Uses of Class
com.actelion.research.chem.StereoMolecule
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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)
StereoMolecule
SmilesParser. parseMolecule(byte[] smiles)
Convenience method to quickly obtain a StereoMolecule from a SMILES string.StereoMolecule
SmilesParser. parseMolecule(java.lang.String smiles)
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 java.lang.String
IsomericSmilesCreator. createSmarts(StereoMolecule mol)
Convenience method to generate a canonical and isomeric SMILES from a given molecule.static java.lang.String
IsomericSmilesCreator. createSmiles(StereoMolecule mol)
Convenience method to generate a canonical and isomeric SMILES from a given molecule.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 probabilitiesstatic 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-cyanostatic 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)
Standardises a molecule and fixes some structural errors.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)
Deprecated.Depictor(StereoMolecule mol, int displayMode)
Deprecated.Depictor2D(StereoMolecule mol)
Depictor2D(StereoMolecule mol, int displayMode)
ExtendedDepictor(StereoMolecule[] mol, int markushCoreCount, DrawingObjectList drawingObjectList)
Use this constructor for markush structures.ExtendedDepictor(StereoMolecule[] mol, DrawingObjectList drawingObjectList)
ExtendedDepictor(StereoMolecule mol, DrawingObjectList drawingObjectList)
IsomericSmilesCreator(StereoMolecule mol)
Creates an IsomericSmilesCreator, which doesn't include atom mapping into generated smiles.IsomericSmilesCreator(StereoMolecule mol, boolean includeAtomMapping)
Deprecated.IsomericSmilesCreator(StereoMolecule mol, int mode)
Creates an IsomericSmilesCreator with the given mode.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 molecule 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)
SubstructureFilter(StereoMolecule substructure, int matchMode)
SVGDepictor(StereoMolecule mol, int displayMode, java.lang.String id)
SVGDepictor(StereoMolecule mol, java.lang.String id)
TautomerHelper(StereoMolecule mol)
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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 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)
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Uses of StereoMolecule in com.actelion.research.chem.alignment3d.transformation
Methods in com.actelion.research.chem.alignment3d.transformation with parameters of type StereoMolecule Modifier and Type Method Description default void
Transformation. apply(StereoMolecule mol)
void
TransformationSequence. apply(StereoMolecule mol)
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Uses of StereoMolecule in com.actelion.research.chem.chemicalspaces
Methods in com.actelion.research.chem.chemicalspaces with parameters of type StereoMolecule Modifier and Type Method Description static boolean
ChemicalSpaceCreator. matchesReactionRole(Reaction rxn, SSSearcherWithIndex[] searchers, int component, StereoMolecule reactant, long[] index)
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Uses of StereoMolecule in com.actelion.research.chem.chemicalspaces.synthon
Methods in com.actelion.research.chem.chemicalspaces.synthon that return StereoMolecule Modifier and Type Method Description static StereoMolecule
SynthonReactor. react(java.util.List<StereoMolecule> synthons)
Method parameters in com.actelion.research.chem.chemicalspaces.synthon with type arguments of type StereoMolecule Modifier and Type Method Description static StereoMolecule
SynthonReactor. react(java.util.List<StereoMolecule> synthons)
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Uses of StereoMolecule in com.actelion.research.chem.combinatorialspace
Methods in com.actelion.research.chem.combinatorialspace that return StereoMolecule Modifier and Type Method Description StereoMolecule
Synthon. getOrigBB()
StereoMolecule
Synthon. getSynthon()
Constructors in com.actelion.research.chem.combinatorialspace with parameters of type StereoMolecule Constructor Description Synthon(StereoMolecule origBB, StereoMolecule synthon)
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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)
Generates a set of distinct conformers of the canonical largest fragment of the passed molecule.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)
BondRotationHelper(StereoMolecule mol, boolean includeTerminalPolarH)
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)
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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 diastereotopicstatic 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 atomsstatic java.lang.String
DiastereotopicAtomID. test(StereoMolecule molecule)
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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, boolean keepMarkedAtoms)
InventorTemplate(StereoMolecule fragment, long[] ffp, boolean keepAbsoluteOrientation)
