention.`inventCoordinates(StereoMolecule mol)`
`static boolean`	ExtendedMoleculeFunctions.`isAcceptor(StereoMolecule mol, int atom)`
`static boolean`	AtomFunctionAnalyzer.`isAcidicOxygen(StereoMolecule mol, int atom)`
`static boolean`	AtomFunctionAnalyzer.`isAcidicOxygenAtPhosphoricAcid(StereoMolecule mol, int atom)`
`static boolean`	ExtendedMoleculeFunctions.`isAlcoholicOxygen(StereoMolecule mol, int atom)`
`static boolean`	ExtendedMoleculeFunctions.`isAliphaticAtom(StereoMolecule mol, int atm)`
`static boolean`	AtomFunctionAnalyzer.`isAlkylAmine(StereoMolecule mol, int atom)`
`static boolean`	AtomFunctionAnalyzer.`isAmide(StereoMolecule mol, int atom)`
`static boolean`	AtomFunctionAnalyzer.`isAmine(StereoMolecule mol, int atom)`
`static boolean`	AtomFunctionAnalyzer.`isArylAmine(StereoMolecule mol, int atom)`
`static boolean`	AtomFunctionAnalyzer.`isBasicNitrogen(StereoMolecule mol, int atom)`
`static boolean`	ExtendedMoleculeFunctions.`isCarbonConnected2Hetero(StereoMolecule mol, int atomIndex)`
`static boolean`	ExtendedMoleculeFunctions.`isCarbonOnlyConnected2Hetero(StereoMolecule mol)`
`static boolean`	ExtendedMoleculeFunctions.`isCarbonTwoValencesMinimum(StereoMolecule mol)`
`static boolean`	ExtendedMoleculeFunctions.`isCarboxyC(StereoMolecule mol, int atom)`
`static boolean`	ExtendedMoleculeFunctions.`isConnected2Hetero(StereoMolecule mol, int[] arrAtomIndex)`
`boolean`	StereoIsomerEnumerator.`isCorrectStereoIsomer(StereoMolecule mol, int index)`	Checks, whether the given molecule's atom and bond parities are the expected one's for the given stereo isomer index.
`static boolean`	ExtendedMoleculeFunctions.`isCyanoN(StereoMolecule mol, int atom)`
`static boolean`	ExtendedMoleculeFunctions.`isDonor(StereoMolecule mol, int atom)`
`static boolean`	ExtendedMoleculeFunctions.`isEtherOxygenAtAromatic(StereoMolecule mol, int atom)`
`static boolean`	ExtendedMoleculeFunctions.`isIsolatedCarbon(StereoMolecule mol, int indexAtCentral, int[] arrIndexAt)`
`static boolean`	AtomFunctionAnalyzer.`isMemberOfNitroGroup(StereoMolecule mol, int atom)`
`static boolean`	AtomFunctionAnalyzer.`isNitroGroupN(StereoMolecule mol, int atom)`
`static boolean`	ExtendedMoleculeFunctions.`isRingExclusively(StereoMolecule mol)`
`static boolean`	ExtendedMoleculeFunctions.`isRingInMolecule(StereoMolecule mol)`
`static boolean`	ExtendedMoleculeFunctions.`isSulfoxyGroup(StereoMolecule mol, int atom)`
`static boolean`	ExtendedMoleculeFunctions.`isThioEther(StereoMolecule mol, int atom)`
`static boolean`	ExtendedMoleculeFunctions.`isWildcard(StereoMolecule mol, int atom)`
`static void`	ExtendedMoleculeFunctions.`makeSkeleton(StereoMolecule mol)`
`boolean`	MoleculeFilter.`moleculeQualifies(StereoMolecule mol)`
`boolean`	SubstructureFilter.`moleculeQualifies(StereoMolecule mol)`
`java.util.ArrayList<Mutation>`	Mutator.`mutate(StereoMolecule mol)`	Does an in-place mutation of the molecule allowing any kind of mutation at any of the molecules non-selected atoms aiming for 4-24 non-H atoms with an optimum of 9 atoms.
`java.util.ArrayList<Mutation>`	Mutator.`mutate(StereoMolecule mol, int mutationType, boolean regulateSize)`	Does an in-place mutation of the molecule allowing the defined mutation kinds at any of the molecules unselected atoms.
`void`	Mutator.`mutate(StereoMolecule mol, java.util.ArrayList<Mutation> mutationList)`	Selects a likely mutation from the list, performs the mutation and removes it from the list.
`int`	MoleculeNeutralizer.`neutralizeChargedMolecule(StereoMolecule mol)`	Tries to neutralize all charged atoms of the molecule unless a charged atom has a neighbour atom with opposite charge.
`void`	IDCodeParserWithoutCoordinateInvention.`parse(StereoMolecule mol, byte[] idcode)`	Parses the idcode and populates the given molecule to represent the passed idcode.
`void`	IDCodeParserWithoutCoordinateInvention.`parse(StereoMolecule mol, byte[] idcode, byte[] coordinates)`	Parses the idcode and populates the given molecule to represent the passed idcode.
`void`	IDCodeParserWithoutCoordinateInvention.`parse(StereoMolecule mol, byte[] idcode, byte[] coordinates, int idcodeStart, int coordsStart)`	Parses the idcode and populates the given molecule to represent the passed idcode.
`void`	IDCodeParserWithoutCoordinateInvention.`parse(StereoMolecule mol, byte[] idcode, int idcodeStart)`	Parses the idcode and populates the given molecule to represent the passed idcode.
`void`	IDCodeParserWithoutCoordinateInvention.`parse(StereoMolecule mol, java.lang.String idcode)`	Parses the idcode and populates the given molecule to represent the passed idcode.
`void`	IDCodeParserWithoutCoordinateInvention.`parse(StereoMolecule mol, java.lang.String idcode, java.lang.String coordinates)`	Parses the idcode and populates the given molecule to represent the passed idcode.
`boolean`	MolfileParser.`parse(StereoMolecule m, java.io.BufferedReader rd)`
`boolean`	MolfileParser.`parse(StereoMolecule mol, java.io.File file)`
`boolean`	MolfileParser.`parse(StereoMolecule mol, java.lang.String molFile)`
`boolean`	MolfileParser.`parse(StereoMolecule mol, java.lang.StringBuffer molFile)`
`void`	SmilesParser.`parse(StereoMolecule mol, byte[] smiles)`
`void`	SmilesParser.`parse(StereoMolecule mol, byte[] smiles, boolean createCoordinates, boolean readStereoFeatures)`
`void`	SmilesParser.`parse(StereoMolecule mol, byte[] smiles, int position, int endIndex)`
`void`	SmilesParser.`parse(StereoMolecule mol, byte[] smiles, int position, int endIndex, boolean createCoordinates, boolean readStereoFeatures)`
`void`	SmilesParser.`parse(StereoMolecule mol, java.lang.String smiles)`	Parses the given smiles into the molecule, creates proper atom coordinates to reflect correct double bond geometries and translates tetrahedral and allene parities into up/down-bonds.
`void`	IDCodeParserWithoutCoordinateInvention.`parseCoordinates(byte[] encodedCoords, int coordsStart, StereoMolecule mol, Coordinates[] coords)`	This method parses an id-coordinate string (new format only) and writes the coordinates into a Coordinates array.
`void`	Mutator.`performMutation(StereoMolecule mol, Mutation mutation)`	Performs the given mutation on the molecule, updates atom coordinates, and updates stereo bonds to reflect lost or new stereo centers.
`static void`	AtomTypeCalculator.`printAtomType(StereoMolecule mol, int atom)`
`void`	AtomTypeList.`processMolecule(StereoMolecule mol, java.util.TreeSet<java.lang.String> moleculeCache)`
`static StereoMolecule`	ExtendedMoleculeFunctions.`removeSubstructureFromMolecule(StereoMolecule mol, StereoMolecule frag)`
`static StereoMolecule`	ExtendedMoleculeFunctions.`removeSubstructuresFromMolecule(StereoMolecule mol, java.util.List<StereoMolecule> liFragment)`	Deletes the substructures, if found, in the molecule.
`static StereoMolecule`	ExtendedMoleculeFunctions.`removeWildcards(StereoMolecule mol)`
`void`	MutationBiasProvider.`setBiasReference(StereoMolecule referenceMolecule)`
`static void`	ExtendedMoleculeFunctions.`setColorMCS2Molecule(StereoMolecule mol, StereoMolecule molMCS)`
`static void`	ExtendedMoleculeFunctions.`setColorMolecule(StereoMolecule mol, int[] arrIndexMatch)`
`static void`	ExtendedMoleculeFunctions.`setColorMoleculeFromBondIndex(StereoMolecule mol, int[] arrIndexBonds, int color)`
`static void`	ExtendedMoleculeFunctions.`setCoordinatesNull(StereoMolecule mol)`
`void`	SSSearcher.`setFragment(StereoMolecule fragment)`	Defines the fragment to be used in isFragmentInMolecule(...) or findFragmentInMolecule(...).
`void`	SSSearcherWithIndex.`setFragment(StereoMolecule fragment, int[] index)`	Deprecated.
`void`	SSSearcherWithIndex.`setFragment(StereoMolecule fragment, long[] index)`
`void`	SSSearcher.`setMol(StereoMolecule fragment, StereoMolecule molecule)`	Defines fragment and molecule before calling isFragmentInMolecule(...) or findFragmentInMolecule(...).
`void`	SSSearcher.`setMolecule(StereoMolecule molecule)`	Defines the molecule to be used in isFragmentInMolecule(...) or findFragmentInMolecule(...).
`void`	SSSearcherWithIndex.`setMolecule(StereoMolecule molecule, int[] index)`	Deprecated.
`void`	SSSearcherWithIndex.`setMolecule(StereoMolecule molecule, long[] index)`
`static void`	MoleculeStandardizer.`standardize(StereoMolecule mol, int mode)`
`static java.lang.String`	MolfileV3Creator.`writeCTAB(StereoMolecule mol, double scalingFactor)`

Method parameters in com.actelion.research.chem with type arguments of type StereoMolecule
Modifier and Type	Method	Description
`static java.util.LinkedList<StereoMolecule>`	ExtendedMoleculeFunctions.`removeSubStructures(java.util.List<StereoMolecule> liInput)`	Removes all molecules that are a substructure of one of the molecules in the input list.
`static StereoMolecule`	ExtendedMoleculeFunctions.`removeSubstructuresFromMolecule(StereoMolecule mol, java.util.List<StereoMolecule> liFragment)`	Deletes the substructures, if found, in the molecule.

