public class RDKFuncs extends java.lang.Object implements RDKFuncsConstants
M_PI, RDKIT_VERSION
Constructor and Description |
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RDKFuncs() |
Modifier and Type | Method and Description |
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static ROMol |
addHs(ROMol mol)
returns a copy of a molecule with hydrogens added in as explicit Atoms
|
static ROMol |
addHs(ROMol mol,
boolean explicitOnly)
returns a copy of a molecule with hydrogens added in as explicit Atoms
|
static ROMol |
addHs(ROMol mol,
boolean explicitOnly,
boolean addCoords)
returns a copy of a molecule with hydrogens added in as explicit Atoms
|
static ROMol |
addHs(ROMol mol,
boolean explicitOnly,
boolean addCoords,
UInt_Vect onlyOnAtoms) |
static ROMol |
addHs(ROMol mol,
boolean explicitOnly,
boolean addCoords,
UInt_Vect onlyOnAtoms,
boolean addResidueInfo) |
static void |
addHs(RWMol mol) |
static void |
addHs(RWMol mol,
boolean explicitOnly) |
static void |
addHs(RWMol mol,
boolean explicitOnly,
boolean addCoords) |
static void |
addHs(RWMol mol,
boolean explicitOnly,
boolean addCoords,
UInt_Vect onlyOnAtoms) |
static void |
addHs(RWMol mol,
boolean explicitOnly,
boolean addCoords,
UInt_Vect onlyOnAtoms,
boolean addResidueInfo) |
static void |
addRecursiveQueries(ROMol mol,
StringMolMap queries,
java.lang.String propName) |
static void |
addRecursiveQueries(ROMol mol,
StringMolMap queries,
java.lang.String propName,
SWIGTYPE_p_std__vectorT_std__pairT_unsigned_int_std__string_t_t reactantLabels) |
static void |
addRecursiveQueriesToReaction(ChemicalReaction rxn,
StringMolMap queries,
java.lang.String propName) |
static void |
addRecursiveQueriesToReaction(ChemicalReaction rxn,
StringMolMap queries,
java.lang.String propName,
SWIGTYPE_p_std__vectorT_std__vectorT_std__pairT_unsigned_int_std__string_t_t_t reactantLabels) |
static void |
adjustHs(RWMol mol)
adjust the number of implicit and explicit Hs for special cases
|
static ROMol |
adjustQueryProperties(ROMol mol) |
static ROMol |
adjustQueryProperties(ROMol mol,
AdjustQueryParameters params) |
static void |
adjustQueryProperties(RWMol mol) |
static void |
adjustQueryProperties(RWMol mol,
AdjustQueryParameters params) |
static double |
AllBitSimilarity(ExplicitBitVect bv1,
ExplicitBitVect bv2) |
static boolean |
AllProbeBitsMatch(ExplicitBitVect probe,
ExplicitBitVect ref) |
static boolean |
AllProbeBitsMatch(ExplicitBitVect probe,
java.lang.String pkl) |
static boolean |
AllProbeBitsMatch(java.lang.String probe,
java.lang.String ref) |
static void |
assignBWPalette(ColourPalette palette) |
static void |
assignChiralTypesFrom3D(ROMol mol)
Uses a conformer to assign ChiralType to a molecule's atoms.
|
static void |
assignChiralTypesFrom3D(ROMol mol,
int confId)
Uses a conformer to assign ChiralType to a molecule's atoms.
|
static void |
assignChiralTypesFrom3D(ROMol mol,
int confId,
boolean replaceExistingTags)
Uses a conformer to assign ChiralType to a molecule's atoms.
|
static void |
assignChiralTypesFromBondDirs(ROMol mol) |
static void |
assignChiralTypesFromBondDirs(ROMol mol,
int confId) |
static void |
assignChiralTypesFromBondDirs(ROMol mol,
int confId,
boolean replaceExistingTags) |
static void |
assignDefaultPalette(ColourPalette palette) |
static void |
assignRadicals(RWMol mol) |
static void |
assignStereochemistry(ROMol mol)
Assign stereochemistry tags to atoms (i.e.
|
static void |
assignStereochemistry(ROMol mol,
boolean cleanIt)
Assign stereochemistry tags to atoms (i.e.
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static void |
assignStereochemistry(ROMol mol,
boolean cleanIt,
boolean force)
Assign stereochemistry tags to atoms (i.e.
|
static void |
assignStereochemistry(ROMol mol,
boolean cleanIt,
boolean force,
boolean flagPossibleStereoCenters) |
static void |
assignStereochemistryFrom3D(ROMol mol) |
static void |
assignStereochemistryFrom3D(ROMol mol,
int confId) |
static void |
assignStereochemistryFrom3D(ROMol mol,
int confId,
boolean replaceExistingTags) |
static double |
AsymmetricSimilarity(ExplicitBitVect bv1,
ExplicitBitVect bv2) |
static boolean |
atomHasConjugatedBond(Atom at) |
static java.lang.String |
BitVectToFPSText(ExplicitBitVect bv1) |
static java.lang.String |
BitVectToText(ExplicitBitVect bv1) |
static Int_Vect |
bondListFromAtomList(ROMol mol,
Int_Vect atomIds) |
static double |
BraunBlanquetSimilarity(ExplicitBitVect bv1,
ExplicitBitVect bv2) |
static void |
buildDefaultRDKitFingerprintAtomInvariants(ROMol mol,
UInt_Vect lAtomInvariants) |
static double |
calcAMW(ROMol mol) |
static double |
calcAMW(ROMol mol,
boolean onlyHeavy) |
static void |
calcAngleBendGrad(Point3D r,
SWIGTYPE_p_double dist,
SWIGTYPE_p_p_double g,
SWIGTYPE_p_double dE_dTheta,
SWIGTYPE_p_double cosTheta,
SWIGTYPE_p_double sinTheta) |
static double |
calcAngleForceConstant(double theta0,
double bondOrder12,
double bondOrder23,
AtomicParams at1Params,
AtomicParams at2Params,
AtomicParams at3Params) |
static boolean |
CalcBitmapAllProbeBitsMatch(SWIGTYPE_p_unsigned_char probe,
SWIGTYPE_p_unsigned_char ref,
long nBytes) |
static double |
CalcBitmapDice(SWIGTYPE_p_unsigned_char bv1,
SWIGTYPE_p_unsigned_char bv2,
long nBytes) |
static long |
CalcBitmapPopcount(SWIGTYPE_p_unsigned_char bv1,
long nBytes) |
static double |
CalcBitmapTanimoto(SWIGTYPE_p_unsigned_char bv1,
SWIGTYPE_p_unsigned_char bv2,
long nBytes) |
static double |
CalcBitmapTversky(SWIGTYPE_p_unsigned_char bv1,
SWIGTYPE_p_unsigned_char bv2,
long nBytes,
double ca,
double cb) |
static double |
calcBondForceConstant(double restLength,
AtomicParams end1Params,
AtomicParams end2Params) |
static double |
calcBondRestLength(double bondOrder,
AtomicParams end1Params,
AtomicParams end2Params) |
static double |
calcChi0n(ROMol mol) |
static double |
calcChi0n(ROMol mol,
boolean force) |
static double |
calcChi0v(ROMol mol) |
static double |
calcChi0v(ROMol mol,
boolean force) |
static double |
calcChi1n(ROMol mol) |
static double |
calcChi1n(ROMol mol,
boolean force) |
static double |
calcChi1v(ROMol mol) |
static double |
calcChi1v(ROMol mol,
boolean force) |
static double |
calcChi2n(ROMol mol) |
static double |
calcChi2n(ROMol mol,
boolean force) |
static double |
calcChi2v(ROMol mol) |
static double |
calcChi2v(ROMol mol,
boolean force) |
static double |
calcChi3n(ROMol mol) |
static double |
calcChi3n(ROMol mol,
boolean force) |
static double |
calcChi3v(ROMol mol) |
static double |
calcChi3v(ROMol mol,
boolean force) |
static double |
calcChi4n(ROMol mol) |
static double |
calcChi4n(ROMol mol,
boolean force) |
static double |
calcChi4v(ROMol mol) |
static double |
calcChi4v(ROMol mol,
boolean force) |
static double |
calcChiNn(ROMol mol,
long n) |
static double |
calcChiNn(ROMol mol,
long n,
boolean force) |
static double |
calcChiNv(ROMol mol,
long n) |
static double |
calcChiNv(ROMol mol,
long n,
boolean force) |
static Double_Pair |
calcCrippenDescriptors(ROMol mol) |
static Double_Pair |
calcCrippenDescriptors(ROMol mol,
boolean includeHs) |
static Double_Pair |
calcCrippenDescriptors(ROMol mol,
boolean includeHs,
boolean force) |
static Double_Vect |
calcCustomProp_VSA(ROMol mol,
java.lang.String customPropName,
Double_Vect bins) |
static Double_Vect |
calcCustomProp_VSA(ROMol mol,
java.lang.String customPropName,
Double_Vect bins,
boolean force) |
static double |
calcExactMW(ROMol mol) |
static double |
calcExactMW(ROMol mol,
boolean onlyHeavy) |
static double |
calcFractionCSP3(ROMol mol) |
static double |
calcHallKierAlpha(ROMol mol) |
static double |
calcHallKierAlpha(ROMol mol,
Double_Vect atomContribs) |
static SWIGTYPE_p_boost__tupleT_double_double_double_double_t |
calcInversionCoefficientsAndForceConstant(int at2AtomicNum,
boolean isCBoundToO) |
static double |
calcKappa1(ROMol mol) |
static double |
calcKappa2(ROMol mol) |
static double |
calcKappa3(ROMol mol) |
static double |
calcLabuteASA(ROMol mol) |
static double |
calcLabuteASA(ROMol mol,
boolean includeHs) |
static double |
calcLabuteASA(ROMol mol,
boolean includeHs,
boolean force) |
static long |
calcLipinskiHBA(ROMol mol) |
static long |
calcLipinskiHBD(ROMol mol) |
static java.lang.String |
calcMolFormula(ROMol mol) |
static java.lang.String |
calcMolFormula(ROMol mol,
boolean separateIsotopes) |
static java.lang.String |
calcMolFormula(ROMol mol,
boolean separateIsotopes,
boolean abbreviateHIsotopes) |
static double |
calcMolLogP(ROMol mol) |
static double |
calcMolMR(ROMol mol) |
static UInt_Vect |
calcMQNs(ROMol mol) |
static UInt_Vect |
calcMQNs(ROMol mol,
boolean force) |
static double |
calcNonbondedDepth(AtomicParams at1Params,
AtomicParams at2Params) |
static double |
calcNonbondedMinimum(AtomicParams at1Params,
AtomicParams at2Params) |
static long |
calcNumAliphaticCarbocycles(ROMol mol) |
static long |
calcNumAliphaticHeterocycles(ROMol mol) |
static long |
calcNumAliphaticRings(ROMol mol) |
static long |
calcNumAmideBonds(ROMol mol) |
static long |
calcNumAromaticCarbocycles(ROMol mol) |
static long |
calcNumAromaticHeterocycles(ROMol mol) |
static long |
calcNumAromaticRings(ROMol mol) |
static long |
calcNumBridgeheadAtoms(ROMol mol) |
static long |
calcNumBridgeheadAtoms(ROMol mol,
UInt_Vect atoms) |
static long |
calcNumHBA(ROMol mol) |
static long |
calcNumHBD(ROMol mol) |
static long |
calcNumHeteroatoms(ROMol mol) |
static long |
calcNumHeterocycles(ROMol mol) |
static long |
calcNumRings(ROMol mol) |
static long |
calcNumRotatableBonds(ROMol mol) |
static long |
calcNumRotatableBonds(ROMol mol,
boolean strict) |
static long |
calcNumRotatableBonds(ROMol mol,
NumRotatableBondsOptions useStrictDefinition) |
static long |
calcNumSaturatedCarbocycles(ROMol mol) |
static long |
calcNumSaturatedHeterocycles(ROMol mol) |
static long |
calcNumSaturatedRings(ROMol mol) |
static long |
calcNumSpiroAtoms(ROMol mol) |