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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 ExtendedMoleculejava.util.BitSet
FingerPrintGenerator. getFingerprint(StereoMolecule mol, int size)
Generates the fingerprint of a moleculeMethod parameters in com.actelion.research.chem.descriptor with type arguments of type StereoMolecule Modifier and Type Method Description static <T> T
DescriptorHelper. create(DescriptorHandler<T,StereoMolecule> dh, java.lang.String idcode)
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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)
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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)
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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)
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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 reactstatic 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)
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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 static void
DockingUtils. addImplicitHydrogens(StereoMolecule mol)
static void
DockingUtils. assignLikelyProtonationStates(StereoMolecule mol)
static double
ScoringTask. calcScore(StereoMolecule receptor, int probeAtomType, Coordinates c, int[] receptorAtomTypes)
calculate interaction of probe atom with receptorstatic double
ScoringTask. calcScore(StereoMolecule receptor, StereoMolecule ligand, int[] receptorAtomTypes, int[] ligandAtomTypes)
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. repairMolecule3D(StereoMolecule lig)
void
DockingEngine. setMCSReference(StereoMolecule referencePose)
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)
DockingResult(StereoMolecule pose, double score, java.util.Map<java.lang.String,java.lang.Double> contributions)
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Uses of StereoMolecule in com.actelion.research.chem.docking.receptorpharmacophore
Methods in com.actelion.research.chem.docking.receptorpharmacophore with parameters of type StereoMolecule Modifier and Type Method Description static ShapeVolume
NegativeReceptorImageCreator. create(StereoMolecule lig, StereoMolecule rec, TransformationSequence transformation)
Constructors in com.actelion.research.chem.docking.receptorpharmacophore with parameters of type StereoMolecule Constructor Description NegativeReceptorImage(StereoMolecule ligand, StereoMolecule receptor)
NegativeReceptorImage(StereoMolecule ligand, StereoMolecule receptor, double gridWidth, Coordinates extension)
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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)
ProbeScanning(StereoMolecule receptor, java.util.Set<java.lang.Integer> bindingSiteAtoms, MoleculeGrid grid)
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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)
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Uses of StereoMolecule in com.actelion.research.chem.docking.shape
Methods in com.actelion.research.chem.docking.shape that return types with arguments of type StereoMolecule Modifier and Type Method Description java.util.List<StereoMolecule>
ShapeDocking. dock(StereoMolecule candidate)
Methods in com.actelion.research.chem.docking.shape with parameters of type StereoMolecule Modifier and Type Method Description java.util.List<StereoMolecule>
ShapeDocking. dock(StereoMolecule candidate)
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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)
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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)
MMFFPositionConstraint(StereoMolecule mol, double k, double d)
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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)
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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 atomsstatic Coordinates[]
GeometryCalculator. getBounds(StereoMolecule molecule)
Gets the Bounds of a moleculestatic Coordinates
GeometryCalculator. getCenterGravity(StereoMolecule mol)
Gets the center of Gravity of a moleculestatic 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 atomsstatic void
GeometryCalculator. translate(StereoMolecule molecule, Coordinates c)
Translate a Moleculevoid
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
SubStructSearchExhaustiveTreeWalker. setFragment(StereoMolecule frag)
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)
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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 resolutionstatic 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 tripstatic 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
PheSAMolecule. getConformer(int index)
StereoMolecule
PheSAMolecule. getConformer(MolecularVolume molVol)
Returns the corresponding conformer of a molecular volumeStereoMolecule
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 algorithmvoid