Constructors in com.actelion.research.chem with parameters of type StereoMolecule
Constructor	Description
`AbstractDepictor(StereoMolecule mol)`
`AbstractDepictor(StereoMolecule mol, int displayMode)`
`Canonizer(StereoMolecule mol)`	Runs a canonicalization procedure for the given molecule that creates unique atom ranks, which takes stereo features, ESR settings and query features into account.
`Canonizer(StereoMolecule mol, int mode)`	Runs a canonicalization procedure for the given molecule that creates unique atom ranks, which takes stereo features, ESR settings and query features into account.
`Depictor(StereoMolecule mol)`
`Depictor(StereoMolecule mol, int displayMode)`
`Depictor2D(StereoMolecule mol)`
`Depictor2D(StereoMolecule mol, int displayMode)`
`ExtendedDepictor(StereoMolecule[] mol, int markushCoreCount, DrawingObjectList drawingObjectList, boolean useGraphics2D)`	Use this constructor for markush structures.
`ExtendedDepictor(StereoMolecule[] mol, DrawingObjectList drawingObjectList, boolean useGraphics2D)`
`ExtendedDepictor(StereoMolecule mol, DrawingObjectList drawingObjectList, boolean useGraphics2D)`
`IsomericSmilesCreator(StereoMolecule mol)`	Creates an IsomericSmilesCreator, which doesn't include atom mapping into generated smiles.
`IsomericSmilesCreator(StereoMolecule mol, boolean includeAtomMapping)`	Creates an IsomericSmilesCreator, which may include atom mapping numbers into generated smiles.
`MarkushStructure(StereoMolecule[] fragment, int coreCount)`
`Molecule3D(StereoMolecule mol)`
`MolfileV3Creator(StereoMolecule mol)`	This creates a new molfile version 3 from the given molecule.
`MolfileV3Creator(StereoMolecule mol, boolean allowScaling)`	This creates a new molfile version 3 from the given molecule.
`MolfileV3Creator(StereoMolecule mol, boolean allowScaling, double scalingFactor, java.lang.StringBuilder builder)`	This creates a new molfile version 3 from the given molecule.
`MolfileV3Creator(StereoMolecule mol, boolean allowScaling, java.lang.StringBuilder builder)`	This creates a new molfile version 3 from the given molecule.
`PropertyCalculator(StereoMolecule mol)`
`StereoIsomerEnumerator(StereoMolecule mol, boolean skipEnantiomers)`	If the passed molecules has stereo-chemically undefined configurations (double bonds, stereo centers) or/and one or more AND/OR groups of defined relative stereo configurations, then it represents multiple stereo isomers.
`SubstructureFilter(StereoMolecule substructure)`
`SVGDepictor(StereoMolecule mol, int displayMode, java.lang.String id)`
`SVGDepictor(StereoMolecule mol, java.lang.String id)`
`TautomerHelper(StereoMolecule mol)`

Uses of StereoMolecule in com.actelion.research.chem.alignment3d

Methods in com.actelion.research.chem.alignment3d with parameters of type StereoMolecule
Modifier and Type	Method	Description
`static double`	PheSAAlignmentOptimizer.`align(PheSAMolecule fitShape, MolecularVolume refVol, MolecularVolume fitVol, StereoMolecule aligned, double ppWeight)`
`static double[]`	PheSAAlignmentOptimizer.`align(PheSAMolecule refShape, PheSAMolecule fitShape, StereoMolecule[] bestAlignment, double ppWeight, boolean optimize)`
`static double`	PheSAAlignmentOptimizer.`alignTwoMolsInPlace(StereoMolecule refMol, StereoMolecule fitMol)`
`static double`	PheSAAlignmentOptimizer.`alignTwoMolsInPlace(StereoMolecule refMol, StereoMolecule fitMol, double ppWeight)`

Uses of StereoMolecule in com.actelion.research.chem.conf

Methods in com.actelion.research.chem.conf that return StereoMolecule
Modifier and Type	Method	Description
`StereoMolecule`	TorsionDetail.`getFragment()`	Returns the direct surrounding of the previously classified rotatable bond.
`StereoMolecule`	Conformer.`getMolecule()`
`StereoMolecule`	Conformer.`toMolecule()`	Copies this Conformer's atom coordinates to the associated molecule.
`StereoMolecule`	Conformer.`toMolecule(StereoMolecule mol)`	Copies this Conformer's atom coordinates to the given molecule.

Methods in com.actelion.research.chem.conf with parameters of type StereoMolecule
Modifier and Type	Method	Description
`float`	MolecularFlexibilityCalculator.`calculateMolecularFlexibility(StereoMolecule mol)`	Calculates a molecular flexibility as a value from 0.0 to 1.0 considering torsion statistics derived from the CSD database (torsion maxima, frequencies, and 50% intervals) of rotatable bonds.
`static double`	TorsionDB.`calculateTorsionExtended(StereoMolecule mol, int[] atom)`	Calculates a signed torsion like calculateTorsion().
`boolean`	TorsionDetail.`classify(StereoMolecule mol, int bond)`	Determines uniquely an identifying name for the rotatable bond and its vicinity.
`void`	Conformer.`copyFrom(StereoMolecule mol)`	Copies the molecule's atom coordinates to this Conformer.
`void`	Conformer.`copyTo(StereoMolecule mol)`	Copies this conformer's atom coordinates to mol.
`static int[]`	TorsionDB.`findRearAtoms(StereoMolecule mol, int[] torsionAtom)`	If the atom sequence contains a straight chain of sp-hybridized atoms, then the atom array contain the first two and last two atoms of a sequence of 2n+4 atoms (n: number of conjugated triple bonds).
`static int`	TorsionDB.`findRotatableBonds(StereoMolecule mol, boolean skipAllRingBonds, boolean[] isRotatableBond)`	Locates all relevant rotatable bonds, i.e.
`static int[]`	TorsionDescriptorHelper.`findRotatableBonds(StereoMolecule mol)`	Calculates an array of all rotatable bonds that can be used multiple times as parameter to calculateDescriptor().
`ConformerSet`	ConformerSetGenerator.`generateConformerSet(StereoMolecule mol)`
`static int`	BondLengthSet.`getAtomPi(StereoMolecule mol, int atom)`	Returns an atom's pi electron count for the purpose of classifying a connected bond to determine its length.
`static int`	BondLengthSet.`getBondID(StereoMolecule mol, int bond)`	Constructs a bond classification index from a specific bond in a molecule.
`static int`	BondLengthSet.`getBondIndex(StereoMolecule mol, int bond)`	Constructs a bond classification ID from a specific bond in a molecule and returns the ID's index in the sorted list of bond length information.
`static float`	BondLengthSet.`getBondLengthFromCovalentRadii(StereoMolecule mol, int bond)`	Returns an estimate of the bond length based on atom and bond characteristics.
`static int[]`	TorsionDB.`getExtendedAtomSequence(StereoMolecule mol, int[] atom)`	If the atom sequence contains a straight chain of sp-hybridized atoms, then the atom array contain the first two and last two atoms of a sequence of 2n+4 atoms (n: number of conjugated triple bonds).
`static float[]`	TorsionRelevanceHelper.`getRelevance(StereoMolecule mol, boolean[] isRotatableBond)`	The relevance of a rotatable bond and its torsion angle for creating substantially different conformers depends on how close the bond is to the center of the molecule.
`static float[]`	TorsionRelevanceHelper.`getRelevance(StereoMolecule mol, int[] rotatableBond)`	The relevance of a rotatable bond and its torsion angle for creating substantially different conformers depends on how close the bond is to the center of the molecule.
`static float[]`	TorsionDescriptor.`getRotatableBondWeights(StereoMolecule mol, int[] rotatableBond)`	The relevance of a rotatable bond and its torsion angle for creating substantially different conformers depends on how close the bond is to the center of the molecule.
`static float`	BondLengthSet.`getStdDevFromCovalentRadii(StereoMolecule mol, int bond)`	Returns an the standard deviation of bond lengths from bonds with similar characteristics from crystallographic data.
`static java.lang.String`	TorsionDB.`getTorsionID(StereoMolecule mol, int bond, int[] torsionAtom, TorsionDetail detail)`	Determines uniquely an identifying name for the rotatable bond and its vicinity.
`static float`	BondLengthSet.`lookupBondLength(StereoMolecule mol, int bond)`	Returns an estimate of the bond length based on atom and bond characteristics.
`static void`	BondRotationHelper.`predictAtomSequence(StereoMolecule mol, int bond, int[] torsionAtoms, int[] rearAtoms)`
`StereoMolecule`	Conformer.`toMolecule(StereoMolecule mol)`	Copies this Conformer's atom coordinates to the given molecule.