static long |
calcNumSpiroAtoms(ROMol mol,
UInt_Vect atoms) |
static Int_Vect |
calcPathDiscriminators(ROMol mol,
Int_Vect path) |
static Double_Vect |
calcPEOE_VSA(ROMol mol) |
static Double_Vect |
calcPEOE_VSA(ROMol mol,
Double_Vect bins) |
static Double_Vect |
calcPEOE_VSA(ROMol mol,
Double_Vect bins,
boolean force) |
static Double_Vect |
calcSlogP_VSA(ROMol mol) |
static Double_Vect |
calcSlogP_VSA(ROMol mol,
Double_Vect bins) |
static Double_Vect |
calcSlogP_VSA(ROMol mol,
Double_Vect bins,
boolean force) |
static Double_Vect |
calcSMR_VSA(ROMol mol) |
static Double_Vect |
calcSMR_VSA(ROMol mol,
Double_Vect bins) |
static Double_Vect |
calcSMR_VSA(ROMol mol,
Double_Vect bins,
boolean force) |
static void |
calcTorsionGrad(Point3D r,
Point3D t,
SWIGTYPE_p_double d,
SWIGTYPE_p_p_double g,
SWIGTYPE_p_double sinTerm,
SWIGTYPE_p_double cosPhi) |
static double |
calcTPSA(ROMol mol) |
static double |
calcTPSA(ROMol mol,
boolean force) |
static double |
calcTPSA(ROMol mol,
boolean force,
boolean includeSandP) |
static double |
calculateCosTorsion(Point3D p1,
Point3D p2,
Point3D p3,
Point3D p4) |
static double |
calculateCosY(Point3D iPoint,
Point3D jPoint,
Point3D kPoint,
Point3D lPoint) |
static void |
canonicalizeConformer(Conformer conf) |
static void |
canonicalizeConformer(Conformer conf,
Point3D center) |
static void |
canonicalizeConformer(Conformer conf,
Point3D center,
boolean normalizeCovar) |
static void |
canonicalizeConformer(Conformer conf,
Point3D center,
boolean normalizeCovar,
boolean ignoreHs) |
static void |
canonicalizeFragment(ROMol mol,
int atomIdx,
SWIGTYPE_p_std__vectorT_RDKit__Canon__AtomColors_t colors,
UInt_Vect ranks,
SWIGTYPE_p_std__vectorT_RDKit__Canon__MolStackElem_t molStack) |
static void |
canonicalizeFragment(ROMol mol,
int atomIdx,
SWIGTYPE_p_std__vectorT_RDKit__Canon__AtomColors_t colors,
UInt_Vect ranks,
SWIGTYPE_p_std__vectorT_RDKit__Canon__MolStackElem_t molStack,
SWIGTYPE_p_boost__dynamic_bitsetT_t bondsInPlay) |
static void |
canonicalizeFragment(ROMol mol,
int atomIdx,
SWIGTYPE_p_std__vectorT_RDKit__Canon__AtomColors_t colors,
UInt_Vect ranks,
SWIGTYPE_p_std__vectorT_RDKit__Canon__MolStackElem_t molStack,
SWIGTYPE_p_boost__dynamic_bitsetT_t bondsInPlay,
Str_Vect bondSymbols) |
static void |
canonicalizeFragment(ROMol mol,
int atomIdx,
SWIGTYPE_p_std__vectorT_RDKit__Canon__AtomColors_t colors,
UInt_Vect ranks,
SWIGTYPE_p_std__vectorT_RDKit__Canon__MolStackElem_t molStack,
SWIGTYPE_p_boost__dynamic_bitsetT_t bondsInPlay,
Str_Vect bondSymbols,
boolean doIsomericSmiles) |
static void |
canonicalizeFragment(ROMol mol,
int atomIdx,
SWIGTYPE_p_std__vectorT_RDKit__Canon__AtomColors_t colors,
UInt_Vect ranks,
SWIGTYPE_p_std__vectorT_RDKit__Canon__MolStackElem_t molStack,
SWIGTYPE_p_boost__dynamic_bitsetT_t bondsInPlay,
Str_Vect bondSymbols,
boolean doIsomericSmiles,
boolean doRandom) |
static void |
canonicalizeMol(ROMol mol) |
static void |
canonicalizeMol(ROMol mol,
boolean normalizeCovar) |
static void |
canonicalizeMol(ROMol mol,
boolean normalizeCovar,
boolean ignoreHs) |
static RWMol |
chargeParent(RWMol mol) |
static RWMol |
chargeParent(RWMol mol,
CleanupParameters params) |
static RWMol |
chargeParent(RWMol mol,
CleanupParameters params,
boolean skip_standardize) |
static ROMol |
checkMol(SWIGTYPE_p_int errors,
ROMol inMol) |
static ROMol |
checkMol(SWIGTYPE_p_int errors,
java.lang.String data,
boolean isSmiles) |
static StringInt_Pair |
checkMolString(java.lang.String data,
boolean isSmiles) |
static java.lang.String |
ChemicalReactionToRxnBlock(ChemicalReaction rxn) |
static java.lang.String |
ChemicalReactionToRxnBlock(ChemicalReaction rxn,
boolean separateAgents) |
static ROMol |
ChemicalReactionToRxnMol(ChemicalReaction rxn) |
static java.lang.String |
ChemicalReactionToRxnSmarts(ChemicalReaction rxn) |
static java.lang.String |
ChemicalReactionToRxnSmiles(ChemicalReaction rxn) |
static java.lang.String |
ChemicalReactionToRxnSmiles(ChemicalReaction rxn,
boolean canonical) |
static boolean |
chiralAtomNeedsTagInversion(ROMol mol,
Atom atom,
boolean isAtomFirst,
long numClosures) |
static RWMol |
cleanup(RWMol mol) |
static void |
cleanUp(RWMol mol)
Designed to be called by the sanitizer to handle special cases before anything is done.
|
static RWMol |
cleanup(RWMol mol,
CleanupParameters params) |
static void |
cleanupChirality(RWMol mol) |
static void |
clipToOne(SWIGTYPE_p_double x) |
static void |
closeCheckMolFiles() |
static void |
collectBondsAndAngles(ROMol mol,
Match_Vect bonds,
Int_Vect_Vect angles) |
static ROMol |
combineMols(ROMol mol1,
ROMol mol2) |
static ROMol |
combineMols(ROMol mol1,
ROMol mol2,
Point3D offset) |
static void |
compute2DCoordsForReaction(ChemicalReaction rxn) |
static void |
compute2DCoordsForReaction(ChemicalReaction rxn,
double spacing) |
static void |
compute2DCoordsForReaction(ChemicalReaction rxn,
double spacing,
boolean updateProps) |
static void |
compute2DCoordsForReaction(ChemicalReaction rxn,
double spacing,
boolean updateProps,
boolean canonOrient) |
static void |
compute2DCoordsForReaction(ChemicalReaction rxn,
double spacing,
boolean updateProps,
boolean canonOrient,
long nFlipsPerSample) |
static void |
compute2DCoordsForReaction(ChemicalReaction rxn,
double spacing,
boolean updateProps,
boolean canonOrient,
long nFlipsPerSample,
long nSamples) |
static void |
compute2DCoordsForReaction(ChemicalReaction rxn,
double spacing,
boolean updateProps,
boolean canonOrient,
long nFlipsPerSample,
long nSamples,
int sampleSeed) |
static void |
compute2DCoordsForReaction(ChemicalReaction rxn,
double spacing,
boolean updateProps,
boolean canonOrient,
long nFlipsPerSample,
long nSamples,
int sampleSeed,
boolean permuteDeg4Nodes) |
static double |
computeBalabanJ(ROMol mol)
calculates Balaban's J index for the molecule
|
static double |
computeBalabanJ(ROMol mol,
boolean useBO)
calculates Balaban's J index for the molecule
|
static double |
computeBalabanJ(ROMol mol,
boolean useBO,
boolean force)
calculates Balaban's J index for the molecule
|
static double |
computeBalabanJ(ROMol mol,
boolean useBO,
boolean force,
Int_Vect bondPath)
calculates Balaban's J index for the molecule
|
static double |
computeBalabanJ(ROMol mol,
boolean useBO,
boolean force,
Int_Vect bondPath,
boolean cacheIt)
calculates Balaban's J index for the molecule
|
static double |
computeBalabanJ(SWIGTYPE_p_double distMat,
int nb,
int nAts)
This is an overloaded member function, provided for convenience.
|
static Transform3D |
computeCanonicalTransform(Conformer conf) |
static Transform3D |
computeCanonicalTransform(Conformer conf,
Point3D center) |
static Transform3D |
computeCanonicalTransform(Conformer conf,
Point3D center,
boolean normalizeCovar) |
static Transform3D |
computeCanonicalTransform(Conformer conf,
Point3D center,
boolean normalizeCovar,
boolean ignoreHs) |
static Point3D |
computeCentroid(Conformer conf) |
static Point3D |
computeCentroid(Conformer conf,
boolean ignoreHs) |
static void |
computeDihedral(Point_Vect pos,
long idx1,
long idx2,
long idx3,
long idx4) |
static void |
computeDihedral(Point_Vect pos,
long idx1,
long idx2,
long idx3,
long idx4,
SWIGTYPE_p_double dihedral) |
static void |
computeDihedral(Point_Vect pos,
long idx1,
long idx2,
long idx3,
long idx4,
SWIGTYPE_p_double dihedral,
SWIGTYPE_p_double cosPhi) |
static void |
computeDihedral(Point_Vect pos,
long idx1,
long idx2,
long idx3,
long idx4,
SWIGTYPE_p_double dihedral,
SWIGTYPE_p_double cosPhi,
Point3D r) |
static void |
computeDihedral(Point_Vect pos,
long idx1,
long idx2,
long idx3,
long idx4,
SWIGTYPE_p_double dihedral,
SWIGTYPE_p_double cosPhi,
Point3D r,
Point3D t) |
static void |
computeDihedral(Point_Vect pos,
long idx1,
long idx2,
long idx3,
long idx4,
SWIGTYPE_p_double dihedral,
SWIGTYPE_p_double cosPhi,
Point3D r,
Point3D t,
SWIGTYPE_p_double d) |
static void |
computeDihedral(Point3D p1,
Point3D p2,
Point3D p3,
Point3D p4) |
static void |
computeDihedral(Point3D p1,
Point3D p2,
Point3D p3,
Point3D p4,
SWIGTYPE_p_double dihedral) |
static void |
computeDihedral(Point3D p1,
Point3D p2,
Point3D p3,
Point3D p4,
SWIGTYPE_p_double dihedral,
SWIGTYPE_p_double cosPhi) |
static void |
computeDihedral(Point3D p1,
Point3D p2,
Point3D p3,
Point3D p4,
SWIGTYPE_p_double dihedral,
SWIGTYPE_p_double cosPhi,
Point3D r) |
static void |
computeDihedral(Point3D p1,
Point3D p2,
Point3D p3,
Point3D p4,
SWIGTYPE_p_double dihedral,
SWIGTYPE_p_double cosPhi,
Point3D r,
Point3D t) |
static void |
computeDihedral(Point3D p1,
Point3D p2,
Point3D p3,
Point3D p4,
SWIGTYPE_p_double dihedral,
SWIGTYPE_p_double cosPhi,
Point3D r,
Point3D t,
SWIGTYPE_p_double d) |
static void |
computeDihedral(SWIGTYPE_p_double pos,
long idx1,
long idx2,
long idx3,
long idx4) |
static void |
computeDihedral(SWIGTYPE_p_double pos,
long idx1,
long idx2,
long idx3,
long idx4,
SWIGTYPE_p_double dihedral) |
static void |
computeDihedral(SWIGTYPE_p_double pos,
long idx1,
long idx2,
long idx3,
long idx4,
SWIGTYPE_p_double dihedral,
SWIGTYPE_p_double cosPhi) |
static void |
computeDihedral(SWIGTYPE_p_double pos,
long idx1,
long idx2,
long idx3,
long idx4,
SWIGTYPE_p_double dihedral,
SWIGTYPE_p_double cosPhi,
Point3D r) |
static void |
computeDihedral(SWIGTYPE_p_double pos,
long idx1,
long idx2,
long idx3,
long idx4,
SWIGTYPE_p_double dihedral,
SWIGTYPE_p_double cosPhi,
Point3D r,
Point3D t) |
static void |
computeDihedral(SWIGTYPE_p_double pos,
long idx1,
long idx2,
long idx3,
long idx4,
SWIGTYPE_p_double dihedral,
SWIGTYPE_p_double cosPhi,
Point3D r,
Point3D t,
SWIGTYPE_p_double d) |
static double |
computeDihedralAngle(Point3D pt1,
Point3D pt2,
Point3D pt3,
Point3D pt4) |
static boolean |
computeInitialCoords(DoubleSymmMatrix distmat,
Point_Vect positions) |
static boolean |
computeInitialCoords(DoubleSymmMatrix distmat,
Point_Vect positions,
boolean randNegEig) |