VolumeGaussian. decode(java.lang.String string64, StereoMolecule mol)
static MolecularVolume
MolecularVolume. decodeFull(java.lang.String string, StereoMolecule refMol)
static VolumeGaussian
VolumeGaussian. fromString(java.lang.String encodedGaussian, StereoMolecule mol)
static void
PheSAAlignment. rotateMol(StereoMolecule mol, double[][] m)
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
ShapeVolume. update(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)
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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 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)
Constructors in com.actelion.research.chem.phesa.pharmacophore with parameters of type StereoMolecule Constructor Description ChargedGroupDetector(StereoMolecule mol)
IonizableGroupDetector(StereoMolecule mol)
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Uses of StereoMolecule in com.actelion.research.chem.phesa.pharmacophore.pp
Methods in com.actelion.research.chem.phesa.pharmacophore.pp 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 AliphaticPoint
AliphaticPoint. 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 SimplePharmacophorePoint
SimplePharmacophorePoint. fromString(java.lang.String ppString, StereoMolecule mol)
Constructors in com.actelion.research.chem.phesa.pharmacophore.pp 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)
AliphaticPoint(StereoMolecule mol, int a, java.util.List<java.lang.Integer> atoms)
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)
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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)
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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)
static double
GlobularityCalculator. assessGlobularity(StereoMolecule mol, int maxConformerCount)
Generates conformers from a 2D- or 3D-molecule and then calculates the globularity (flat=0, round=1) from the conformer's atom coordinates.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)
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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)
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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)
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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)
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Uses of StereoMolecule in com.actelion.research.chem.reaction.mapping
Methods in com.actelion.research.chem.reaction.mapping that return StereoMolecule Modifier and Type Method Description StereoMolecule
ChemicalRule. getProduct()
StereoMolecule
SimilarityGraphBasedReactionMapper. getProduct()
StereoMolecule
ChemicalRule. getReactant()
StereoMolecule
SimilarityGraphBasedReactionMapper. getReactant()
Methods in com.actelion.research.chem.reaction.mapping with parameters of type StereoMolecule Modifier and Type Method Description void
ChemicalRule. apply(StereoMolecule reactant, int[] match)
static boolean
SimilarityGraphBasedReactionMapper. hasNonCarbonNeighbour(StereoMolecule mol, int atom)
static boolean
SimilarityGraphBasedReactionMapper. hasNonCarbonNeighbour(StereoMolecule mol, int atom, int notThisAtom)
static boolean
SimilarityGraphBasedReactionMapper. hasOxo(StereoMolecule mol, int atom)
static boolean
SimilarityGraphBasedReactionMapper. hasOxo(StereoMolecule mol, int atom, int notThisAtom)
void
SimilarityGraphBasedReactionMapper. map(StereoMolecule reactant, StereoMolecule product, int[] reactantMapNo, int[] productMapNo)
Entirely maps the given reaction by setting all reactant's and product's mapping numbers.Constructors in com.actelion.research.chem.reaction.mapping with parameters of type StereoMolecule Constructor Description MappingScorer(StereoMolecule reactant, StereoMolecule product)
Instantiates a mapping scorer that judges the quality of a mapping by adding penalties for every bond being broken, created, or changed.ReactionCenterMapper(StereoMolecule reactant, StereoMolecule product, int[] reactantMapNo, int[] productMapNo, int mapNo)
RootAtomPairSource(StereoMolecule reactant, StereoMolecule product, int[] reactantMapNo, int[] productMapNo)
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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)
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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()
Deprecated.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()
Deprecated.StereoMolecule
JStructureView. getMolecule()
StereoMolecule
CompoundCollectionModel. getMoleculeForDisplay(int index)
StereoMolecule
DefaultCompoundCollectionModel. getMoleculeForDisplay(int index)
StereoMolecule
JDrawDialog. getStructure()
Deprecated.StereoMolecule[]
JEditableChemistryView. getStructures()
If chemistryType isMethods 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)
protected JDrawDialog
JEditableChemistryView. createDrawDialog(java.lang.String title, 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)