Constructors in com.actelion.research.chem.conf with parameters of type StereoMolecule
Constructor	Description
`AtomAssembler(StereoMolecule mol)`
`BondAngleSet(StereoMolecule mol, BondLengthSet set)`	Calculates and caches a list of bond angle estimates for any two neighbours of any atom of the molecule.
`BondLengthSet(StereoMolecule mol)`	Calculates and caches a list of bond length estimates from molecule.
`BondRotationHelper(StereoMolecule mol)`
`Conformer(Conformer c, StereoMolecule mol)`	Use at own risk!! Initializes the conformer as a copy of c but replaces the StereoMolecule by the supplied molecule.
`Conformer(StereoMolecule mol)`	Creates a Conformer, i.e.
`TorsionDescriptorHelper(StereoMolecule mol)`
`TorsionDescriptorHelper(StereoMolecule mol, int[] rotatableBond)`
`TorsionPrediction(StereoMolecule mol, int[] torsionAtom)`

Uses of StereoMolecule in com.actelion.research.chem.contrib

Methods in com.actelion.research.chem.contrib with parameters of type StereoMolecule
Modifier and Type	Method	Description
`static void`	HydrogenHandler.`addImplicitHydrogens(StereoMolecule molecule)`
`static void`	HydrogenHandler.`addImplicitHydrogens(StereoMolecule molecule, int iAtom)`
`static void`	DiastereotopicAtomID.`addMissingChirality(StereoMolecule molecule)`
`static void`	DiastereotopicAtomID.`addMissingChirality(StereoMolecule molecule, int esrType)`	The problem is that sometimes we need to add chiral bond that was not planned because it is the same group This is the case for example for the valine where the 2 C of the methyl groups are diastereotopic
`static java.lang.String[]`	DiastereotopicAtomID.`getAtomIds(StereoMolecule molecule)`
`static java.lang.String[][]`	HoseCodeCreator.`getHoseCodes(StereoMolecule mol, int maxSphereSize, int type)`	This descriptor requires proper up/down bonds, because it encodes stereo parities.
`static int`	HydrogenHandler.`getNumberOfHydrogens(StereoMolecule molecule)`
`static void`	DiastereotopicAtomID.`markDiastereotopicAtoms(StereoMolecule molecule)`	In order to debug we could number the group of diastereotopic atoms
`static java.lang.String`	DiastereotopicAtomID.`test(StereoMolecule molecule)`

Uses of StereoMolecule in com.actelion.research.chem.coords

Methods in com.actelion.research.chem.coords that return StereoMolecule
Modifier and Type	Method	Description
`StereoMolecule`	InventorTemplate.`getFragment()`

Methods in com.actelion.research.chem.coords with parameters of type StereoMolecule
Modifier and Type	Method	Description
`void`	CoordinateInventor.`invent(StereoMolecule mol)`	Creates new atom 2D-coordinates for a molecule or a part of a molecule.
`void`	CoordinateInventor.`invent(StereoMolecule mol, long[] ffp)`	Creates new atom 2D-coordinates for a molecule or a part of a molecule.

Constructors in com.actelion.research.chem.coords with parameters of type StereoMolecule
Constructor	Description
`InventorFragment(StereoMolecule mol, int atoms, int mode)`
`InventorTemplate(StereoMolecule fragment, long[] ffp)`

Uses of StereoMolecule in com.actelion.research.chem.descriptor

Methods in com.actelion.research.chem.descriptor that return types with arguments of type StereoMolecule
Modifier and Type	Method	Description
`DescriptorHandler<int[],StereoMolecule>`	DescriptorHandlerFFP512.`getThreadSafeCopy()`
`DescriptorHandler<int[][],StereoMolecule>`	DescriptorHandlerFunctionalGroups.`getThreadSafeCopy()`
`DescriptorHandler<int[],StereoMolecule>`	DescriptorHandlerHashedCFp.`getThreadSafeCopy()`
`DescriptorHandler<long[],StereoMolecule>`	DescriptorHandlerLongCFP.`getThreadSafeCopy()`
`DescriptorHandler<long[],StereoMolecule>`	DescriptorHandlerLongFFP512.`getThreadSafeCopy()`
`DescriptorHandler<long[],StereoMolecule>`	DescriptorHandlerLongPFP512.`getThreadSafeCopy()`
`DescriptorHandler<int[],StereoMolecule>`	DescriptorHandlerPFP512.`getThreadSafeCopy()`
`DescriptorHandler<byte[],StereoMolecule>`	DescriptorHandlerSkeletonSpheres.`getThreadSafeCopy()`

Methods in com.actelion.research.chem.descriptor with parameters of type StereoMolecule
Modifier and Type	Method	Description
`int[]`	DescriptorHandlerFFP512.`createDescriptor(StereoMolecule mol)`
`int[][]`	DescriptorHandlerFunctionalGroups.`createDescriptor(StereoMolecule mol)`	This descriptor contains non-hashed counts of predefined overlapping small fragments of organic functional groups.
`int[]`	DescriptorHandlerHashedCFp.`createDescriptor(StereoMolecule mol)`	This descriptor requires proper up/down bonds, because it encodes stereo parities.
`long[]`	DescriptorHandlerLongCFP.`createDescriptor(StereoMolecule mol)`	This descriptor requires proper up/down bonds, because it encodes stereo parities.
`long[]`	DescriptorHandlerLongFFP512.`createDescriptor(StereoMolecule mol)`
`long[]`	DescriptorHandlerLongPFP512.`createDescriptor(StereoMolecule mol)`
`int[]`	DescriptorHandlerPFP512.`createDescriptor(StereoMolecule mol)`
`byte[]`	DescriptorHandlerSkeletonSpheres.`createDescriptor(StereoMolecule mol)`	This descriptor requires proper up/down bonds, because it encodes stereo parities.
`MolDistHist`	DescriptorHandlerFlexophore.`createDescriptorSingleConf(StereoMolecule mol)`
`MolDistHistViz`	DescriptorHandlerFlexophore.`createVisualDescriptor(StereoMolecule fragBiggest)`	This descriptor contains the molecule used for construction.
`java.util.BitSet`	FingerPrintGenerator.`getFingerprint(StereoMolecule mol)`	Generates a fingerprint of the default size for the given ExtendedMolecule
`java.util.BitSet`	FingerPrintGenerator.`getFingerprint(StereoMolecule mol, int size)`	Generates the fingerprint of a molecule

Uses of StereoMolecule in com.actelion.research.chem.descriptor.flexophore

Methods in com.actelion.research.chem.descriptor.flexophore with parameters of type StereoMolecule
Modifier and Type	Method	Description
`MolDistHistViz`	IDescriptorHandlerFlexophore.`createVisualDescriptor(StereoMolecule mol)`

Uses of StereoMolecule in com.actelion.research.chem.descriptor.flexophore.generator

Methods in com.actelion.research.chem.descriptor.flexophore.generator with parameters of type StereoMolecule
Modifier and Type	Method	Description
`MolDistHistViz`	CreatorMolDistHistViz.`create(StereoMolecule molOrig)`
`static MolDistHistViz`	FlexophoreCreateFunctions.`createDescriptor(StereoMolecule mol)`
`MolDistHistViz`	CreatorMolDistHistViz.`createFromGivenConformation(StereoMolecule molOrig)`
`MolDistHistViz`	CreatorMolDistHistViz.`createMultipleConformations(StereoMolecule molOrig)`	Conformation generator of Thomas Sander

Uses of StereoMolecule in com.actelion.research.chem.descriptor.flexophore.redgraph

Methods in com.actelion.research.chem.descriptor.flexophore.redgraph with parameters of type StereoMolecule
Modifier and Type	Method	Description
`java.util.List<SubGraphIndices>`	SubGraphExtractor.`extract(StereoMolecule molOrig)`	Delivers a list of indices that describes sub structures of the given molecule.
`java.util.List<SubGraphIndices>`	SubGraphExtractor.`extractAliphaticRingsAndEndStandingAliphaticGroups(StereoMolecule molOrig)`

Uses of StereoMolecule in com.actelion.research.chem.descriptor.pharmacophoregraph

Methods in com.actelion.research.chem.descriptor.pharmacophoregraph that return StereoMolecule
Modifier and Type	Method	Description
`StereoMolecule`	PharmGraphGenerator.`generateDescriptor(StereoMolecule mol)`

Methods in com.actelion.research.chem.descriptor.pharmacophoregraph with parameters of type StereoMolecule
Modifier and Type	Method	Description
`StereoMolecule`	PharmGraphGenerator.`generateDescriptor(StereoMolecule mol)`

Uses of StereoMolecule in com.actelion.research.chem.descriptor.pharmacophoretree

Methods in com.actelion.research.chem.descriptor.pharmacophoretree that return types with arguments of type StereoMolecule
Modifier and Type	Method	Description
`DescriptorHandler<PharmacophoreTree,StereoMolecule>`	DescriptorHandlerPTree.`getThreadSafeCopy()`

Methods in com.actelion.research.chem.descriptor.pharmacophoretree with parameters of type StereoMolecule
Modifier and Type	Method	Description
`PharmacophoreTree`	DescriptorHandlerPTree.`createDescriptor(StereoMolecule mol)`
`static PharmacophoreTree`	PharmacophoreTreeGenerator.`generate(StereoMolecule mol)`
`static PharmacophoreTree`	PharmacophoreTreeGenerator.`generate(StereoMolecule mol, java.util.Map<java.lang.Integer,java.util.List<java.lang.Integer>> atomToNodes, java.util.List<java.util.Set<java.lang.Integer>> rings)`	the parameter rings can be used for fragments/building blocks to submit atoms that will belong to a ring after they react
`static double[]`	PharmacophoreTreeGenerator.`getAtomVolumes(StereoMolecule mol)`

Constructors in com.actelion.research.chem.descriptor.pharmacophoretree with parameters of type StereoMolecule
Constructor	Description
`FeatureCalculator(StereoMolecule mol)`
`IonizableGroupDetector2D(StereoMolecule mol)`

Uses of StereoMolecule in com.actelion.research.chem.docking

Methods in com.actelion.research.chem.docking that return StereoMolecule
Modifier and Type	Method	Description
`StereoMolecule`	DockingEngine.DockingResult.`getPose()`