static boolean |
computeInitialCoords(DoubleSymmMatrix distmat,
Point_Vect positions,
boolean randNegEig,
long numZeroFail) |
static boolean |
computeInitialCoords(DoubleSymmMatrix distmat,
Point_Vect positions,
boolean randNegEig,
long numZeroFail,
int seed) |
static boolean |
computeInitialCoords(DoubleSymmMatrix distmat,
Point_Vect positions,
SWIGTYPE_p_RDKit__double_source_type rng) |
static boolean |
computeInitialCoords(DoubleSymmMatrix distmat,
Point_Vect positions,
SWIGTYPE_p_RDKit__double_source_type rng,
boolean randNegEig) |
static boolean |
computeInitialCoords(DoubleSymmMatrix distmat,
Point_Vect positions,
SWIGTYPE_p_RDKit__double_source_type rng,
boolean randNegEig,
long numZeroFail) |
static boolean |
computeRandomCoords(Point_Vect positions,
double boxSize) |
static boolean |
computeRandomCoords(Point_Vect positions,
double boxSize,
int seed) |
static boolean |
computeRandomCoords(Point_Vect positions,
double boxSize,
SWIGTYPE_p_RDKit__double_source_type rng) |
static double |
computeSignedDihedralAngle(Point3D pt1,
Point3D pt2,
Point3D pt3,
Point3D pt4) |
static ForceField |
construct3DForceField(BoundsMatrix mmat,
Point3D_Vect positions,
SWIGTYPE_p_ForceFields__CrystalFF__CrystalFFDetails etkdgDetails) |
static ForceField |
construct3DImproperForceField(BoundsMatrix mmat,
Point3D_Vect positions,
Int_Vect_Vect improperAtoms,
Int_Vect atomNums) |
static ForceField |
constructPlain3DForceField(BoundsMatrix mmat,
Point3D_Vect positions,
SWIGTYPE_p_ForceFields__CrystalFF__CrystalFFDetails etkdgDetails) |
static void |
contourAndDrawGaussians(MolDraw2D drawer,
SWIGTYPE_p_std__vectorT_RDGeom__Point2D_t locs,
Double_Vect heights,
Double_Vect widths) |
static void |
contourAndDrawGaussians(MolDraw2D drawer,
SWIGTYPE_p_std__vectorT_RDGeom__Point2D_t locs,
Double_Vect heights,
Double_Vect widths,
long nContours) |
static void |
contourAndDrawGaussians(MolDraw2D drawer,
SWIGTYPE_p_std__vectorT_RDGeom__Point2D_t locs,
Double_Vect heights,
Double_Vect widths,
long nContours,
ContourParams ps) |
static void |
contourAndDrawGaussians(MolDraw2D drawer,
SWIGTYPE_p_std__vectorT_RDGeom__Point2D_t locs,
Double_Vect heights,
Double_Vect widths,
long nContours,
Double_Vect levels) |
static void |
contourAndDrawGaussians(MolDraw2D drawer,
SWIGTYPE_p_std__vectorT_RDGeom__Point2D_t locs,
Double_Vect heights,
Double_Vect widths,
long nContours,
Double_Vect levels,
ContourParams ps) |
static void |
contourAndDrawGrid(MolDraw2D drawer,
SWIGTYPE_p_double grid,
Double_Vect xcoords,
Double_Vect ycoords) |
static void |
contourAndDrawGrid(MolDraw2D drawer,
SWIGTYPE_p_double grid,
Double_Vect xcoords,
Double_Vect ycoords,
long nContours) |
static void |
contourAndDrawGrid(MolDraw2D drawer,
SWIGTYPE_p_double grid,
Double_Vect xcoords,
Double_Vect ycoords,
long nContours,
ContourParams ps) |
static void |
contourAndDrawGrid(MolDraw2D drawer,
SWIGTYPE_p_double grid,
Double_Vect xcoords,
Double_Vect ycoords,
long nContours,
Double_Vect levels) |
static void |
contourAndDrawGrid(MolDraw2D drawer,
SWIGTYPE_p_double grid,
Double_Vect xcoords,
Double_Vect ycoords,
long nContours,
Double_Vect levels,
ContourParams ps) |
static void |
convertToBonds(Int_Vect_Vect res,
Int_Vect_Vect brings,
ROMol mol) |
static ExplicitBitVect |
convertToExplicit(SWIGTYPE_p_SparseBitVect sbv) |
static double |
CosineSimilarity(ExplicitBitVect bv1,
ExplicitBitVect bv2) |
static int |
countAtomElec(Atom at)
return the number of electrons available on an atom to donate for aromaticity
|
static ROMol |
deleteSubstructs(ROMol mol,
ROMol query) |
static ROMol |
deleteSubstructs(ROMol mol,
ROMol query,
boolean onlyFrags) |
static ROMol |
deleteSubstructs(ROMol mol,
ROMol query,
boolean onlyFrags,
boolean useChirality) |
static java.lang.String |
describeQuery(Atom atom) |
static java.lang.String |
describeQuery(Bond bond) |
static void |
detectBondStereochemistry(ROMol mol) |
static void |
detectBondStereochemistry(ROMol mol,
int confId) |
static MolSanitizeException_Vect |
detectChemistryProblems(ROMol mol) |
static MolSanitizeException_Vect |
detectChemistryProblems(ROMol mol,
int sanitizeOps) |
static double |
DiceSimilarity(ExplicitBitVect bv1,
ExplicitBitVect bv2) |
static double |
DiceSimilarity(SparseIntVect32 v1,
SparseIntVect32 v2) |
static double |
DiceSimilarity(SparseIntVect32 v1,
SparseIntVect32 v2,
boolean returnDistance) |
static double |
DiceSimilarity(SparseIntVect32 v1,
SparseIntVect32 v2,
boolean returnDistance,
double bounds) |
static double |
DiceSimilarity(SparseIntVect64 v1,
SparseIntVect64 v2) |
static double |
DiceSimilarity(SparseIntVect64 v1,
SparseIntVect64 v2,
boolean returnDistance) |
static double |
DiceSimilarity(SparseIntVect64 v1,
SparseIntVect64 v2,
boolean returnDistance,
double bounds) |
static double |
DiceSimilarity(SparseIntVectu32 v1,
SparseIntVectu32 v2) |
static double |
DiceSimilarity(SparseIntVectu32 v1,
SparseIntVectu32 v2,
boolean returnDistance) |
static double |
DiceSimilarity(SparseIntVectu32 v1,
SparseIntVectu32 v2,
boolean returnDistance,
double bounds) |
static SparseIntVectu32 |
DifferenceFingerprintChemReaction(ChemicalReaction rxn) |
static SparseIntVectu32 |
DifferenceFingerprintChemReaction(ChemicalReaction rxn,
ReactionFingerprintParams params) |
static Str_Vect |
enumerateTautomerSmiles(java.lang.String smiles) |
static Str_Vect |
enumerateTautomerSmiles(java.lang.String smiles,
CleanupParameters params) |
static double |
equation17(double bondOrder23,
AtomicParams at2Params,
AtomicParams at3Params) |
static void |
fastFindRings(ROMol mol) |
static boolean |
FilterCatalogCanSerialize() |
static FilterCatalog |
FilterCatalogDeserialize(byte[] b) |
static Int_Vect_List |
findAllPathsOfLengthN(ROMol mol,
long targetLen) |
static Int_Vect_List |
findAllPathsOfLengthN(ROMol mol,
long targetLen,
boolean useBonds) |
static Int_Vect_List |
findAllPathsOfLengthN(ROMol mol,
long targetLen,
boolean useBonds,
boolean useHs) |
static Int_Vect_List |
findAllPathsOfLengthN(ROMol mol,
long targetLen,
boolean useBonds,
boolean useHs,
int rootedAtAtom) |
static Int_Int_Vect_List_Map |
findAllPathsOfLengthsMtoN(ROMol mol,
long lowerLen,
long upperLen) |
static Int_Int_Vect_List_Map |
findAllPathsOfLengthsMtoN(ROMol mol,
long lowerLen,
long upperLen,
boolean useBonds) |
static Int_Int_Vect_List_Map |
findAllPathsOfLengthsMtoN(ROMol mol,
long lowerLen,
long upperLen,
boolean useBonds,
boolean useHs) |
static Int_Int_Vect_List_Map |
findAllPathsOfLengthsMtoN(ROMol mol,
long lowerLen,
long upperLen,
boolean useBonds,
boolean useHs,
int rootedAtAtom) |
static Int_Vect_List |
findAllSubgraphsOfLengthN(ROMol mol,
long targetLen) |
static Int_Vect_List |
findAllSubgraphsOfLengthN(ROMol mol,
long targetLen,
boolean useHs) |
static Int_Vect_List |
findAllSubgraphsOfLengthN(ROMol mol,
long targetLen,
boolean useHs,
int rootedAtAtom) |
static Int_Int_Vect_List_Map |
findAllSubgraphsOfLengthsMtoN(ROMol mol,
long lowerLen,
long upperLen) |
static Int_Int_Vect_List_Map |
findAllSubgraphsOfLengthsMtoN(ROMol mol,
long lowerLen,
long upperLen,
boolean useHs) |
static Int_Int_Vect_List_Map |
findAllSubgraphsOfLengthsMtoN(ROMol mol,
long lowerLen,
long upperLen,
boolean useHs,
int rootedAtAtom) |
static Int_Vect |
findAtomEnvironmentOfRadiusN(ROMol mol,
long radius,
long rootedAtAtom) |
static Int_Vect |
findAtomEnvironmentOfRadiusN(ROMol mol,
long radius,
long rootedAtAtom,
boolean useHs) |
static MCSResult |
findMCS_P(ROMol_Vect mols,
java.lang.String params_json) |
static MCSResult |
findMCS(ROMol_Vect mols) |
static MCSResult |
findMCS(ROMol_Vect mols,
boolean maximizeBonds) |
static MCSResult |
findMCS(ROMol_Vect mols,
boolean maximizeBonds,
double threshold) |
static MCSResult |
findMCS(ROMol_Vect mols,
boolean maximizeBonds,
double threshold,
long timeout) |
static MCSResult |
findMCS(ROMol_Vect mols,
boolean maximizeBonds,
double threshold,
long timeout,
boolean verbose) |
static MCSResult |
findMCS(ROMol_Vect mols,
boolean maximizeBonds,
double threshold,
long timeout,
boolean verbose,
boolean matchValences) |
static MCSResult |
findMCS(ROMol_Vect mols,
boolean maximizeBonds,
double threshold,
long timeout,
boolean verbose,
boolean matchValences,
boolean ringMatchesRingOnly) |
static MCSResult |
findMCS(ROMol_Vect mols,
boolean maximizeBonds,
double threshold,
long timeout,
boolean verbose,
boolean matchValences,
boolean ringMatchesRingOnly,
boolean completeRingsOnly) |
static MCSResult |
findMCS(ROMol_Vect mols,
boolean maximizeBonds,
double threshold,
long timeout,
boolean verbose,
boolean matchValences,
boolean ringMatchesRingOnly,
boolean completeRingsOnly,
boolean matchChiralTag) |
static MCSResult |
findMCS(ROMol_Vect mols,
boolean maximizeBonds,
double threshold,
long timeout,
boolean verbose,
boolean matchValences,
boolean ringMatchesRingOnly,
boolean completeRingsOnly,
boolean matchChiralTag,
AtomComparator atomComp) |
static MCSResult |
findMCS(ROMol_Vect mols,
boolean maximizeBonds,
double threshold,
long timeout,
boolean verbose,
boolean matchValences,
boolean ringMatchesRingOnly,
boolean completeRingsOnly,
boolean matchChiralTag,
AtomComparator atomComp,
BondComparator bondComp) |
static MCSResult |
findMCS(ROMol_Vect mols,
boolean maximizeBonds,
double threshold,
long timeout,
boolean verbose,
boolean matchValences,
boolean ringMatchesRingOnly,
boolean completeRingsOnly,
boolean matchChiralTag,
AtomComparator atomComp,
BondComparator bondComp,
RingComparator ringComp) |
static void |
findPotentialStereoBonds(ROMol mol)
finds bonds that could be cis/trans in a molecule and mark them as Bond::STEREOANY
|
static void |
findPotentialStereoBonds(ROMol mol,
boolean cleanIt)
finds bonds that could be cis/trans in a molecule and mark them as Bond::STEREOANY
|
static int |
findSSSR(ROMol mol)
This is an overloaded member function, provided for convenience.