Deprecated.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)
Deprecated.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)
Deprecated.JDrawDialog(java.awt.Dialog owner, StereoMolecule mol)
Deprecated.JDrawDialog(java.awt.Dialog owner, StereoMolecule[] mol, java.lang.String title, java.awt.Dialog.ModalityType modalityType)
Deprecated.JDrawDialog(java.awt.Dialog owner, StereoMolecule mol, java.awt.Dialog.ModalityType modalityType)
Deprecated.JDrawDialog(java.awt.Dialog owner, StereoMolecule mol, java.lang.String title)
Deprecated.JDrawDialog(java.awt.Dialog owner, StereoMolecule mol, java.lang.String title, java.awt.Dialog.ModalityType modalityType)
Deprecated.JDrawDialog(java.awt.Frame owner, StereoMolecule mol)
Deprecated.JDrawDialog(java.awt.Frame owner, StereoMolecule[] mol)
Deprecated.JDrawDialog(java.awt.Frame owner, StereoMolecule[] mol, java.awt.Dialog.ModalityType modalityType)
Deprecated.JDrawDialog(java.awt.Frame owner, StereoMolecule[] mol, java.lang.String title)
Deprecated.JDrawDialog(java.awt.Frame owner, StereoMolecule[] mol, java.lang.String title, java.awt.Dialog.ModalityType modalityType)
Deprecated.JDrawDialog(java.awt.Frame owner, StereoMolecule mol, java.awt.Dialog.ModalityType modalityType)
Deprecated.JDrawDialog(java.awt.Frame owner, StereoMolecule mol, java.lang.String title)
Deprecated.JDrawDialog(java.awt.Frame owner, StereoMolecule mol, java.lang.String title, java.awt.Dialog.ModalityType modalityType)
Deprecated.JDrawPanel(StereoMolecule mol)
Deprecated.JDrawPanel(StereoMolecule mol, boolean isReaction)
Deprecated.JDrawPanel(StereoMolecule mol, int mode)
Deprecated.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, int smartsMode)
StereoMolecule
IClipboardHandler. pasteMolecule()
StereoMolecule
IClipboardHandler. pasteMolecule(boolean prefer2D, int smartsMode)
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 molfileboolean
IClipboardHandler. copyMolecule(StereoMolecule mol)
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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)
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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)
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Uses of StereoMolecule in com.actelion.research.gui.editor
Methods in com.actelion.research.gui.editor that return StereoMolecule Modifier and Type Method Description StereoMolecule[]
GenericDrawArea. getFragments()
StereoMolecule
GenericDrawArea. getMolecule()
StereoMolecule
SwingEditorDialog. getStructure()
Methods in com.actelion.research.gui.editor with parameters of type StereoMolecule Modifier and Type Method Description boolean
GenericDrawArea. addPastedOrDropped(StereoMolecule mol, java.awt.Point p)
void
GenericDrawArea. setFragments(StereoMolecule[] fragment)
void
GenericDrawArea. setMolecule(StereoMolecule theMolecule)
Constructors in com.actelion.research.gui.editor with parameters of type StereoMolecule Constructor Description GenericDrawArea(StereoMolecule mol, int mode, GenericDialogHelper helper, GenericCanvas canvas)
SwingEditorArea(StereoMolecule mol, int mode)
SwingEditorDialog(java.awt.Dialog owner, StereoMolecule mol)
Creates a modal chemical editor dialog to edit a single molecule, which may, of course, consist of multiple disconnected fragments.SwingEditorDialog(java.awt.Dialog owner, StereoMolecule[] mol, java.awt.Dialog.ModalityType modalityType)
Creates a modal chemical editor dialog to edit multiple molecules in one editor pane.SwingEditorDialog(java.awt.Dialog owner, StereoMolecule mol, java.awt.Dialog.ModalityType modalityType)
Creates a chemical editor dialog to edit a single molecule, which may, of course, consist of multiple disconnected fragments.SwingEditorDialog(java.awt.Frame owner, StereoMolecule mol)
Creates a modal chemical editor dialog to edit a single molecule, which may, of course, consist of multiple disconnected fragments.SwingEditorDialog(java.awt.Frame owner, StereoMolecule[] mol, java.awt.Dialog.ModalityType modalityType)
Creates a modal chemical editor dialog to edit multiple molecules in one editor pane.SwingEditorDialog(java.awt.Frame owner, StereoMolecule mol, java.awt.Dialog.ModalityType modalityType)
Creates a chemical editor dialog to edit a single molecule, which may, of course, consist of multiple disconnected fragments.SwingEditorPanel(StereoMolecule mol)
Creates a chemical editor panel to edit the given molecule.SwingEditorPanel(StereoMolecule[] mol)
Creates a chemical editor panel to edit multiple molecules.SwingEditorPanel(StereoMolecule mol, int mode)
Creates a chemical editor panel to draw a molecule, reaction, or set of molecules, depending on the mode. -
Uses of StereoMolecule in com.actelion.research.gui.generic
Constructors in com.actelion.research.gui.generic with parameters of type StereoMolecule Constructor Description GenericDepictor(StereoMolecule mol)
GenericDepictor(StereoMolecule mol, int displayMode)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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