Methods in com.actelion.research.chem.docking with parameters of type StereoMolecule
Modifier and Type	Method	Description
`DockingEngine.DockingResult`	DockingEngine.`dockMolecule(StereoMolecule mol)`
`static void`	DockingEngine.`getBindingSiteAtoms(StereoMolecule receptor, java.util.Set<java.lang.Integer> bindingSiteAtoms, MoleculeGrid grid, boolean includeHydrogens)`
`static Coordinates`	DockingUtils.`getCOM(StereoMolecule conf)`
`static int[]`	DockingEngine.`getReceptorAtomTypes(StereoMolecule receptor)`
`static void`	DockingUtils.`repairLig(StereoMolecule lig)`

Constructors in com.actelion.research.chem.docking with parameters of type StereoMolecule
Constructor	Description
`DockingEngine(StereoMolecule receptor, StereoMolecule nativeLigand)`
`DockingEngine(StereoMolecule rec, StereoMolecule nativeLig, int mcSteps, int startPositions, DockingEngine.ScoringFunction scoringFunction, DockingEngine.StartPosition startPosition)`
`DockingResult(StereoMolecule pose, double score)`

Uses of StereoMolecule in com.actelion.research.chem.docking.scoring

Methods in com.actelion.research.chem.docking.scoring with parameters of type StereoMolecule
Modifier and Type	Method	Description
`static void`	ChemPLP.`identifyHBondFunctionality(StereoMolecule mol, java.util.Set<java.lang.Integer> acceptors, java.util.Set<java.lang.Integer> donorHs, java.util.Set<java.lang.Integer> donors, java.util.Set<java.lang.Integer> metals, java.util.Set<java.lang.Integer> chargedAcceptors, java.util.Set<java.lang.Integer> chargedDonorHs)`

Constructors in com.actelion.research.chem.docking.scoring with parameters of type StereoMolecule
Constructor	Description
`AbstractScoringEngine(StereoMolecule receptor, java.util.Set<java.lang.Integer> bindingSiteAtoms, MoleculeGrid grid)`
`IdoScore(StereoMolecule receptor, java.util.Set<java.lang.Integer> bindingSiteAtoms, int[] receptorAtomTypes, MoleculeGrid grid)`

Uses of StereoMolecule in com.actelion.research.chem.docking.scoring.idoscore

Constructors in com.actelion.research.chem.docking.scoring.idoscore with parameters of type StereoMolecule
Constructor	Description
`StrainTerm(StereoMolecule mol)`

Uses of StereoMolecule in com.actelion.research.chem.forcefield

Fields in com.actelion.research.chem.forcefield declared as StereoMolecule
Modifier and Type	Field	Description
`protected StereoMolecule`	AbstractForceField.`mMol`

Constructors in com.actelion.research.chem.forcefield with parameters of type StereoMolecule
Constructor	Description
`AbstractForceField(StereoMolecule mol)`

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

Subclasses of StereoMolecule 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 StereoMolecule
Constructor	Description
`ForceFieldMMFF94(StereoMolecule mol, java.lang.String tablename)`	Forcefield constructor.
`ForceFieldMMFF94(StereoMolecule m, java.lang.String tablename, java.util.Map<java.lang.String,java.lang.Object> options)`	Forcefield constructor.
`MMFFMolecule(StereoMolecule mol)`
`PositionConstraint(StereoMolecule mol, double k, double d)`

Uses of StereoMolecule in com.actelion.research.chem.interactionstatistics

Methods in com.actelion.research.chem.interactionstatistics with parameters of type StereoMolecule
Modifier and Type	Method	Description
`static int`	InteractionAtomTypeCalculator.`getAtomType(StereoMolecule mol, int atom)`

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

Methods in com.actelion.research.chem.io that return StereoMolecule
Modifier and Type	Method	Description
`StereoMolecule`	CompoundFileParser.`getMolecule()`	Either this method or getIDCode() and getCoordinates() must be overwritten!!!
`StereoMolecule`	SDFileParser.`getMolecule()`
`StereoMolecule`	RDFileParser.`getNextMolecule()`	RD-files may contains lists of molecules or lists of reactions.

Methods in com.actelion.research.chem.io that return types with arguments of type StereoMolecule
Modifier and Type	Method	Description
`java.util.ArrayList<StereoMolecule>`	CompoundFileHelper.`readStructuresFromFile(boolean readIdentifier)`
`java.util.ArrayList<StereoMolecule>`	CompoundFileHelper.`readStructuresFromFile(java.io.File file, boolean readIdentifier)`

Methods in com.actelion.research.chem.io with parameters of type StereoMolecule
Modifier and Type	Method	Description
`void`	DWARFileCreator.`setRowStructure(StereoMolecule mol, int idcodeColumn, int coordsColumn)`	Calculates the canonical structure representation as idcode from mol and puts it into the given idcodeColumn.

Uses of StereoMolecule in com.actelion.research.chem.io.pdb.converter

Fields in com.actelion.research.chem.io.pdb.converter declared as StereoMolecule
Modifier and Type	Field	Description
`protected StereoMolecule`	MoleculeGrid.`mol`

Methods in com.actelion.research.chem.io.pdb.converter with parameters of type StereoMolecule
Modifier and Type	Method	Description
`static boolean`	BondsCalculator.`aromatize(StereoMolecule mol, java.util.ArrayList<java.lang.Integer>[] atomToRings, RingCollection ringSet, java.util.Set<java.lang.Integer> aromaticAtoms, java.util.Set<java.lang.Integer> aromaticBonds)`
`static boolean`	BondsCalculator.`aromatize(StereoMolecule mol, java.util.Set<java.lang.Integer> aromaticAtoms, java.util.Set<java.lang.Integer> aromaticBonds)`
`static void`	BondsCalculator.`calculateBondOrders(StereoMolecule mol, boolean lenient)`	Calculate the bond orders of the molecule (without knowing the hydrogens).
`static int`	BondsCalculator.`connected(StereoMolecule mol, int a, int atomicNo, int bondOrder)`
`static void`	BondsCalculator.`createBonds(StereoMolecule mol, boolean lenient, java.util.Map<java.lang.Integer,java.lang.String> atomToGroup)`	Calculates the bonds of a molecule by checking the distance between all atoms.
`static double`	GeometryCalculator.`getAngle(StereoMolecule mol, int a1, int a2, int a3)`	Gets the Angle between 3 atoms
`static Coordinates[]`	GeometryCalculator.`getBounds(StereoMolecule molecule)`	Gets the Bounds of a molecule
`static Coordinates`	GeometryCalculator.`getCenterGravity(StereoMolecule mol)`	Gets the center of Gravity of a molecule
`static Coordinates`	GeometryCalculator.`getCoordinates(StereoMolecule mol, int atm)`
`static double`	GeometryCalculator.`getDihedral(StereoMolecule mol, int a1, int a2, int a3, int a4)`	Gets the Dihedral Angle between 4 atoms
`static void`	GeometryCalculator.`translate(StereoMolecule molecule, Coordinates c)`	Translate a Molecule
`void`	MoleculeGrid.`updateGrid(StereoMolecule mol)`

Constructors in com.actelion.research.chem.io.pdb.converter with parameters of type StereoMolecule
Constructor	Description
`AminoAcidLabeled(StereoMolecule mol, java.lang.String name, java.lang.String abbreviation)`
`MoleculeGrid(StereoMolecule mol)`
`MoleculeGrid(StereoMolecule mol, double gridWidth, Coordinates extension)`	Creates the Grid: Complexity O(nAtoms)

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

Methods in com.actelion.research.chem.mcs that return StereoMolecule
Modifier and Type	Method	Description
`StereoMolecule`	MCSFunctions.`getMaximumCommonSubstructure(java.util.List<StereoMolecule> li)`
`StereoMolecule`	MCS.`getMCS()`
`StereoMolecule`	MCSFast.`getMCS()`
`StereoMolecule`	MCSFunctions.`getRemainingStructure(StereoMolecule molProduct, StereoMolecule molEduct1)`

Methods in com.actelion.research.chem.mcs that return types with arguments of type StereoMolecule
Modifier and Type	Method	Description
`java.util.LinkedList<StereoMolecule>`	MCS.`getAllCommonSubstructures()`	All molecules which are sub structures of an other molecule in the list are removed.
`java.util.List<StereoMolecule>`	MCSFast.`getAllCommonSubstructures()`	All molecules which are sub structures of an other molecule in the list are removed.
`java.util.List<StereoMolecule>`	ExhaustiveMCSGeneratorParallel.`process(java.util.List<StereoMolecule> liMol, java.io.File workdir)`

Methods in com.actelion.research.chem.mcs with parameters of type StereoMolecule
Modifier and Type	Method	Description
`static java.lang.String`	ExhaustiveFragmentGeneratorAtoms.`getIdCodeFromFragment(StereoMolecule mol, ListWithIntVec livIndexAtom)`
`StereoMolecule`	MCSFunctions.`getRemainingStructure(StereoMolecule molProduct, StereoMolecule molEduct1)`
`double`	MCSFunctions.`getScore(StereoMolecule mol, StereoMolecule frag)`
`void`	RunBondVector2IdCode.`init(StereoMolecule mol)`
`void`	MCS.`set(StereoMolecule mol, StereoMolecule frag)`	mol should contain equal or more bonds than frag.
`void`	MCS.`set(StereoMolecule mol, StereoMolecule frag, boolean[] excluded)`	mol should contain equal or more bonds than frag.
`void`	MCSFast.`set(StereoMolecule mol, StereoMolecule frag)`
`void`	SubStructSearchBondIndex.`setFragment(StereoMolecule frag)`
`void`	SubStructSearchExhaustiveTreeWalker.`setFragment(StereoMolecule frag)`
`void`	SubStructSearchBondIndex.`setMolecule(StereoMolecule mol)`
`void`	SubStructSearchExhaustiveTreeWalker.`setMolecule(StereoMolecule mol)`

Method parameters in com.actelion.research.chem.mcs with type arguments of type StereoMolecule
Modifier and Type	Method	Description
`StereoMolecule`	MCSFunctions.`getMaximumCommonSubstructure(java.util.List<StereoMolecule> li)`
`void`	ExhaustiveFragmentGeneratorParallizer.`process(Pipeline<StereoMolecule> queuePipe, int maxSizeFrag, boolean cleaveRingBonds, boolean addWildcards)`
`java.util.List<StereoMolecule>`	ExhaustiveMCSGeneratorParallel.`process(java.util.List<StereoMolecule> liMol, java.io.File workdir)`

Constructors in com.actelion.research.chem.mcs with parameters of type StereoMolecule
Constructor	Description
`BondVector2IdCode(StereoMolecule mol)`

Uses of StereoMolecule in com.actelion.research.chem.name

Methods in com.actelion.research.chem.name that return StereoMolecule
Modifier and Type	Method	Description
`static StereoMolecule`	StructureNameResolver.`resolve(java.lang.String name)`
`StereoMolecule`	IStructureNameResolver.`resolveLocal(java.lang.String name)`	Local and typically quick name resolution
`static StereoMolecule`	StructureNameResolver.`resolveLocal(java.lang.String name)`	If a IStructureNameResolver instance was instantiated and given to this class, then that is asked to try to resolve the given chemical name, i.e.
`StereoMolecule`	IStructureNameResolver.`resolveRemote(java.lang.String name)`	Typically remote server based name resolution that requires a network round trip
`static StereoMolecule`	StructureNameResolver.`resolveRemote(java.lang.String name)`	If a IStructureNameResolver instance was instantiated and given to this class, then that is asked to try to resolve the given chemical name, i.e.