|
static int |
findSSSR(ROMol mol,
Int_Vect_Vect res) |
static Int_Vect_List |
findUniqueSubgraphsOfLengthN(ROMol mol,
long targetLen) |
static Int_Vect_List |
findUniqueSubgraphsOfLengthN(ROMol mol,
long targetLen,
boolean useHs) |
static Int_Vect_List |
findUniqueSubgraphsOfLengthN(ROMol mol,
long targetLen,
boolean useHs,
boolean useBO) |
static Int_Vect_List |
findUniqueSubgraphsOfLengthN(ROMol mol,
long targetLen,
boolean useHs,
boolean useBO,
int rootedAtAtom) |
static ExplicitBitVect |
FoldFingerprint(ExplicitBitVect bv1) |
static ExplicitBitVect |
FoldFingerprint(ExplicitBitVect bv1,
long factor) |
static ROMol |
fragmentOnBRICSBonds(ROMol mol) |
static RWMol |
fragmentParent(RWMol mol) |
static RWMol |
fragmentParent(RWMol mol,
CleanupParameters params) |
static RWMol |
fragmentParent(RWMol mol,
CleanupParameters params,
boolean skip_standardize) |
static void |
FromBitString(ExplicitBitVect sbv,
java.lang.String s) |
static void |
FromDaylightString(ExplicitBitVect sbv,
java.lang.String s) |
static UInt_Vect |
generateBondHashes(ROMol mol,
SWIGTYPE_p_boost__dynamic_bitsetT_t atomsInPath,
SWIGTYPE_p_std__vectorT_RDKit__Bond_const_p_t bondCache,
SWIGTYPE_p_std__vectorT_short_t isQueryBond,
Int_Vect path,
boolean useBondOrder,
UInt_Vect atomInvariants) |
static java.lang.String |
get_2DConf() |
static java.lang.String |
get_3DConf() |
static java.lang.String |
get_AtomID() |
static java.lang.String |
get_BondsPotentialStereo() |
static java.lang.String |
get_brokenChirality() |
static java.lang.String |
get_ChiralityPossible() |
static java.lang.String |
get_CIPCode() |
static java.lang.String |
get_CIPRank() |
static java.lang.String |
get_connectivityHKDeltas() |
static java.lang.String |
get_connectivityNVals() |
static java.lang.String |
get_crippenLogP() |
static java.lang.String |
get_CrippenLogP() |
static java.lang.String |
get_crippenLogPContribs() |
static java.lang.String |
get_crippenMR() |
static java.lang.String |
get_CrippenMR() |
static java.lang.String |
get_crippenMRContribs() |
static java.lang.String |
get_doIsoSmiles() |
static java.lang.String |
get_fragSMARTS() |
static java.lang.String |
get_GasteigerCharge() |
static java.lang.String |
get_GasteigerHCharge() |
static java.lang.String |
get_hasMassQuery() |
static java.lang.String |
get_labuteASA() |
static java.lang.String |
get_labuteAtomContribs() |
static java.lang.String |
get_labuteAtomHContrib() |
static java.lang.String |
get_MMFFSanitized() |
static java.lang.String |
get_MolFileAtomQuery() |
static java.lang.String |
get_MolFileBondAttach() |
static java.lang.String |
get_MolFileBondCfg() |
static java.lang.String |
get_MolFileBondEndPts() |
static java.lang.String |
get_MolFileBondQuery() |
static java.lang.String |
get_MolFileBondStereo() |
static java.lang.String |
get_MolFileBondType() |
static java.lang.String |
get_MolFileChiralFlag() |
static java.lang.String |
get_MolFileRLabel() |
static java.lang.String |
get_Name() |
static java.lang.String |
get_NeedsQueryScan() |
static java.lang.String |
get_protected() |
static java.lang.String |
get_QueryFormalCharge() |
static java.lang.String |
get_QueryHCount() |
static java.lang.String |
get_QueryIsotope() |
static java.lang.String |
get_QueryMass() |
static java.lang.String |
get_queryRootAtom() |
static java.lang.String |
get_ReactionDegreeChanged() |
static java.lang.String |
get_rgroupAtomMaps() |
static java.lang.String |
get_rgroupBonds() |
static java.lang.String |
get_RingClosures() |
static java.lang.String |
get_ringStereoAtoms() |
static java.lang.String |
get_ringStereochemCand() |
static java.lang.String |
get_ringStereoWarning() |
static java.lang.String |
get_SLN_s() |
static java.lang.String |
get_smilesAtomOutputOrder() |
static java.lang.String |
get_SmilesStart() |
static java.lang.String |
get_starred() |
static java.lang.String |
get_StereochemDone() |
static java.lang.String |
get_supplementalSmilesLabel() |
static java.lang.String |
get_tpsa() |
static java.lang.String |
get_tpsaAtomContribs() |
static java.lang.String |
get_TraversalBondIndexOrder() |
static java.lang.String |
get_TraversalRingClosureBond() |
static java.lang.String |
get_TraversalStartPoint() |
static java.lang.String |
get_TriposAtomType() |
static java.lang.String |
get_Unfinished_SLN_() |
static java.lang.String |
get_UnknownStereo() |
static java.lang.String |
get_unspecifiedOrder() |
static SWIGTYPE_p_double |
get3DDistanceMat(ROMol mol) |
static SWIGTYPE_p_double |
get3DDistanceMat(ROMol mol,
int confId) |
static SWIGTYPE_p_double |
get3DDistanceMat(ROMol mol,
int confId,
boolean useAtomWts) |
static SWIGTYPE_p_double |
get3DDistanceMat(ROMol mol,
int confId,
boolean useAtomWts,
boolean force) |
static SWIGTYPE_p_double |
get3DDistanceMat(ROMol mol,
int confId,
boolean useAtomWts,
boolean force,
java.lang.String propNamePrefix) |
static SWIGTYPE_p_double |
getAdjacencyMatrix(ROMol mol)
returns a molecule's adjacency matrix
|
static SWIGTYPE_p_double |
getAdjacencyMatrix(ROMol mol,
boolean useBO)
returns a molecule's adjacency matrix
|
static SWIGTYPE_p_double |
getAdjacencyMatrix(ROMol mol,
boolean useBO,
int emptyVal)
returns a molecule's adjacency matrix
|
static SWIGTYPE_p_double |
getAdjacencyMatrix(ROMol mol,
boolean useBO,
int emptyVal,
boolean force)
returns a molecule's adjacency matrix
|
static SWIGTYPE_p_double |
getAdjacencyMatrix(ROMol mol,
boolean useBO,
int emptyVal,
boolean force,
java.lang.String propNamePrefix)
returns a molecule's adjacency matrix
|
static SWIGTYPE_p_double |
getAdjacencyMatrix(ROMol mol,
boolean useBO,
int emptyVal,
boolean force,
java.lang.String propNamePrefix,
SWIGTYPE_p_boost__dynamic_bitsetT_t bondsToUse) |
static double |
getAmideBondOrder() |
static java.lang.String |
getAmwVersion() |
static double |
getAngleDeg(Conformer conf,
long iAtomId,
long jAtomId,
long kAtomId) |
static double |
getAngleRad(Conformer conf,
long iAtomId,
long jAtomId,
long kAtomId) |
static java.lang.String |
getAtomAlias(Atom atom) |
static long |
getAtomCode(Atom atom) |
static long |
getAtomCode(Atom atom,
long branchSubtract) |
static long |
getAtomCode(Atom atom,
long branchSubtract,
boolean includeChirality) |
static java.lang.String |
getAtomLabel() |
static SWIGTYPE_p_unsigned_int |
getAtomNumberTypes() |
static long |
getAtomPairCode(long codeI,
long codeJ,
long dist) |
static long |
getAtomPairCode(long codeI,
long codeJ,
long dist,
boolean includeChirality) |
static SparseIntVect32 |
getAtomPairFingerprint(ROMol mol) |
static SparseIntVect32 |
getAtomPairFingerprint(ROMol mol,
long minLength,
long maxLength) |
static SparseIntVect32 |
getAtomPairFingerprint(ROMol mol,
long minLength,
long maxLength,
UInt_Vect fromAtoms) |
static SparseIntVect32 |
getAtomPairFingerprint(ROMol mol,
long minLength,
long maxLength,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms) |
static SparseIntVect32 |
getAtomPairFingerprint(ROMol mol,
long minLength,
long maxLength,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants) |
static SparseIntVect32 |
getAtomPairFingerprint(ROMol mol,
long minLength,
long maxLength,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants,
boolean includeChirality) |
static SparseIntVect32 |
getAtomPairFingerprint(ROMol mol,
long minLength,
long maxLength,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants,
boolean includeChirality,
boolean use2D) |
static SparseIntVect32 |
getAtomPairFingerprint(ROMol mol,
long minLength,
long maxLength,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants,
boolean includeChirality,
boolean use2D,
int confId) |
static SparseIntVect32 |
getAtomPairFingerprint(ROMol mol,
UInt_Vect fromAtoms) |
static SparseIntVect32 |
getAtomPairFingerprint(ROMol mol,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms) |
static SparseIntVect32 |
getAtomPairFingerprint(ROMol mol,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants) |
static SparseIntVect32 |
getAtomPairFingerprint(ROMol mol,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants,
boolean includeChirality) |
static SparseIntVect32 |
getAtomPairFingerprint(ROMol mol,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants,
boolean includeChirality,
boolean use2D) |
static SparseIntVect32 |
getAtomPairFingerprint(ROMol mol,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants,
boolean includeChirality,
boolean use2D,
int confId) |
static java.lang.String |
getAtomPairsVersion() |
static int |
getAtomRLabel(Atom atm) |
static java.lang.String |
GetAtomSmarts(QueryAtom qatom) |
static java.lang.String |
GetAtomSmiles(Atom atom) |
static java.lang.String |
GetAtomSmiles(Atom atom,
boolean doKekule) |
static java.lang.String |
GetAtomSmiles(Atom atom,
boolean doKekule,
Bond bondIn) |
static java.lang.String |
GetAtomSmiles(Atom atom,
boolean doKekule,
Bond bondIn,
boolean allHsExplicit) |
static java.lang.String |
GetAtomSmiles(Atom atom,
boolean doKekule,
Bond bondIn,
boolean allHsExplicit,
boolean isomericSmiles) |
static int |
getAtomTypeAtomicNum(int val) |
static boolean |
getAtomTypeIsAromatic(int val) |
static java.lang.String |
getAtomValue(Atom atom) |
static void |
getAvalonCountFP(ROMol mol,
SparseIntVectu32 res) |
static void |
getAvalonCountFP(ROMol mol,
SparseIntVectu32 res,
long nBits) |
static void |
getAvalonCountFP(ROMol mol,
SparseIntVectu32 res,
long nBits,
boolean isQuery) |
static void |
getAvalonCountFP(ROMol mol,
SparseIntVectu32 res,
long nBits,
boolean isQuery,
boolean resetVect) |
static void |
getAvalonCountFP(ROMol mol,
SparseIntVectu32 res,
long nBits,
boolean isQuery,
boolean resetVect,
long bitFlags) |
static void |
getAvalonCountFP(java.lang.String data,
boolean isSmiles,
SparseIntVectu32 res) |
static void |
getAvalonCountFP(java.lang.String data,
boolean isSmiles,
SparseIntVectu32 res,
long nBits) |
static void |
getAvalonCountFP(java.lang.String data,
boolean isSmiles,
SparseIntVectu32 res,
long nBits,
boolean isQuery) |
static void |
getAvalonCountFP(java.lang.String data,
boolean isSmiles,
SparseIntVectu32 res,
long nBits,
boolean isQuery,
long bitFlags) |
static void |
getAvalonFP(ROMol mol,
ExplicitBitVect res) |
static void |
getAvalonFP(ROMol mol,
ExplicitBitVect res,
long nBits) |
static void |
getAvalonFP(ROMol mol,
ExplicitBitVect res,
long nBits,
boolean isQuery) |
static void |
getAvalonFP(ROMol mol,
ExplicitBitVect res,
long nBits,
boolean isQuery,
boolean resetVect) |
static void |
getAvalonFP(ROMol mol,
ExplicitBitVect res,
long nBits,
boolean isQuery,
boolean resetVect,
long bitFlags) |
static void |
getAvalonFP(ROMol mol,
UInt_Vect res) |
static void |
getAvalonFP(ROMol mol,
UInt_Vect res,
long nBits) |
static void |
getAvalonFP(ROMol mol,
UInt_Vect res,
long nBits,
boolean isQuery) |
static void |
getAvalonFP(ROMol mol,
UInt_Vect res,
long nBits,
boolean isQuery,
boolean resetVect) |
static void |
getAvalonFP(ROMol mol,
UInt_Vect res,
long nBits,
boolean isQuery,
boolean resetVect,
long bitFlags) |
static void |
getAvalonFP(java.lang.String data,
boolean isSmiles,
ExplicitBitVect res) |
static void |
getAvalonFP(java.lang.String data,
boolean isSmiles,
ExplicitBitVect res,
long nBits) |
static void |
getAvalonFP(java.lang.String data,
boolean isSmiles,
ExplicitBitVect res,
long nBits,
boolean isQuery) |
static void |
getAvalonFP(java.lang.String data,
boolean isSmiles,
ExplicitBitVect res,
long nBits,
boolean isQuery,
boolean resetVect) |
static void |
getAvalonFP(java.lang.String data,
boolean isSmiles,
ExplicitBitVect res,
long nBits,
boolean isQuery,
boolean resetVect,
long bitFlags) |
static void |
getAvalonFP(java.lang.String data,
boolean isSmiles,
UInt_Vect res) |
static void |
getAvalonFP(java.lang.String data,
boolean isSmiles,
UInt_Vect res,
long nBits) |
static void |
getAvalonFP(java.lang.String data,
boolean isSmiles,
UInt_Vect res,
long nBits,
boolean isQuery) |
static void |
getAvalonFP(java.lang.String data,
boolean isSmiles,
UInt_Vect res,
long nBits,
boolean isQuery,
boolean resetVect) |
static void |
getAvalonFP(java.lang.String data,
boolean isSmiles,
UInt_Vect res,
long nBits,
boolean isQuery,
boolean resetVect,
long bitFlags) |
static int |
getAvalonSimilarityBits() |
static int |
getAvalonSSSBits() |
static java.lang.String |
getBalabanJ() |
static java.lang.String |
getBalanbanJ() |
static double |
getBondLength(Conformer conf,
long iAtomId,
long jAtomId) |
static java.lang.String |
GetBondSmarts(QueryBond qbond) |
static java.lang.String |
GetBondSmarts(QueryBond qbond,
int atomToLeftIdx) |
static java.lang.String |
GetBondSmiles(Bond bond) |
static java.lang.String |
GetBondSmiles(Bond bond,
int atomToLeftIdx) |
static java.lang.String |
GetBondSmiles(Bond bond,
int atomToLeftIdx,
boolean doKekule) |
static java.lang.String |
GetBondSmiles(Bond bond,
int atomToLeftIdx,
boolean doKekule,
boolean allBondsExplicit) |
static java.lang.String |
getBoostVersion() |
static java.lang.String |
getCanonSmiles(ROMol mol) |
static java.lang.String |
getCanonSmiles(ROMol mol,
int flags) |
static java.lang.String |
getCanonSmiles(java.lang.String data,
boolean isSmiles) |
static java.lang.String |
getCanonSmiles(java.lang.String data,
boolean isSmiles,
int flags) |
static java.lang.String |
getCheckMolLog() |
static java.lang.String |
getChi0nVersion() |
static java.lang.String |
getChi0vVersion() |
static java.lang.String |
getChi1nVersion() |
static java.lang.String |
getChi1vVersion() |
static java.lang.String |
getChi2nVersion() |
static java.lang.String |
getChi2vVersion() |
static java.lang.String |
getChi3nVersion() |
static java.lang.String |
getChi3vVersion() |
static java.lang.String |
getChi4nVersion() |
static java.lang.String |
getChi4vVersion() |
static java.lang.String |
getChiNnVersion() |
static java.lang.String |
getChiNvVersion() |
static int |
getCi_ATOM_HOLDER() |
static int |
getCi_BITVECT_VERSION() |
static int |
getCi_LEADING_BOND() |
static int |
getCi_LOCAL_INF() |
static int |
getCi_RIGHTMOST_ATOM() |
static int |
getCi_SPARSEINTVECT_VERSION() |
static long |
getCodeSize() |
static java.lang.String |
getComputedPropName() |
static void |
getConnectivityInvariants(ROMol mol,
UInt_Vect invars) |
static void |
getConnectivityInvariants(ROMol mol,
UInt_Vect invars,
boolean includeRingMembership) |
static java.lang.String |
getCXExtensions(ROMol mol) |
static java.lang.String |
getDEFAULT_FILTERMATCHERBASE_NAME() |
static CleanupParameters |
getDefaultCleanupParameters() |
static int |
getDefaultConfId() |
static ReactionFingerprintParams |
getDefaultDifferenceFPParams() |
static Str_Vect |
getDefaultFeatureSmarts() |
static ReactionFingerprintParams |
getDefaultStructuralFPParams() |
static double |
getDEG2RAD() |
static double |
getDihedralDeg(Conformer conf,
long iAtomId,
long jAtomId,
long kAtomId,
long lAtomId) |
static double |
getDihedralRad(Conformer conf,
long iAtomId,
long jAtomId,
long kAtomId,
long lAtomId) |
static long |
getDIM_2D() |
static long |
getDIM_3D() |
static java.lang.String |
getDiscrims() |
static SWIGTYPE_p_double |
getDistanceMat(ROMol mol)
Computes the molecule's topological distance matrix.
|
static SWIGTYPE_p_double |
getDistanceMat(ROMol mol,
boolean useBO)
Computes the molecule's topological distance matrix.
|
static SWIGTYPE_p_double |
getDistanceMat(ROMol mol,
boolean useBO,
boolean useAtomWts)
Computes the molecule's topological distance matrix.
|
static SWIGTYPE_p_double |
getDistanceMat(ROMol mol,
boolean useBO,
boolean useAtomWts,
boolean force)
Computes the molecule's topological distance matrix.
|
static SWIGTYPE_p_double |
getDistanceMat(ROMol mol,
boolean useBO,
boolean useAtomWts,
boolean force,
java.lang.String propNamePrefix)
Computes the molecule's topological distance matrix.
|
static SWIGTYPE_p_double |
getDistanceMat(ROMol mol,
Int_Vect activeAtoms,
SWIGTYPE_p_std__vectorT_RDKit__Bond_const_p_t bonds)
Computes the molecule's topological distance matrix.
|
static SWIGTYPE_p_double |
getDistanceMat(ROMol mol,
Int_Vect activeAtoms,
SWIGTYPE_p_std__vectorT_RDKit__Bond_const_p_t bonds,
boolean useBO)
Computes the molecule's topological distance matrix.
|
static SWIGTYPE_p_double |
getDistanceMat(ROMol mol,
Int_Vect activeAtoms,
SWIGTYPE_p_std__vectorT_RDKit__Bond_const_p_t bonds,
boolean useBO,
boolean useAtomWts)
Computes the molecule's topological distance matrix.
|
static java.lang.String |
getDistanceMatrix_Paths() |
static java.lang.String |
getDummyLabel() |
static double |
getElectronMass() |
static int |
getEndianId() |
static double |
getEPS_DOUBLE() |
static EmbedParameters |
getETDG() |
static EmbedParameters |
getETKDG() |
static EmbedParameters |
getETKDGv2() |
static java.lang.String |
getExactmwVersion() |
static java.lang.String |
getExtraRings() |
static SparseIntVectu32 |
getFeatureFingerprint(ROMol mol,
long radius) |
static SparseIntVectu32 |
getFeatureFingerprint(ROMol mol,
long radius,
boolean useChirality) |
static SparseIntVectu32 |
getFeatureFingerprint(ROMol mol,
long radius,
boolean useChirality,
boolean useBondTypes) |
static SparseIntVectu32 |
getFeatureFingerprint(ROMol mol,
long radius,
boolean useChirality,
boolean useBondTypes,
boolean useCounts) |
static void |
getFeatureInvariants(ROMol mol,
UInt_Vect invars) |
static void |
getFeatureInvariants(ROMol mol,
UInt_Vect invars,
SWIGTYPE_p_std__vectorT_RDKit__ROMol_const_p_t patterns) |
static int |
getFormalCharge(ROMol mol) |
static java.lang.String |
getFractionCSP3Version() |
static double |
getG() |
static java.lang.String |
getHallKierAlphaVersion() |
static SparseIntVect32 |
getHashedAtomPairFingerprint(ROMol mol) |
static SparseIntVect32 |
getHashedAtomPairFingerprint(ROMol mol,
long nBits) |
static SparseIntVect32 |
getHashedAtomPairFingerprint(ROMol mol,
long nBits,
long minLength) |
static SparseIntVect32 |
getHashedAtomPairFingerprint(ROMol mol,
long nBits,
long minLength,
long maxLength) |
static SparseIntVect32 |
getHashedAtomPairFingerprint(ROMol mol,
long nBits,
long minLength,
long maxLength,
UInt_Vect fromAtoms) |
static SparseIntVect32 |
getHashedAtomPairFingerprint(ROMol mol,
long nBits,
long minLength,
long maxLength,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms) |
static SparseIntVect32 |
getHashedAtomPairFingerprint(ROMol mol,
long nBits,
long minLength,
long maxLength,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants) |
static SparseIntVect32 |
getHashedAtomPairFingerprint(ROMol mol,
long nBits,
long minLength,
long maxLength,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants,
boolean includeChirality) |
static SparseIntVect32 |
getHashedAtomPairFingerprint(ROMol mol,
long nBits,
long minLength,
long maxLength,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants,
boolean includeChirality,
boolean use2D) |
static SparseIntVect32 |
getHashedAtomPairFingerprint(ROMol mol,
long nBits,
long minLength,
long maxLength,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants,
boolean includeChirality,
boolean use2D,
int confId) |
static ExplicitBitVect |
getHashedAtomPairFingerprintAsBitVect(ROMol mol) |
static ExplicitBitVect |
getHashedAtomPairFingerprintAsBitVect(ROMol mol,
long nBits) |
static ExplicitBitVect |
getHashedAtomPairFingerprintAsBitVect(ROMol mol,
long nBits,
long minLength) |
static ExplicitBitVect |
getHashedAtomPairFingerprintAsBitVect(ROMol mol,
long nBits,
long minLength,
long maxLength) |
static ExplicitBitVect |
getHashedAtomPairFingerprintAsBitVect(ROMol mol,
long nBits,
long minLength,
long maxLength,
UInt_Vect fromAtoms) |
static ExplicitBitVect |
getHashedAtomPairFingerprintAsBitVect(ROMol mol,
long nBits,
long minLength,
long maxLength,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms) |
static ExplicitBitVect |
getHashedAtomPairFingerprintAsBitVect(ROMol mol,
long nBits,
long minLength,
long maxLength,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants) |
static ExplicitBitVect |
getHashedAtomPairFingerprintAsBitVect(ROMol mol,
long nBits,
long minLength,
long maxLength,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants,
long nBitsPerEntry) |
static ExplicitBitVect |
getHashedAtomPairFingerprintAsBitVect(ROMol mol,
long nBits,
long minLength,
long maxLength,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants,