Uses of StereoMolecule in com.actelion.research.chem.phesa

Methods in com.actelion.research.chem.phesa that return StereoMolecule
Modifier and Type	Method	Description
`StereoMolecule[][]`	PheSABindingHypothesis.`generate()`
`StereoMolecule`	PheSAMolecule.`getConformer(MolecularVolume molVol)`	Returns the corresponding conformer of a molecular volume
`StereoMolecule`	PheSAAlignment.PheSAResult.`getFitMol()`
`StereoMolecule`	PheSAMolecule.`getMolecule()`
`StereoMolecule[]`	DescriptorHandlerShape.`getPreviousAlignment()`
`StereoMolecule`	PheSAAlignment.PheSAResult.`getRefMol()`

Methods in com.actelion.research.chem.phesa with parameters of type StereoMolecule
Modifier and Type	Method	Description
`PheSAMolecule`	DescriptorHandlerShape.`createDescriptor(StereoMolecule mol)`	the ShapeDescriptor consists of a whole ensemble of MolecularVolumes (MolecularGaussians), obtained from a conformational search algorithm
`static MolecularVolume`	MolecularVolume.`decodeFull(java.lang.String string, StereoMolecule refMol)`
`static void`	PheSAAlignment.`rotateMol(StereoMolecule mol, double[] transform)`
`static void`	PheSAAlignment.`rotateMol(StereoMolecule mol, double[][] m)`
`static void`	PheSAAlignment.`rotateMol(StereoMolecule mol, Matrix rotMat)`
`static void`	PheSAAlignment.`rotateMol(StereoMolecule mol, Quaternion rotor, double[] transl)`
`void`	DescriptorHandlerShape.`setPreviousAlignment(StereoMolecule[] previousAlignment)`
`static void`	PheSAAlignment.`translateMol(StereoMolecule mol, double[] translate)`
`void`	MolecularVolume.`update(StereoMolecule mol)`
`void`	Gaussian3D.`updateCoordinates(StereoMolecule mol)`
`void`	VolumeGaussian.`updateCoordinates(StereoMolecule mol)`

Constructors in com.actelion.research.chem.phesa with parameters of type StereoMolecule
Constructor	Description
`MolecularVolume(StereoMolecule mol)`
`PheSAAlignment(StereoMolecule refMol, StereoMolecule mol)`
`PheSAAlignment(StereoMolecule refMol, StereoMolecule mol, double ppWeight)`
`PheSAMolecule(StereoMolecule mol, MolecularVolume shape)`
`PheSAMolecule(StereoMolecule mol, java.util.ArrayList<MolecularVolume> shape)`
`PheSAResult(StereoMolecule refMol, StereoMolecule fitMol, double sim)`

Constructor parameters in com.actelion.research.chem.phesa with type arguments of type StereoMolecule
Constructor	Description
`PheSABindingHypothesis(java.util.List<StereoMolecule> actives)`
`PheSABindingHypothesis(java.util.List<StereoMolecule> actives, int nProcesses)`

Uses of StereoMolecule in com.actelion.research.chem.phesa.pharmacophore

Methods in com.actelion.research.chem.phesa.pharmacophore with parameters of type StereoMolecule
Modifier and Type	Method	Description
`void`	PPGaussian.`decode(java.lang.String string64, StereoMolecule mol)`
`static AcceptorPoint`	AcceptorPoint.`fromString(java.lang.String ppString, StereoMolecule mol)`
`static AromRingPoint`	AromRingPoint.`fromString(java.lang.String ppString, StereoMolecule mol)`
`static ChargePoint`	ChargePoint.`fromString(java.lang.String ppString, StereoMolecule mol)`
`static DonorPoint`	DonorPoint.`fromString(java.lang.String ppString, StereoMolecule mol)`
`static ExitVectorPoint`	ExitVectorPoint.`fromString(java.lang.String ppString, StereoMolecule mol)`
`static IPharmacophorePoint`	PharmacophorePointFactory.`fromString(java.lang.String ppString, StereoMolecule mol)`
`static PPGaussian`	PPGaussian.`fromString(java.lang.String encodedGaussian, StereoMolecule mol)`
`static java.util.List<IPharmacophorePoint>`	PharmacophoreCalculator.`getPharmacophorePoints(StereoMolecule mol)`
`static boolean`	PharmacophoreCalculator.`isAcceptor(StereoMolecule mol, int a)`
`static boolean`	PharmacophoreCalculator.`isDonorHeavyAtom(StereoMolecule mol, int d)`
`static boolean`	PharmacophoreCalculator.`isDonorHydrogen(StereoMolecule mol, int h)`
`void`	AcceptorPoint.`updateCoordinates(StereoMolecule mol)`
`void`	AromRingPoint.`updateCoordinates(StereoMolecule mol)`
`void`	ChargePoint.`updateCoordinates(StereoMolecule mol)`
`void`	DonorPoint.`updateCoordinates(StereoMolecule mol)`
`void`	ExitVectorPoint.`updateCoordinates(StereoMolecule mol)`
`void`	IPharmacophorePoint.`updateCoordinates(StereoMolecule mol)`
`void`	PPGaussian.`updateCoordinates(StereoMolecule mol)`

Constructors in com.actelion.research.chem.phesa.pharmacophore with parameters of type StereoMolecule
Constructor	Description
`AcceptorPoint(StereoMolecule mol, int a, java.util.List<java.lang.Integer> neighbours, int interactionClass)`
`AcceptorPoint(StereoMolecule mol, int a, java.util.List<java.lang.Integer> neighbours, int interactionClass, int acceptorID)`
`AromRingPoint(StereoMolecule mol, int a, java.util.List<java.lang.Integer> ringAtoms)`
`ChargePoint(StereoMolecule mol, int a, java.util.List<java.lang.Integer> neighbours, int charge)`
`DonorPoint(StereoMolecule mol, int d, int h, int interactionClass)`
`ExitVectorPoint(StereoMolecule mol, int c, int e)`
`IonizableGroupDetector(StereoMolecule mol)`

Uses of StereoMolecule in com.actelion.research.chem.phesaflex

Methods in com.actelion.research.chem.phesaflex with parameters of type StereoMolecule
Modifier and Type	Method	Description
`double`	FlexibleShapeAlignment.`calcMin(StereoMolecule fitMol)`
`void`	FlexibleShapeAlignment.`restrainedRelaxation(StereoMolecule fitMol, double e0)`

Constructors in com.actelion.research.chem.phesaflex with parameters of type StereoMolecule
Constructor	Description
`EvaluableFlexibleOverlap(PheSAAlignment shapeAlign, StereoMolecule refMol, StereoMolecule fitMol, double ppWeight, boolean[] isHydrogen, double[] v, java.util.Map<java.lang.String,java.lang.Object> ffOptions)`
`FlexibleShapeAlignment(StereoMolecule refMol, StereoMolecule fitMol)`
`FlexibleShapeAlignment(StereoMolecule refMol, StereoMolecule fitMol, double ppWeight)`
`FlexibleShapeAlignment(StereoMolecule refMol, StereoMolecule fitMol, MolecularVolume refVol, MolecularVolume fitVol, double ppWeight)`
`MetropolisMonteCarloHelper(StereoMolecule mol)`

Uses of StereoMolecule in com.actelion.research.chem.prediction

Methods in com.actelion.research.chem.prediction with parameters of type StereoMolecule
Modifier and Type	Method	Description
`float`	CLogPPredictor.`assessCLogP(StereoMolecule mol)`	Ambiguous bonds are normalized.
`static float`	FastMolecularComplexityCalculator.`assessComplexity(StereoMolecule mol)`	Ambiguous bonds are normalized.
`double`	DruglikenessPredictor.`assessDruglikeness(StereoMolecule testMolecule, ThreadMaster threadMaster)`
`double`	DruglikenessPredictorWithIndex.`assessDruglikeness(StereoMolecule mol, long[] index, ThreadMaster threadMaster)`
`float`	TotalSurfaceAreaPredictor.`assessNonPolarSurfaceArea(StereoMolecule mol)`	Calculates the topological non-polar surface area (TPSA) of a molecule as a sum of contributions of its non-polar atom-types.
`float`	TotalSurfaceAreaPredictor.`assessPolarSurfaceArea(StereoMolecule mol)`	Calculates the topological polar surface area (TPSA) of a molecule as a sum of contributions of its polar atom-types.
`float`	PolarSurfaceAreaPredictor.`assessPSA(StereoMolecule mol)`	Calculates the topological polar surface area (TPSA) of a molecule as a sum of contributions of its polar atom-types.
`float`	TotalSurfaceAreaPredictor.`assessRelativePolarSurfaceArea(StereoMolecule mol)`	Calculates the relative (fractional) polar surface area from polar and non-polar atom contributions.
`int`	ToxicityPredictor.`assessRisk(StereoMolecule testMolecule, int riskType, ThreadMaster threadMaster)`
`static float`	MolecularShapeCalculator.`assessShape(StereoMolecule mol)`	Returns the number of bonds of the shortest path between those two atoms with the largest topological distance divided by the number of non-hydrogen atoms.
`float`	SolubilityPredictor.`assessSolubility(StereoMolecule mol)`
`float`	TotalSurfaceAreaPredictor.`assessTotalSurfaceArea(StereoMolecule mol)`	Calculates the topological total surface area (TPSA) of a molecule as a sum of contributions of its polar and non-atom-types.
`static float`	MolecularPropertyHelper.`calculateProperty(StereoMolecule mol, int type)`
`void`	CLogPPredictor.`getCLogPIncrements(StereoMolecule mol, float[] increment)`	Normalizes ambiguous bonds and assigns cLogP increments to every atom based on its enhanced atom type.
`ParameterizedStringList`	CLogPPredictor.`getDetail(StereoMolecule mol)`
`ParameterizedStringList`	PolarSurfaceAreaPredictor.`getDetail(StereoMolecule mol)`
`ParameterizedStringList`	SolubilityPredictor.`getDetail(StereoMolecule mol)`
`ParameterizedStringList`	TotalSurfaceAreaPredictor.`getDetail(StereoMolecule mol)`
`ParameterizedStringList`	ToxicityPredictor.`getDetail(StereoMolecule testMolecule, int riskType)`
`java.lang.String`	DruglikenessPredictor.`getDruglikenessString(StereoMolecule testMolecule)`
`int[]`	TotalSurfaceAreaPredictor.`getNonPolarAtomTypeCounts(StereoMolecule mol)`
`int[]`	PolarSurfaceAreaPredictor.`getPolarAtomTypeCounts(StereoMolecule mol)`

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

Methods in com.actelion.research.chem.properties.complexity that return StereoMolecule
Modifier and Type	Method	Description
`StereoMolecule`	ResultFragmentsStatistic.`getMol()`
`StereoMolecule`	SummaryFragments.`getMol()`

Methods in com.actelion.research.chem.properties.complexity with parameters of type StereoMolecule
Modifier and Type	Method	Description
`double`	MolecularComplexityCalculator.`calculate(StereoMolecule mol)`
`ResultFragmentsStatistic`	ExhaustiveFragmentsStatistics.`create(StereoMolecule mol, int maxNumBondsFragmentDesired)`	Creates a list with ModelExhaustiveStatistics.
`static int`	ObjectiveExhaustiveStatistics.`getNeededNumberOfBondsInFragment(StereoMolecule mol)`
`static double`	SymmetryCalculator.`getRatioSymmetricAtoms(StereoMolecule mol)`

Constructors in com.actelion.research.chem.properties.complexity with parameters of type StereoMolecule
Constructor	Description
`ResultFragmentsStatistic(StereoMolecule mol, java.util.List<ModelExhaustiveStatistics> liModelExhaustiveStatistics)`

Uses of StereoMolecule in com.actelion.research.chem.properties.fractaldimension

Constructors in com.actelion.research.chem.properties.fractaldimension with parameters of type StereoMolecule
Constructor	Description
`InputObjectFracDimCalc(StereoMolecule data, long id, java.lang.String smiles)`

Uses of StereoMolecule in com.actelion.research.chem.reaction

Methods in com.actelion.research.chem.reaction that return StereoMolecule
Modifier and Type	Method	Description
`static StereoMolecule[]`	ReactionEncoder.`decodeCatalysts(byte[] rxnBytes)`	Generates an array of all catalysts of the encoded reaction string as bytes.
`static StereoMolecule[]`	ReactionEncoder.`decodeMolecules(byte[] rxnBytes, byte[] coords, byte[] mapping, boolean includeReactants, boolean includeProducts)`	Generates an array of all reactants and/or products of the encoded reaction string as bytes.
`static StereoMolecule[]`	ReactionEncoder.`decodeMolecules(java.lang.String s, boolean includeCoords, boolean includeMapping, boolean includeReactants, boolean includeProducts)`	Generates an array of all reactants and/or products of the encoded reaction string as bytes.
`StereoMolecule`	Reaction.`getCatalyst(int no)`
`StereoMolecule`	Reaction.`getMolecule(int no)`
`StereoMolecule`	Reaction.`getProduct(int no)`
`StereoMolecule[][]`	Reactor.`getProducts()`
`StereoMolecule`	Reaction.`getReactant(int no)`

Methods in com.actelion.research.chem.reaction with parameters of type StereoMolecule
Modifier and Type	Method	Description
`void`	Reaction.`addCatalyst(StereoMolecule catalyst)`
`void`	Reaction.`addCatalyst(StereoMolecule catalyst, int position)`
`void`	Reaction.`addProduct(StereoMolecule product)`
`void`	Reaction.`addProduct(StereoMolecule product, int position)`
`void`	Reaction.`addReactant(StereoMolecule reactant)`
`void`	Reaction.`addReactant(StereoMolecule reactant, int position)`
`void`	Reactor.`setReactant(int no, StereoMolecule reactant)`	Defines a real world reactant.

Constructors in com.actelion.research.chem.reaction with parameters of type StereoMolecule
Constructor	Description
`FunctionalGroupClassifier(StereoMolecule mol)`
`MoleculeAutoMapper(StereoMolecule mol)`
`Reaction(StereoMolecule[] mol, int reactantCount)`

Uses of StereoMolecule in com.actelion.research.chem.shredder

Methods in com.actelion.research.chem.shredder that return StereoMolecule
Modifier and Type	Method	Description
`StereoMolecule`	Fragment.`getMol()`

Methods in com.actelion.research.chem.shredder with parameters of type StereoMolecule
Modifier and Type	Method	Description
`java.util.ArrayList<Fragment3D>`	Fragmenter3D.`getFragments(StereoMolecule mol)`	Applying the constraints passed to the Fragmenter3D constructor, this method shredders the given 3D-molecule and returns all generated 3D-fragments as an ArrayList.
`void`	Fragment.`setMol(StereoMolecule mol)`

Uses of StereoMolecule in com.actelion.research.gui

Methods in com.actelion.research.gui that return StereoMolecule
Modifier and Type	Method	Description
`StereoMolecule`	JStructureView.`getDisplayMolecule()`
`StereoMolecule[]`	JDrawArea.`getFragments()`
`StereoMolecule`	CompoundCollectionModel.`getMolecule(int index)`
`abstract StereoMolecule`	DefaultCompoundCollectionModel.`getMolecule(int index)`
`StereoMolecule`	DefaultCompoundCollectionModel.IDCode.`getMolecule(int index)`
`StereoMolecule`	DefaultCompoundCollectionModel.IDCodeWithName.`getMolecule(int index)`
`StereoMolecule`	DefaultCompoundCollectionModel.Molecule.`getMolecule(int index)`
`StereoMolecule`	DefaultCompoundCollectionModel.Native.`getMolecule(int index)`
`StereoMolecule`	JDrawArea.`getMolecule()`
`StereoMolecule`	JStructureView.`getMolecule()`
`StereoMolecule`	CompoundCollectionModel.`getMoleculeForDisplay(int index)`
`StereoMolecule`	DefaultCompoundCollectionModel.`getMoleculeForDisplay(int index)`
`StereoMolecule`	JDrawDialog.`getStructure()`
`StereoMolecule[]`	JEditableChemistryView.`getStructures()`	If chemistryType is

Methods in com.actelion.research.gui with parameters of type StereoMolecule
Modifier and Type	Method	Description
`void`	CompoundCollectionModel.`addMolecule(int index, StereoMolecule mol)`
`abstract void`	DefaultCompoundCollectionModel.`addMolecule(int index, StereoMolecule mol)`
`void`	DefaultCompoundCollectionModel.IDCode.`addMolecule(int index, StereoMolecule mol)`
`void`	DefaultCompoundCollectionModel.IDCodeWithName.`addMolecule(int index, StereoMolecule mol)`
`void`	DefaultCompoundCollectionModel.Molecule.`addMolecule(int index, StereoMolecule mol)`
`void`	DefaultCompoundCollectionModel.Native.`addMolecule(int index, StereoMolecule mol)`
`void`	JChemistryView.`setContent(StereoMolecule mol)`
`void`	JChemistryView.`setContent(StereoMolecule[] mol)`
`void`	JChemistryView.`setContent(StereoMolecule[] mol, DrawingObjectList drawingObjectList)`
`void`	JChemistryView.`setContent(StereoMolecule mol, DrawingObjectList drawingObjectList)`
`void`	JEditableChemistryView.`setContent(StereoMolecule[] mol)`
`void`	JEditableChemistryView.`setContent(StereoMolecule[] mol, DrawingObjectList drawingObjectList)`
`void`	JDrawArea.`setFragments(StereoMolecule[] fragment)`
`void`	CompoundCollectionModel.`setMolecule(int index, StereoMolecule mol)`
`void`	DefaultCompoundCollectionModel.IDCode.`setMolecule(int index, StereoMolecule mol)`
`void`	DefaultCompoundCollectionModel.IDCodeWithName.`setMolecule(int index, StereoMolecule mol)`
`void`	DefaultCompoundCollectionModel.Molecule.`setMolecule(int index, StereoMolecule mol)`
`void`	DefaultCompoundCollectionModel.Native.`setMolecule(int index, StereoMolecule mol)`
`abstract void`	DefaultCompoundCollectionModel.`setMolecule(int index, StereoMolecule mol)`
`void`	JDrawArea.`setMolecule(StereoMolecule theMolecule)`
`void`	CompoundCollectionPane.`structureChanged(StereoMolecule mol)`
`void`	JStructureView.`structureChanged(StereoMolecule mol)`	Updates the molecule used for display, drag & drop and clipboard transfer.
`void`	JStructureView.`structureChanged(StereoMolecule mol, StereoMolecule displayMol)`	Updates both molecules used for display and for drag & drop/clipboard transfer.
`void`	StructureListener.`structureChanged(StereoMolecule mol)`