long nBitsPerEntry,
boolean includeChirality) |
static ExplicitBitVect |
getHashedAtomPairFingerprintAsBitVect(ROMol mol,
long nBits,
long minLength,
long maxLength,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants,
long nBitsPerEntry,
boolean includeChirality,
boolean use2D) |
static ExplicitBitVect |
getHashedAtomPairFingerprintAsBitVect(ROMol mol,
long nBits,
long minLength,
long maxLength,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants,
long nBitsPerEntry,
boolean includeChirality,
boolean use2D,
int confId) |
static SparseIntVectu32 |
getHashedFingerprint(ROMol mol,
long radius) |
static SparseIntVectu32 |
getHashedFingerprint(ROMol mol,
long radius,
long nBits) |
static SparseIntVectu32 |
getHashedFingerprint(ROMol mol,
long radius,
long nBits,
UInt_Vect invariants) |
static SparseIntVectu32 |
getHashedFingerprint(ROMol mol,
long radius,
long nBits,
UInt_Vect invariants,
UInt_Vect fromAtoms) |
static SparseIntVectu32 |
getHashedFingerprint(ROMol mol,
long radius,
long nBits,
UInt_Vect invariants,
UInt_Vect fromAtoms,
boolean useChirality) |
static SparseIntVectu32 |
getHashedFingerprint(ROMol mol,
long radius,
long nBits,
UInt_Vect invariants,
UInt_Vect fromAtoms,
boolean useChirality,
boolean useBondTypes) |
static SparseIntVectu32 |
getHashedFingerprint(ROMol mol,
long radius,
long nBits,
UInt_Vect invariants,
UInt_Vect fromAtoms,
boolean useChirality,
boolean useBondTypes,
boolean onlyNonzeroInvariants) |
static SparseIntVectu32 |
getHashedFingerprint(ROMol mol,
long radius,
long nBits,
UInt_Vect invariants,
UInt_Vect fromAtoms,
boolean useChirality,
boolean useBondTypes,
boolean onlyNonzeroInvariants,
BitInfoMap atomsSettingBits) |
static SparseIntVect64 |
getHashedTopologicalTorsionFingerprint(ROMol mol) |
static SparseIntVect64 |
getHashedTopologicalTorsionFingerprint(ROMol mol,
long nBits) |
static SparseIntVect64 |
getHashedTopologicalTorsionFingerprint(ROMol mol,
long nBits,
long targetSize) |
static SparseIntVect64 |
getHashedTopologicalTorsionFingerprint(ROMol mol,
long nBits,
long targetSize,
UInt_Vect fromAtoms) |
static SparseIntVect64 |
getHashedTopologicalTorsionFingerprint(ROMol mol,
long nBits,
long targetSize,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms) |
static SparseIntVect64 |
getHashedTopologicalTorsionFingerprint(ROMol mol,
long nBits,
long targetSize,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants) |
static SparseIntVect64 |
getHashedTopologicalTorsionFingerprint(ROMol mol,
long nBits,
long targetSize,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants,
boolean includeChirality) |
static ExplicitBitVect |
getHashedTopologicalTorsionFingerprintAsBitVect(ROMol mol) |
static ExplicitBitVect |
getHashedTopologicalTorsionFingerprintAsBitVect(ROMol mol,
long nBits) |
static ExplicitBitVect |
getHashedTopologicalTorsionFingerprintAsBitVect(ROMol mol,
long nBits,
long targetSize) |
static ExplicitBitVect |
getHashedTopologicalTorsionFingerprintAsBitVect(ROMol mol,
long nBits,
long targetSize,
UInt_Vect fromAtoms) |
static ExplicitBitVect |
getHashedTopologicalTorsionFingerprintAsBitVect(ROMol mol,
long nBits,
long targetSize,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms) |
static ExplicitBitVect |
getHashedTopologicalTorsionFingerprintAsBitVect(ROMol mol,
long nBits,
long targetSize,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants) |
static ExplicitBitVect |
getHashedTopologicalTorsionFingerprintAsBitVect(ROMol mol,
long nBits,
long targetSize,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants,
long nBitsPerEntry) |
static ExplicitBitVect |
getHashedTopologicalTorsionFingerprintAsBitVect(ROMol mol,
long nBits,
long targetSize,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants,
long nBitsPerEntry,
boolean includeChirality) |
static java.lang.String |
getInternalRgroupSmiles() |
static java.lang.String |
getIsImplicit() |
static SWIGTYPE_p_std__string |
getIsotopesAtomData() |
static java.lang.String |
getKappa1Version() |
static java.lang.String |
getKappa2Version() |
static java.lang.String |
getKappa3Version() |
static EmbedParameters |
getKDG() |
static java.lang.String |
getLabuteASAVersion() |
static double |
getLabuteAtomContribs(ROMol mol,
Double_Vect Vi,
SWIGTYPE_p_double hContrib) |
static double |
getLabuteAtomContribs(ROMol mol,
Double_Vect Vi,
SWIGTYPE_p_double hContrib,
boolean includeHs) |
static double |
getLabuteAtomContribs(ROMol mol,
Double_Vect Vi,
SWIGTYPE_p_double hContrib,
boolean includeHs,
boolean force) |
static double |
getLambda() |
static java.lang.String |
getLayeredFingerprintMolVersion() |
static java.lang.String |
getLipinskiHBAVersion() |
static java.lang.String |
getLipinskiHBDVersion() |
static java.lang.String |
getMaccsFingerprintVersion() |
static int |
getMassIntegerConversionFactor() |
static int |
getMAX_BONDTYPE() |
static int |
getMAX_CYCLES() |
static double |
getMAX_DOUBLE() |
static double |
getMAX_INT() |
static double |
getMAX_LONGINT() |
static int |
getMAX_NATOMS() |
static java.lang.String |
getMaxAttachIdx() |
static long |
getMaxFingerprintLayers() |
static long |
getMaxNumBranches() |
static long |
getMaxNumPi() |
static long |
getMaxPathLen() |
static java.lang.String |
getMolAtomMapNumber() |
static int |
getMOLFILE_MAXLINE() |
static java.lang.String |
getMolFileAlias() |
static java.lang.String |
getMolFileComments() |
static java.lang.String |
getMolFileInfo() |
static java.lang.String |
getMolFileValue() |
static ROMol_Vect |
getMolFrags(ROMol mol)
splits a molecule into its component fragments
|
static ROMol_Vect |
getMolFrags(ROMol mol,
boolean sanitizeFrags)
splits a molecule into its component fragments
|
static ROMol_Vect |
getMolFrags(ROMol mol,
boolean sanitizeFrags,
Int_Vect frags) |
static ROMol_Vect |
getMolFrags(ROMol mol,
boolean sanitizeFrags,
Int_Vect frags,
Int_Vect_Vect fragsMolAtomMapping) |
static ROMol_Vect |
getMolFrags(ROMol mol,
boolean sanitizeFrags,
Int_Vect frags,
Int_Vect_Vect fragsMolAtomMapping,
boolean copyConformers) |
static long |
getMolFrags(ROMol mol,
Int_Vect_Vect frags) |
static long |
getMolFrags(ROMol mol,
Int_Vect mapping) |
static java.lang.String |
getMolInversionFlag() |
static java.lang.String |
getMolParity() |
static java.lang.String |
getMolRxnComponent() |
static java.lang.String |
getMolRxnRole() |
static java.lang.String |
getMolTotValence() |
static java.lang.String |
getMorganConnectivityInvariantVersion() |
static java.lang.String |
getMorganFeatureInvariantVersion() |
static ExplicitBitVect |
getMorganFingerprintAsBitVect(ROMol mol,
long radius,
long nBits) |
static ExplicitBitVect |
getMorganFingerprintAsBitVect(ROMol mol,
long radius,
long nBits,
UInt_Vect invariants) |
static ExplicitBitVect |
getMorganFingerprintAsBitVect(ROMol mol,
long radius,
long nBits,
UInt_Vect invariants,
UInt_Vect fromAtoms) |
static ExplicitBitVect |
getMorganFingerprintAsBitVect(ROMol mol,
long radius,
long nBits,
UInt_Vect invariants,
UInt_Vect fromAtoms,
boolean useChirality) |
static ExplicitBitVect |
getMorganFingerprintAsBitVect(ROMol mol,
long radius,
long nBits,
UInt_Vect invariants,
UInt_Vect fromAtoms,
boolean useChirality,
boolean useBondTypes) |
static ExplicitBitVect |
getMorganFingerprintAsBitVect(ROMol mol,
long radius,
long nBits,
UInt_Vect invariants,
UInt_Vect fromAtoms,
boolean useChirality,
boolean useBondTypes,
boolean onlyNonzeroInvariants) |
static ExplicitBitVect |
getMorganFingerprintAsBitVect(ROMol mol,
long radius,
long nBits,
UInt_Vect invariants,
UInt_Vect fromAtoms,
boolean useChirality,
boolean useBondTypes,
boolean onlyNonzeroInvariants,
BitInfoMap atomsSettingBits) |
static java.lang.String |
getMorganFingerprintVersion() |
static java.lang.String |
getMQNVersion() |
static java.lang.String |
getMRV_SMA() |
static java.lang.String |
getNullBond() |
static java.lang.String |
getNumAliphaticCarbocyclesVersion() |
static java.lang.String |
getNumAliphaticHeterocyclesVersion() |
static java.lang.String |
getNumAliphaticRingsVersion() |
static java.lang.String |
getNumAmideBondsVersion() |
static java.lang.String |
getNumArom() |
static java.lang.String |
getNumAromaticCarbocyclesVersion() |
static java.lang.String |
getNumAromaticHeterocyclesVersion() |
static java.lang.String |
getNumAromaticRingsVersion() |
static long |
getNumAtomPairFingerprintBits() |
static java.lang.String |
getNumAtomStereoCentersVersion() |
static long |
getNumAtomsWithDistinctProperty(ROMol mol,
java.lang.String prop) |
static long |
getNumBranchBits() |
static java.lang.String |
getNumBridgeheadAtomsVersion() |
static long |
getNumChiralBits() |
static java.lang.String |
getNumHBAVersion() |
static java.lang.String |
getNumHBDVersion() |
static java.lang.String |
getNumHeteroatomsVersion() |
static java.lang.String |
getNumHeterocyclesVersion() |
static long |
getNumPathBits() |
static long |
getNumPiBits() |
static java.lang.String |
getNumRingsVersion() |
static java.lang.String |
getNumRotatableBondsVersion() |
static java.lang.String |
getNumSaturatedCarbocyclesVersion() |
static java.lang.String |
getNumSaturatedHeterocyclesVersion() |
static java.lang.String |
getNumSaturatedRingsVersion() |
static java.lang.String |
getNumSpiroAtomsVersion() |
static long |
getNumTypeBits() |
static java.lang.String |
getNumUnspecifiedAtomStereoCentersVersion() |
static java.lang.String |
getOrigNoImplicit() |
static java.lang.String |
getPeriodicTableAtomData() |
static boolean |
getPreferCoordGen() |
static double |
getRAD2DEG() |
static java.lang.String |
getRDKFingerprintMolVersion() |
static java.lang.String |
getRdkitBuild() |
static java.lang.String |
getRdkitVersion() |
static java.lang.String |
getReactantAtomIdx() |
static Int_Vect_Vect |
getReactingAtoms(ChemicalReaction rxn) |
static Int_Vect_Vect |
getReactingAtoms(ChemicalReaction rxn,
boolean mappedAtomsOnly) |
static java.lang.String |
getReactionMapNum() |
static java.lang.String |
getRingMembership() |
static Int_List |
getShortestPath(ROMol mol,
int aid1,
int aid2)
Find the shortest path between two atoms.