Method parameters in com.actelion.research.gui with type arguments of type StereoMolecule
Modifier and Type	Method	Description
`void`	CompoundCollectionModel.`addMoleculeList(java.util.Collection<StereoMolecule> list)`
`void`	DefaultCompoundCollectionModel.`addMoleculeList(java.util.Collection<StereoMolecule> list)`

Constructors in com.actelion.research.gui with parameters of type StereoMolecule
Constructor	Description
`JDrawArea(StereoMolecule mol, int mode)`
`JDrawDialog(java.awt.Dialog owner, StereoMolecule mol)`
`JDrawDialog(java.awt.Dialog owner, StereoMolecule mol, java.lang.String title)`
`JDrawDialog(java.awt.Frame owner, StereoMolecule mol)`
`JDrawDialog(java.awt.Frame owner, StereoMolecule[] mol)`
`JDrawDialog(java.awt.Frame owner, StereoMolecule[] mol, java.lang.String title)`
`JDrawDialog(java.awt.Frame owner, StereoMolecule mol, java.lang.String title)`
`JDrawPanel(StereoMolecule mol)`
`JDrawPanel(StereoMolecule mol, boolean isReaction)`
`JDrawPanel(StereoMolecule mol, int mode)`
`JEditableStructureView(StereoMolecule mol)`
`JEditableStructureView(StereoMolecule mol, int dragAction, int dropAction)`
`JStructureView(StereoMolecule mol)`	This creates a standard structure view where the displayed molecule is used for D&D and clipboard transfer after removing atom colors and bond highlights.
`JStructureView(StereoMolecule mol, int dragAction, int dropAction)`	This creates a standard structure view where the displayed molecule is used for D&D and clipboard transfer after removing atom colors and bond highlights.
`JStructureView(StereoMolecule mol, StereoMolecule displayMol)`	This creates a structure view that distinguishes between displayed molecule and the one being used for D&D and clipboard transfer.
`JStructureView(StereoMolecule mol, StereoMolecule displayMol, int dragAction, int dropAction)`	This creates a structure view that distinguishes between displayed molecule and the one being used for D&D and clipboard transfer.

Uses of StereoMolecule in com.actelion.research.gui.clipboard

Methods in com.actelion.research.gui.clipboard that return StereoMolecule
Modifier and Type	Method	Description
`StereoMolecule`	ClipboardHandler.`pasteMolecule()`	Get one Molecule from the Clipboard.
`StereoMolecule`	ClipboardHandler.`pasteMolecule(boolean prefer2D)`
`StereoMolecule`	IClipboardHandler.`pasteMolecule()`

Methods in com.actelion.research.gui.clipboard that return types with arguments of type StereoMolecule
Modifier and Type	Method	Description
`java.util.ArrayList<StereoMolecule>`	ClipboardHandler.`pasteMolecules()`	Get one or more Molecule(s) from the Clipboard.
`java.util.ArrayList<StereoMolecule>`	IClipboardHandler.`pasteMolecules()`

Methods in com.actelion.research.gui.clipboard with parameters of type StereoMolecule
Modifier and Type	Method	Description
`boolean`	ClipboardHandler.`copyMolecule(StereoMolecule mol)`	Copies a molecule to the clipboard in various formats: ENHMETAFILE with an embedded sketch MDLSK Sketch MDLCT MDL molfile
`boolean`	IClipboardHandler.`copyMolecule(StereoMolecule mol)`

Uses of StereoMolecule in com.actelion.research.gui.clipboard.external

Methods in com.actelion.research.gui.clipboard.external with parameters of type StereoMolecule
Modifier and Type	Method	Description
`byte[]`	ChemDrawCDX.`getChemDrawBuffer(StereoMolecule mol)`

Uses of StereoMolecule in com.actelion.research.gui.dnd

Fields in com.actelion.research.gui.dnd declared as StereoMolecule
Modifier and Type	Field	Description
`protected StereoMolecule`	MoleculeTransferable.`mMol`

Methods in com.actelion.research.gui.dnd that return StereoMolecule
Modifier and Type	Method	Description
`protected StereoMolecule`	MoleculeDropAdapter.`createFromDataFlavor(java.awt.datatransfer.DataFlavor chosen, java.lang.Object o)`
`protected StereoMolecule`	SDFileMoleculeDropAdapter.`createFromDataFlavor(java.awt.datatransfer.DataFlavor chosen, java.lang.Object o)`

Methods in com.actelion.research.gui.dnd with parameters of type StereoMolecule
Modifier and Type	Method	Description
`void`	MoleculeDropAdapter.`onDropMolecule(StereoMolecule m, java.awt.Point pt)`

Constructors in com.actelion.research.gui.dnd with parameters of type StereoMolecule
Constructor	Description
`MoleculeTransferable(StereoMolecule mol)`
`SDFileMoleculeTransferable(StereoMolecule mol, StructureInfo si)`

Uses of StereoMolecule in com.actelion.research.jfx.gui.chem

Methods in com.actelion.research.jfx.gui.chem that return StereoMolecule
Modifier and Type	Method	Description
`StereoMolecule`	MoleculeView.`getValue()`
`StereoMolecule`	MoleculeViewSkin.`getValue()`

Methods in com.actelion.research.jfx.gui.chem that return types with arguments of type StereoMolecule
Modifier and Type	Method	Description
`javafx.beans.property.ObjectProperty<StereoMolecule>`	MoleculeView.`valueProperty()`
`javafx.beans.property.ObjectProperty<StereoMolecule>`	MoleculeViewSkin.`valueProperty()`

Methods in com.actelion.research.jfx.gui.chem with parameters of type StereoMolecule
Modifier and Type	Method	Description
`AbstractDepictor`	MoleculeView.`createDepictor(StereoMolecule value)`
`void`	IMoleculeView.`setMolecule(StereoMolecule mol)`
`void`	MoleculeView.`setMolecule(StereoMolecule r)`
`void`	MoleculeViewSkin.`setMolecule(StereoMolecule mol)`
`void`	MoleculeView.`setValue(StereoMolecule t)`
`void`	MoleculeViewSkin.`setValue(StereoMolecule value)`

Constructors in com.actelion.research.jfx.gui.chem with parameters of type StereoMolecule
Constructor	Description
`JFXCanvasDepictor(StereoMolecule mol)`
`JFXCanvasDepictor(StereoMolecule mol, int mode)`
`MoleculeView(StereoMolecule mol)`

Uses of StereoMolecule in com.actelion.research.jfx.gui.misc

Methods in com.actelion.research.jfx.gui.misc that return StereoMolecule
Modifier and Type	Method	Description
`static StereoMolecule`	ClipboardHelper.`paste()`
`static StereoMolecule`	ClipboardHelper.`readContent(javafx.scene.input.Clipboard clipboard)`

Methods in com.actelion.research.jfx.gui.misc with parameters of type StereoMolecule
Modifier and Type	Method	Description
`static void`	ClipboardHelper.`copy(StereoMolecule mol)`
`static javafx.scene.input.ClipboardContent`	ClipboardHelper.`writeContent(StereoMolecule mol)`
`static javafx.scene.input.ClipboardContent`	ClipboardHelper.`writeContent(StereoMolecule mol, javafx.scene.input.ClipboardContent content)`

Uses of StereoMolecule in com.actelion.research.share.gui.editor

Methods in com.actelion.research.share.gui.editor that return StereoMolecule
Modifier and Type	Method	Description
`StereoMolecule`	Model.`getFragmentAt(java.awt.geom.Point2D pt, boolean includeBond)`
`StereoMolecule[]`	Model.`getFragments()`
`StereoMolecule`	Model.`getMolecule()`
`StereoMolecule`	Model.`getMoleculeAt(java.awt.geom.Point2D pt, boolean includeBond)`
`StereoMolecule`	Model.`getSelectedCopy(StereoMolecule sourceMol)`
`abstract StereoMolecule`	Model.`pasteMolecule(double cx, double cy)`

Methods in com.actelion.research.share.gui.editor with parameters of type StereoMolecule
Modifier and Type	Method	Description
`void`	Model.`addMolecule(StereoMolecule mol, double x, double y)`
`protected abstract AbstractDepictor`	Model.`createDepictor(StereoMolecule stereoMolecule)`
`void`	Model.`deleteMolecule(StereoMolecule tm)`
`StereoMolecule`	Model.`getSelectedCopy(StereoMolecule sourceMol)`
`void`	Model.`setFragments(StereoMolecule[] fragment)`
`void`	Model.`setValue(StereoMolecule value, boolean b)`

Uses of StereoMolecule in com.actelion.research.share.gui.editor.actions

Methods in com.actelion.research.share.gui.editor.actions with parameters of type StereoMolecule
Modifier and Type	Method	Description
`protected void`	DrawAction.`drawAtomHighlight(IDrawContext ctx, StereoMolecule mol, int theAtom)`
`protected void`	DrawAction.`drawAtomKeyStrokes(IDrawContext ctx, StereoMolecule mol, int theAtom)`
`protected void`	DrawAction.`drawBondHighlight(IDrawContext ctx, StereoMolecule mol, int theBond)`
`int`	AtomHighlightAction.`findAtom(StereoMolecule mol, java.awt.geom.Point2D pt)`
`protected void`	DrawAction.`highlightAtom(StereoMolecule mol, int atom)`

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

Fields in com.actelion.research.share.gui.editor.chem declared as StereoMolecule
Modifier and Type	Field	Description
`protected StereoMolecule[]`	AbstractExtendedDepictor.`mMolecule`

Methods in com.actelion.research.share.gui.editor.chem with parameters of type StereoMolecule
Modifier and Type	Method	Description
`abstract AbstractDepictor`	AbstractExtendedDepictor.`createDepictor(StereoMolecule stereoMolecule, boolean mUseGraphics2D, DrawConfig cfg)`

Constructors in com.actelion.research.share.gui.editor.chem with parameters of type StereoMolecule
Constructor	Description
`AbstractExtendedDepictor(StereoMolecule[] mol, int markushCoreCount, java.util.List<IDrawingObject> drawingObjectList, boolean useGraphics2D, DrawConfig cfg)`	Use this constructor for markush structures.
`AbstractExtendedDepictor(StereoMolecule[] mol, java.util.List<IDrawingObject> drawingObjectList, boolean useGraphics2D, DrawConfig cfg)`
`AbstractExtendedDepictor(StereoMolecule mol, java.util.List<IDrawingObject> drawingObjectList, boolean useGraphics2D, DrawConfig cfg)`

Uses of StereoMolecule in com.actelion.research.share.gui.editor.geom

Methods in com.actelion.research.share.gui.editor.geom with parameters of type StereoMolecule
Modifier and Type	Method	Description
`abstract IAtomPropertiesDialog`	GeomFactory.`createAtomPropertiesDialog(StereoMolecule m, int atom)`
`abstract IAtomQueryFeaturesDialog`	GeomFactory.`createAtomQueryFeatureDialog(StereoMolecule mol, int atom, boolean includeReactionHints)`
`abstract IBondQueryFeaturesDialog`	GeomFactory.`createBondFeaturesDialog(StereoMolecule mol, int bond)`
`abstract java.awt.geom.Rectangle2D`	GeomFactory.`getBoundingRect(StereoMolecule m)`

Uses of StereoMolecule in com.actelion.research.util

Methods in com.actelion.research.util with parameters of type StereoMolecule
Modifier and Type	Method	Description
`static boolean`	Sketch.`createMolFromSketchBuffer(StereoMolecule mol, byte[] buffer)`
`static boolean`	Sketch.`createMolFromSketchFile(StereoMolecule mol, java.lang.String szFileName)`

Uses of StereoMolecule in org.openmolecules.chem.conf.gen

Methods in org.openmolecules.chem.conf.gen that return StereoMolecule
Modifier and Type	Method	Description
`StereoMolecule`	ConformerGenerator.`getNextConformerAsMolecule(StereoMolecule mol)`	Creates the next random, likely or systematic new(!) conformer of the molecule that was passed when calling initializeConformers().
`StereoMolecule`	ConformerGenerator.`getOneConformerAsMolecule(StereoMolecule mol)`	Fills all free valences of mol with explicit hydrogens and tries to create a reasonable conformer by starting with the most likely torsion set.

Methods in org.openmolecules.chem.conf.gen with parameters of type StereoMolecule
Modifier and Type	Method	Description
`static void`	ConformerGenerator.`addHydrogenAtoms(StereoMolecule mol)`	Adds explicit hydrogen atoms where they are implicit by filling valences and adapting for atom charges.
`RigidFragment`	RigidFragmentProvider.`createFragment(StereoMolecule mol, int[] fragmentNo, int fragmentIndex)`
`double`	RigidFragmentProvider.`forceFieldMinimize(StereoMolecule mol)`	For using a different forcefield you may override all three forceField...
`StereoMolecule`	ConformerGenerator.`getNextConformerAsMolecule(StereoMolecule mol)`	Creates the next random, likely or systematic new(!) conformer of the molecule that was passed when calling initializeConformers().
`Conformer`	ConformerGenerator.`getOneConformer(StereoMolecule mol)`	Fills all free valences of mol with explicit hydrogens and tries to create a reasonable conformer by starting with the most likely torsion set.
`StereoMolecule`	ConformerGenerator.`getOneConformerAsMolecule(StereoMolecule mol)`	Fills all free valences of mol with explicit hydrogens and tries to create a reasonable conformer by starting with the most likely torsion set.
`protected boolean`	ConformerGenerator.`initialize(StereoMolecule mol, boolean use60degreeSteps)`	Don't call this method directly.
`boolean`	ConformerGenerator.`initializeConformers(StereoMolecule mol)`	One of the initializeConformers() methods needs to be called, before getting individual conformers of the same molecule by getNextConformer().
`boolean`	ConformerGenerator.`initializeConformers(StereoMolecule mol, int strategy, int maxTorsionSets, boolean use60degreeSteps)`	One of the initializeConformers() methods needs to be called, before getting individual conformers of the same molecule by getNextConformer().

Constructors in org.openmolecules.chem.conf.gen with parameters of type StereoMolecule
Constructor	Description
`RotatableBond(StereoMolecule mol, int bond, int[] fragmentNo, int[] disconnectedFragmentNo, int disconnectedFragmentSize, RigidFragment[] fragment, java.util.Random random)`
`RotatableBond(StereoMolecule mol, int bond, int[] fragmentNo, int[] disconnectedFragmentNo, int disconnectedFragmentSize, RigidFragment[] fragment, java.util.Random random, boolean use60degreeSteps)`

Uses of StereoMolecule in org.openmolecules.chem.conf.so

Methods in org.openmolecules.chem.conf.so that return StereoMolecule
Modifier and Type	Method	Description
`StereoMolecule`	ConformationSelfOrganizer.`generateOneConformerInPlace(long randomSeed)`	This convenience method returns the StereoMolecule that has been passed to the constructor after modifying its atom coordinates to reflect the conformer internally created by generateOneConformer().
`StereoMolecule`	ConformationSelfOrganizer.`getMolecule()`

Methods in org.openmolecules.chem.conf.so with parameters of type StereoMolecule
Modifier and Type	Method	Description
`static void`	AxialStereoRule.`calculateRules(java.util.ArrayList<ConformationRule> ruleList, StereoMolecule mol)`
`static void`	DistanceRule.`calculateRules(java.util.ArrayList<ConformationRule> ruleList, StereoMolecule mol)`
`static void`	PlaneRule.`calculateRules(java.util.ArrayList<ConformationRule> ruleList, StereoMolecule mol)`
`static void`	StraightLineRule.`calculateRules(java.util.ArrayList<ConformationRule> ruleList, StereoMolecule mol)`
`static void`	TetrahedralStereoRule.`calculateRules(java.util.ArrayList<ConformationRule> ruleList, StereoMolecule mol)`
`static void`	TorsionRule.`calculateRules(java.util.ArrayList<ConformationRule> ruleList, StereoMolecule mol)`

Constructors in org.openmolecules.chem.conf.so with parameters of type StereoMolecule
Constructor	Description
`AxialStereoRule(StereoMolecule mol, int[] atom, int[] rearArom, boolean isInRing, boolean positiveTorsionWanted)`
`ConformationSelfOrganizer(StereoMolecule mol, boolean keepHydrogen)`	Generates a new ConformationSelfOrganizer from the given molecule.
`PlaneRule(int[] atom, StereoMolecule mol)`
`SelfOrganizedConformer(StereoMolecule mol)`
`TetrahedralStereoRule(StereoMolecule mol, int[] atom)`

Uses of Classcom.actelion.research.chem.StereoMolecule

Uses of StereoMolecule in com.actelion.research.chem

Uses of StereoMolecule in com.actelion.research.chem.alignment3d

Uses of StereoMolecule in com.actelion.research.chem.conf

Uses of StereoMolecule in com.actelion.research.chem.contrib

Uses of StereoMolecule in com.actelion.research.chem.coords

Uses of StereoMolecule in com.actelion.research.chem.descriptor

Uses of StereoMolecule in com.actelion.research.chem.descriptor.flexophore

Uses of StereoMolecule in com.actelion.research.chem.descriptor.flexophore.generator

Uses of StereoMolecule in com.actelion.research.chem.descriptor.flexophore.redgraph

Uses of StereoMolecule in com.actelion.research.chem.descriptor.pharmacophoregraph

Uses of StereoMolecule in com.actelion.research.chem.descriptor.pharmacophoretree

Uses of StereoMolecule in com.actelion.research.chem.docking

Uses of StereoMolecule in com.actelion.research.chem.docking.scoring

Uses of StereoMolecule in com.actelion.research.chem.docking.scoring.idoscore

Uses of StereoMolecule in com.actelion.research.chem.forcefield

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

Uses of StereoMolecule in com.actelion.research.chem.interactionstatistics

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

Uses of StereoMolecule in com.actelion.research.chem.io.pdb.converter

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

Uses of StereoMolecule in com.actelion.research.chem.name

Uses of StereoMolecule in com.actelion.research.chem.phesa

Uses of StereoMolecule in com.actelion.research.chem.phesa.pharmacophore

Uses of StereoMolecule in com.actelion.research.chem.phesaflex

Uses of StereoMolecule in com.actelion.research.chem.prediction

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

Uses of StereoMolecule in com.actelion.research.chem.properties.fractaldimension

Uses of StereoMolecule in com.actelion.research.chem.reaction

Uses of StereoMolecule in com.actelion.research.chem.shredder

Uses of StereoMolecule in com.actelion.research.gui

Uses of StereoMolecule in com.actelion.research.gui.clipboard

Uses of StereoMolecule in com.actelion.research.gui.clipboard.external

Uses of StereoMolecule in com.actelion.research.gui.dnd

Uses of StereoMolecule in com.actelion.research.jfx.gui.chem

Uses of StereoMolecule in com.actelion.research.jfx.gui.misc

Uses of StereoMolecule in com.actelion.research.share.gui.editor

Uses of StereoMolecule in com.actelion.research.share.gui.editor.actions

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

Uses of StereoMolecule in com.actelion.research.share.gui.editor.geom

Uses of StereoMolecule in com.actelion.research.util

Uses of StereoMolecule in org.openmolecules.chem.conf.gen

Uses of StereoMolecule in org.openmolecules.chem.conf.so

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