|
static double |
getSMALL_DOUBLE() |
static java.lang.String |
getSmilesSymbol() |
static long |
getSubstructLayers() |
static java.lang.String |
getSupplementalSmilesLabel(Atom atom) |
static java.math.BigInteger |
getTopologicalTorsionCode(UInt_Vect atomCodes) |
static java.math.BigInteger |
getTopologicalTorsionCode(UInt_Vect atomCodes,
boolean includeChirality) |
static SparseIntVect64 |
getTopologicalTorsionFingerprint(ROMol mol) |
static SparseIntVect64 |
getTopologicalTorsionFingerprint(ROMol mol,
long targetSize) |
static SparseIntVect64 |
getTopologicalTorsionFingerprint(ROMol mol,
long targetSize,
UInt_Vect fromAtoms) |
static SparseIntVect64 |
getTopologicalTorsionFingerprint(ROMol mol,
long targetSize,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms) |
static SparseIntVect64 |
getTopologicalTorsionFingerprint(ROMol mol,
long targetSize,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants) |
static SparseIntVect64 |
getTopologicalTorsionFingerprint(ROMol mol,
long targetSize,
UInt_Vect fromAtoms,
UInt_Vect ignoreAtoms,
UInt_Vect atomInvariants,
boolean includeChirality) |
static long |
getTopologicalTorsionHash(UInt_Vect pathCodes) |
static double |
getTPSAAtomContribs(ROMol mol,
Double_Vect Vi) |
static double |
getTPSAAtomContribs(ROMol mol,
Double_Vect Vi,
boolean force) |
static double |
getTPSAAtomContribs(ROMol mol,
Double_Vect Vi,
boolean force,
boolean includeSandP) |
static java.lang.String |
getTpsaVersion() |
static java.lang.String |
getTWOD() |
static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t |
getUnfoldedRDKFingerprintMol(ROMol mol) |
static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t |
getUnfoldedRDKFingerprintMol(ROMol mol,
long minPath) |
static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t |
getUnfoldedRDKFingerprintMol(ROMol mol,
long minPath,
long maxPath) |
static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t |
getUnfoldedRDKFingerprintMol(ROMol mol,
long minPath,
long maxPath,
boolean useHs) |
static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t |
getUnfoldedRDKFingerprintMol(ROMol mol,
long minPath,
long maxPath,
boolean useHs,
boolean branchedPaths) |
static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t |
getUnfoldedRDKFingerprintMol(ROMol mol,
long minPath,
long maxPath,
boolean useHs,
boolean branchedPaths,
boolean useBondOrder) |
static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t |
getUnfoldedRDKFingerprintMol(ROMol mol,
long minPath,
long maxPath,
boolean useHs,
boolean branchedPaths,
boolean useBondOrder,
UInt_Vect atomInvariants) |
static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t |
getUnfoldedRDKFingerprintMol(ROMol mol,
long minPath,
long maxPath,
boolean useHs,
boolean branchedPaths,
boolean useBondOrder,
UInt_Vect atomInvariants,
UInt_Vect fromAtoms) |
static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t |
getUnfoldedRDKFingerprintMol(ROMol mol,
long minPath,
long maxPath,
boolean useHs,
boolean branchedPaths,
boolean useBondOrder,
UInt_Vect atomInvariants,
UInt_Vect fromAtoms,
SWIGTYPE_p_std__vectorT_std__vectorT_unsigned_long_long_t_t atomBits) |
static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t |
getUnfoldedRDKFingerprintMol(ROMol mol,
long minPath,
long maxPath,
boolean useHs,
boolean branchedPaths,
boolean useBondOrder,
UInt_Vect atomInvariants,
UInt_Vect fromAtoms,
SWIGTYPE_p_std__vectorT_std__vectorT_unsigned_long_long_t_t atomBits,
SWIGTYPE_p_std__mapT_unsigned_long_long_std__vectorT_std__vectorT_int_t_t_t bitInfo) |
static int |
getVersionMajor() |
static int |
getVersionMinor() |
static int |
getVersionPatch() |
static boolean |
hasNonZeroZCoords(Conformer conf) |
static void |
hkDeltas(ROMol mol,
Double_Vect deltas,
boolean force) |
static void |
identifyQueryBonds(ROMol mol,
SWIGTYPE_p_std__vectorT_RDKit__Bond_const_p_t bondCache,
SWIGTYPE_p_std__vectorT_short_t isQueryBond) |
static java.lang.String |
InchiToInchiKey(java.lang.String inchi) |
static RWMol |
InchiToMol(java.lang.String inchi,
ExtraInchiReturnValues rv) |
static RWMol |
InchiToMol(java.lang.String inchi,
ExtraInchiReturnValues rv,
boolean sanitize) |
static RWMol |
InchiToMol(java.lang.String inchi,
ExtraInchiReturnValues rv,
boolean sanitize,
boolean removeHs) |
static void |
initBoundsMat(BoundsMatrix mmat) |
static void |
initBoundsMat(BoundsMatrix mmat,
double defaultMin) |
static void |
initBoundsMat(BoundsMatrix mmat,
double defaultMin,
double defaultMax) |
static int |
initCheckMol(java.lang.String optString) |
static boolean |
inOrganicSubset(int atomicNumber) |
static void |
Intersect(Int_Vect r1,
Int_Vect r2,
Int_Vect res) |
static boolean |
isAtomAromatic(Atom a) |
static boolean |
isComplexQuery(Atom a) |
static boolean |
isComplexQuery(Bond b) |
static boolean |
isDoubleZero(double x) |
static boolean |
isEarlyAtom(int atomicNum) |
static boolean |
isInGroup6(int num) |
static boolean |
isMoleculeAgentOfReaction(ChemicalReaction rxn,
ROMol mol) |
static boolean |
isMoleculeAgentOfReaction(ChemicalReaction rxn,
ROMol mol,
SWIGTYPE_p_unsigned_int which) |
static boolean |
isMoleculeProductOfReaction(ChemicalReaction rxn,
ROMol mol) |
static boolean |
isMoleculeProductOfReaction(ChemicalReaction rxn,
ROMol mol,
SWIGTYPE_p_unsigned_int which) |
static boolean |
isMoleculeReactantOfReaction(ChemicalReaction rxn,
ROMol mol) |
static boolean |
isMoleculeReactantOfReaction(ChemicalReaction rxn,
ROMol mol,
SWIGTYPE_p_unsigned_int which) |
static void |
isotopeParent(RWMol mol) |
static void |
isotopeParent(RWMol mol,
CleanupParameters params) |
static void |
Kekulize(RWMol mol)
Kekulizes the molecule.
|
static void |
Kekulize(RWMol mol,
boolean markAtomsBonds)
Kekulizes the molecule.
|
static void |
Kekulize(RWMol mol,
boolean markAtomsBonds,
long maxBackTracks)
Kekulizes the molecule.
|
static double |
KulczynskiSimilarity(ExplicitBitVect bv1,
ExplicitBitVect bv2) |
static ExplicitBitVect |
LayeredFingerprintMol(ROMol mol) |
static ExplicitBitVect |
LayeredFingerprintMol(ROMol mol,
long layerFlags) |
static ExplicitBitVect |
LayeredFingerprintMol(ROMol mol,
long layerFlags,
long minPath) |
static ExplicitBitVect |
LayeredFingerprintMol(ROMol mol,
long layerFlags,
long minPath,
long maxPath) |
static ExplicitBitVect |
LayeredFingerprintMol(ROMol mol,
long layerFlags,
long minPath,
long maxPath,
long fpSize) |
static ExplicitBitVect |
LayeredFingerprintMol(ROMol mol,
long layerFlags,
long minPath,
long maxPath,
long fpSize,
UInt_Vect atomCounts) |
static ExplicitBitVect |
LayeredFingerprintMol(ROMol mol,
long layerFlags,
long minPath,
long maxPath,
long fpSize,
UInt_Vect atomCounts,
ExplicitBitVect setOnlyBits) |
static ExplicitBitVect |
LayeredFingerprintMol(ROMol mol,
long layerFlags,
long minPath,
long maxPath,
long fpSize,
UInt_Vect atomCounts,
ExplicitBitVect setOnlyBits,
boolean branchedPaths) |
static ExplicitBitVect |
LayeredFingerprintMol(ROMol mol,
long layerFlags,
long minPath,
long maxPath,
long fpSize,
UInt_Vect atomCounts,
ExplicitBitVect setOnlyBits,
boolean branchedPaths,
UInt_Vect fromAtoms) |
static ExplicitBitVect |
MACCSFingerprintMol(ROMol mol) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAAtomQuery() |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAHAtomQuery() |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomAliphaticQuery() |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomAromaticQuery() |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomExplicitDegreeQuery(int what) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomExplicitValenceQuery(int what) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomFormalChargeQuery(int what) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomHasAliphaticHeteroatomNbrsQuery() |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomHasChiralTagQuery() |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomHasHeteroatomNbrsQuery() |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomHasImplicitHQuery() |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomHasRingBondQuery() |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomHCountQuery(int what) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomHeavyAtomDegreeQuery(int what) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomHybridizationQuery(int what) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomImplicitHCountQuery(int what) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomImplicitValenceQuery(int what) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomInNRingsQuery(int what) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomInRingOfSizeQuery(int tgt) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomInRingQuery() |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomIsotopeQuery(int what) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomMassQuery(int what) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomMinRingSizeQuery(int tgt) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomMissingChiralTagQuery() |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomNegativeFormalChargeQuery(int what) |
static SWIGTYPE_p_Queries__QueryT_int_RDKit__Atom_const_p_true_t |
makeAtomNullQuery() |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomNumAliphaticHeteroatomNbrsQuery(int what) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomNumHeteroatomNbrsQuery(int what) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomNumQuery(int what) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomNumRadicalElectronsQuery(int what) |
static SWIGTYPE_p_Queries__RangeQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomRangeQuery(int lower,
int upper,
boolean lowerOpen,
boolean upperOpen,
SWIGTYPE_p_f_p_q_const__RDKit__Atom__int func) |
static SWIGTYPE_p_Queries__RangeQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomRangeQuery(int lower,
int upper,
boolean lowerOpen,
boolean upperOpen,
SWIGTYPE_p_f_p_q_const__RDKit__Atom__int func,
java.lang.String description) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomRingBondCountQuery(int what) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomTotalDegreeQuery(int what) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomTotalValenceQuery(int what) |
static int |
makeAtomType(int atomic_num,
boolean aromatic) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomTypeQuery(int num,
int aromatic) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeAtomUnsaturatedQuery() |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Bond_const_p_true_t |
makeBondDirEqualsQuery(Bond.BondDir what) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Bond_const_p_true_t |
makeBondHasStereoQuery() |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Bond_const_p_true_t |
makeBondInNRingsQuery(int tgt) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Bond_const_p_true_t |
makeBondInRingOfSizeQuery(int what) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Bond_const_p_true_t |
makeBondIsInRingQuery() |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Bond_const_p_true_t |
makeBondMinRingSizeQuery(int what) |
static SWIGTYPE_p_Queries__QueryT_int_RDKit__Bond_const_p_true_t |
makeBondNullQuery() |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Bond_const_p_true_t |
makeBondOrderEqualsQuery(Bond.BondType what) |
static SWIGTYPE_p_Queries__OrQueryT_int_RDKit__Atom_const_p_true_t |
makeMAtomQuery() |
static SWIGTYPE_p_Queries__OrQueryT_int_RDKit__Atom_const_p_true_t |
makeMHAtomQuery() |
static SWIGTYPE_p_Queries__OrQueryT_int_RDKit__Atom_const_p_true_t |
makeQAtomQuery() |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t |
makeQHAtomQuery() |
static void |
makeRingNeighborMap(Int_Vect_Vect brings,
Int_Int_Vect_Map neighMap) |
static void |
makeRingNeighborMap(Int_Vect_Vect brings,
Int_Int_Vect_Map neighMap,
long maxSize) |
static void |
makeRingNeighborMap(Int_Vect_Vect brings,
Int_Int_Vect_Map neighMap,
long maxSize,
long maxOverlapSize) |
static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Bond_const_p_true_t |
makeSingleOrAromaticBondQuery() |
static SWIGTYPE_p_Queries__OrQueryT_int_RDKit__Atom_const_p_true_t |
makeXAtomQuery() |
static SWIGTYPE_p_Queries__OrQueryT_int_RDKit__Atom_const_p_true_t |
makeXHAtomQuery() |
static double |
McConnaugheySimilarity(ExplicitBitVect bv1,
ExplicitBitVect bv2) |
static boolean |
MCSAtomCompareAny(MCSAtomCompareParameters p,
ROMol mol1,
long atom1,
ROMol mol2,
long atom2,
SWIGTYPE_p_void userData) |
static boolean |
MCSAtomCompareAnyHeavyAtom(MCSAtomCompareParameters p,
ROMol mol1,
long atom1,
ROMol mol2,
long atom2,
SWIGTYPE_p_void userData) |
static boolean |
MCSAtomCompareElements(MCSAtomCompareParameters p,
ROMol mol1,
long atom1,
ROMol mol2,
long atom2,
SWIGTYPE_p_void userData) |
static boolean |
MCSAtomCompareIsotopes(MCSAtomCompareParameters p,
ROMol mol1,
long atom1,
ROMol mol2,
long atom2,
SWIGTYPE_p_void userData) |
static boolean |
MCSBondCompareAny(MCSBondCompareParameters p,
ROMol mol1,
long bond1,
ROMol mol2,
long bond2,
SWIGTYPE_p_void userData) |
static boolean |
MCSBondCompareOrder(MCSBondCompareParameters p,
ROMol mol1,
long bond1,
ROMol mol2,
long bond2,
SWIGTYPE_p_void userData) |
static boolean |
MCSBondCompareOrderExact(MCSBondCompareParameters p,
ROMol mol1,
long bond1,
ROMol mol2,
long bond2,
SWIGTYPE_p_void userData) |
static boolean |
MCSProgressCallbackTimeout(MCSProgressData stat,
SWIGTYPE_p_RDKit__MCSParameters params,
SWIGTYPE_p_void userData) |
static ROMol |
mergeQueryHs(ROMol mol)
returns a copy of a molecule with hydrogens removed and added as queries to the heavy atoms to which they are bound.
|
static ROMol |
mergeQueryHs(ROMol mol,
boolean mergeUnmappedOnly) |
static void |
mergeQueryHs(RWMol mol) |
static void |
mergeQueryHs(RWMol mol,
boolean mergeUnmappedOnly) |
static RWMol |
Mol2BlockToMol(java.lang.String molBlock) |
static RWMol |
Mol2BlockToMol(java.lang.String molBlock,
boolean sanitize) |
static RWMol |
Mol2BlockToMol(java.lang.String molBlock,
boolean sanitize,
boolean removeHs) |
static RWMol |
Mol2BlockToMol(java.lang.String molBlock,
boolean sanitize,
boolean removeHs,
Mol2Type variant) |
static RWMol |
Mol2BlockToMol(java.lang.String molBlock,
boolean sanitize,
boolean removeHs,
Mol2Type variant,
boolean cleanupSubstructures) |
static RWMol |
Mol2DataStreamToMol(SWIGTYPE_p_std__istream inStream) |
static RWMol |
Mol2DataStreamToMol(SWIGTYPE_p_std__istream inStream,
boolean sanitize) |
static RWMol |
Mol2DataStreamToMol(SWIGTYPE_p_std__istream inStream,
boolean sanitize,
boolean removeHs) |
static RWMol |
Mol2DataStreamToMol(SWIGTYPE_p_std__istream inStream,
boolean sanitize,
boolean removeHs,
Mol2Type variant) |
static RWMol |
Mol2DataStreamToMol(SWIGTYPE_p_std__istream inStream,
boolean sanitize,
boolean removeHs,
Mol2Type variant,
boolean cleanupSubstructures) |
static RWMol |
Mol2FileToMol(java.lang.String fName) |
static RWMol |
Mol2FileToMol(java.lang.String fName,
boolean sanitize) |
static RWMol |
Mol2FileToMol(java.lang.String fName,
boolean sanitize,
boolean removeHs) |
static RWMol |
Mol2FileToMol(java.lang.String fName,
boolean sanitize,
boolean removeHs,
Mol2Type variant) |
static RWMol |
Mol2FileToMol(java.lang.String fName,
boolean sanitize,
boolean removeHs,
Mol2Type variant,
boolean cleanupSubstructures) |
static java.lang.String |
MolBlockToInchi(java.lang.String mol,
ExtraInchiReturnValues rv) |
static java.lang.String |
MolBlockToInchi(java.lang.String mol,
ExtraInchiReturnValues rv,
java.lang.String options) |
static RWMol |
MolBlockToMol(java.lang.String molBlock) |
static RWMol |
MolBlockToMol(java.lang.String molBlock,
boolean sanitize) |
static RWMol |
MolBlockToMol(java.lang.String molBlock,
boolean sanitize,
boolean removeHs) |
static RWMol |
MolBlockToMol(java.lang.String molBlock,
boolean sanitize,
boolean removeHs,
boolean strictParsing) |
static RWMol |
MolDataStreamToMol(SWIGTYPE_p_std__istream inStream,
SWIGTYPE_p_unsigned_int line) |
static RWMol |
MolDataStreamToMol(SWIGTYPE_p_std__istream inStream,
SWIGTYPE_p_unsigned_int line,
boolean sanitize) |
static RWMol |
MolDataStreamToMol(SWIGTYPE_p_std__istream inStream,
SWIGTYPE_p_unsigned_int line,
boolean sanitize,
boolean removeHs) |
static RWMol |
MolDataStreamToMol(SWIGTYPE_p_std__istream inStream,
SWIGTYPE_p_unsigned_int line,
boolean sanitize,
boolean removeHs,
boolean strictParsing) |
static RWMol |
MolFileToMol(java.lang.String fName) |
static RWMol |
MolFileToMol(java.lang.String fName,
boolean sanitize) |
static RWMol |
MolFileToMol(java.lang.String fName,
boolean sanitize,
boolean removeHs) |
static RWMol |
MolFileToMol(java.lang.String fName,
boolean sanitize,
boolean removeHs,
boolean strictParsing) |
static java.lang.String |
MolFragmentToCXSmiles(ROMol mol,
Int_Vect atomsToUse) |
static java.lang.String |
MolFragmentToCXSmiles(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse) |
static java.lang.String |
MolFragmentToCXSmiles(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse,
Str_Vect atomSymbols) |
static java.lang.String |
MolFragmentToCXSmiles(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse,
Str_Vect atomSymbols,
Str_Vect bondSymbols) |
static java.lang.String |
MolFragmentToCXSmiles(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse,
Str_Vect atomSymbols,
Str_Vect bondSymbols,
boolean doIsomericSmiles) |
static java.lang.String |
MolFragmentToCXSmiles(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse,
Str_Vect atomSymbols,
Str_Vect bondSymbols,
boolean doIsomericSmiles,
boolean doKekule) |
static java.lang.String |
MolFragmentToCXSmiles(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse,
Str_Vect atomSymbols,
Str_Vect bondSymbols,
boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom) |
static java.lang.String |
MolFragmentToCXSmiles(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse,
Str_Vect atomSymbols,
Str_Vect bondSymbols,
boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom,
boolean canonical) |
static java.lang.String |
MolFragmentToCXSmiles(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse,
Str_Vect atomSymbols,
Str_Vect bondSymbols,
boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom,
boolean canonical,
boolean allBondsExplicit) |
static java.lang.String |
MolFragmentToCXSmiles(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse,
Str_Vect atomSymbols,
Str_Vect bondSymbols,
boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom,
boolean canonical,
boolean allBondsExplicit,
boolean allHsExplicit) |
static java.lang.String |
MolFragmentToSmarts(ROMol mol,
Int_Vect atomsToUse) |
static java.lang.String |
MolFragmentToSmarts(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse) |
static java.lang.String |
MolFragmentToSmarts(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse,
boolean doIsomericSmarts) |
static java.lang.String |
MolFragmentToSmiles(ROMol mol,
Int_Vect atomsToUse) |
static java.lang.String |
MolFragmentToSmiles(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse) |
static java.lang.String |
MolFragmentToSmiles(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse,
Str_Vect atomSymbols) |
static java.lang.String |
MolFragmentToSmiles(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse,
Str_Vect atomSymbols,
Str_Vect bondSymbols) |
static java.lang.String |
MolFragmentToSmiles(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse,
Str_Vect atomSymbols,
Str_Vect bondSymbols,
boolean doIsomericSmiles) |
static java.lang.String |
MolFragmentToSmiles(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse,
Str_Vect atomSymbols,
Str_Vect bondSymbols,
boolean doIsomericSmiles,
boolean doKekule) |
static java.lang.String |
MolFragmentToSmiles(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse,
Str_Vect atomSymbols,
Str_Vect bondSymbols,
boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom) |
static java.lang.String |
MolFragmentToSmiles(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse,
Str_Vect atomSymbols,
Str_Vect bondSymbols,
boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom,
boolean canonical) |
static java.lang.String |
MolFragmentToSmiles(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse,
Str_Vect atomSymbols,
Str_Vect bondSymbols,
boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom,
boolean canonical,
boolean allBondsExplicit) |
static java.lang.String |
MolFragmentToSmiles(ROMol mol,
Int_Vect atomsToUse,
Int_Vect bondsToUse,
Str_Vect atomSymbols,
Str_Vect bondSymbols,
boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom,
boolean canonical,
boolean allBondsExplicit,
boolean allHsExplicit) |
static java.lang.String |
MolHash(RWMol mol,
HashFunction func) |
static java.lang.String |
MolToCXSmiles(ROMol mol) |
static java.lang.String |
MolToCXSmiles(ROMol mol,
boolean doIsomericSmiles) |
static java.lang.String |
MolToCXSmiles(ROMol mol,
boolean doIsomericSmiles,
boolean doKekule) |
static java.lang.String |
MolToCXSmiles(ROMol mol,
boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom) |
static java.lang.String |
MolToCXSmiles(ROMol mol,
boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom,
boolean canonical) |
static java.lang.String |
MolToCXSmiles(ROMol mol,
boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom,
boolean canonical,
boolean allBondsExplicit) |
static java.lang.String |
MolToCXSmiles(ROMol mol,
boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom,
boolean canonical,
boolean allBondsExplicit,
boolean allHsExplicit) |
static java.lang.String |
MolToCXSmiles(ROMol mol,
boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom,
boolean canonical,
boolean allBondsExplicit,
boolean allHsExplicit,
boolean doRandom) |
static java.lang.String |
MolToInchi(ROMol mol,
ExtraInchiReturnValues rv) |
static java.lang.String |
MolToInchi(ROMol mol,
ExtraInchiReturnValues rv,
java.lang.String options) |
static java.lang.String |
MolToInchiKey(ROMol mol) |
static java.lang.String |
MolToInchiKey(ROMol mol,
java.lang.String options) |
static java.lang.String |
MolToMolBlock(ROMol mol) |
static java.lang.String |
MolToMolBlock(ROMol mol,
boolean includeStereo) |
static java.lang.String |
MolToMolBlock(ROMol mol,
boolean includeStereo,
int confId) |
static java.lang.String |
MolToMolBlock(ROMol mol,
boolean includeStereo,
int confId,
boolean kekulize) |
static java.lang.String |
MolToMolBlock(ROMol mol,
boolean includeStereo,
int confId,
boolean kekulize,
boolean forceV3000) |
static void |
MolToMolFile(ROMol mol,
java.lang.String fName) |
static void |
MolToMolFile(ROMol mol,
java.lang.String fName,
boolean includeStereo) |
static void |
MolToMolFile(ROMol mol,
java.lang.String fName,
boolean includeStereo,
int confId) |
static void |
MolToMolFile(ROMol mol,
java.lang.String fName,
boolean includeStereo,
int confId,
boolean kekulize) |
static void |
MolToMolFile(ROMol mol,
java.lang.String fName,
boolean includeStereo,
int confId,
boolean kekulize,
boolean forceV3000) |
static java.lang.String |
MolToPDBBlock(ROMol mol) |
static java.lang.String |
MolToPDBBlock(ROMol mol,
int confId) |
static java.lang.String |
MolToPDBBlock(ROMol mol,
int confId,
long flavor) |
static void |
MolToPDBFile(ROMol mol,
java.lang.String fname) |
static void |
MolToPDBFile(ROMol mol,
java.lang.String fname,
int confId) |
static void |
MolToPDBFile(ROMol mol,
java.lang.String fname,
int confId,
long flavor) |
static java.lang.String |
MolToSmarts(ROMol mol) |
static java.lang.String |
MolToSmarts(ROMol mol,
boolean doIsomericSmarts) |
static java.lang.String |
MolToSmiles(ROMol mol) |
static java.lang.String |
MolToSmiles(ROMol mol,
boolean doIsomericSmiles) |
static java.lang.String |
MolToSmiles(ROMol mol,
boolean doIsomericSmiles,
boolean doKekule) |
static java.lang.String |
MolToSmiles(ROMol mol,
boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom) |
static java.lang.String |
MolToSmiles(ROMol mol,
boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom,
boolean canonical) |
static java.lang.String |
MolToSmiles(ROMol mol,
boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom,
boolean canonical,
boolean allBondsExplicit) |
static java.lang.String |
MolToSmiles(ROMol mol,
boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom,
boolean canonical,
boolean allBondsExplicit,
boolean allHsExplicit) |
static java.lang.String |
MolToSmiles(ROMol mol,
boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom,
boolean canonical,
boolean allBondsExplicit,
boolean allHsExplicit,
boolean doRandom) |
static void |
MolToTPLFile(ROMol mol,
java.lang.String fName) |
static void |
MolToTPLFile(ROMol mol,
java.lang.String fName,
java.lang.String partialChargeProp) |
static void |
MolToTPLFile(ROMol mol,
java.lang.String fName,
java.lang.String partialChargeProp,
boolean writeFirstConfTwice) |
static java.lang.String |
MolToTPLText(ROMol mol) |
static java.lang.String |
MolToTPLText(ROMol mol,
java.lang.String partialChargeProp) |
static java.lang.String |
MolToTPLText(ROMol mol,
java.lang.String partialChargeProp,
boolean writeFirstConfTwice) |
static java.lang.String |
MolToXYZBlock(ROMol mol) |
static java.lang.String |
MolToXYZBlock(ROMol mol,
int confId) |
static void |
MolToXYZFile(ROMol mol,
java.lang.String fName) |
static void |
MolToXYZFile(ROMol mol,
java.lang.String fName,
int confId) |
static SparseIntVectu32 |
MorganFingerprintMol(ROMol mol,
long radius) |
static SparseIntVectu32 |
MorganFingerprintMol(ROMol mol,
long radius,
UInt_Vect invariants) |
static SparseIntVectu32 |
MorganFingerprintMol(ROMol mol,
long radius,
UInt_Vect invariants,
UInt_Vect fromAtoms) |
static SparseIntVectu32 |
MorganFingerprintMol(ROMol mol,
long radius,
UInt_Vect invariants,
UInt_Vect fromAtoms,
boolean useChirality) |
static SparseIntVectu32 |
MorganFingerprintMol(ROMol mol,
long radius,
UInt_Vect invariants,
UInt_Vect fromAtoms,
boolean useChirality,
boolean useBondTypes) |
static SparseIntVectu32 |
MorganFingerprintMol(ROMol mol,
long radius,
UInt_Vect invariants,
UInt_Vect fromAtoms,
boolean useChirality,
boolean useBondTypes,
boolean useCounts) |
static SparseIntVectu32 |
MorganFingerprintMol(ROMol mol,
long radius,
UInt_Vect invariants,
UInt_Vect fromAtoms,
boolean useChirality,
boolean useBondTypes,
boolean useCounts,
boolean onlyNonzeroInvariants) |
static SparseIntVectu32 |
MorganFingerprintMol(ROMol mol,
long radius,
UInt_Vect invariants,
UInt_Vect fromAtoms,
boolean useChirality,
boolean useBondTypes,
boolean useCounts,
boolean onlyNonzeroInvariants,
BitInfoMap atomsSettingBits) |
static ROMol |
MurckoDecompose(ROMol mol) |
static int |
nextCombination(Int_Vect comb,
int tot) |
static RWMol |
normalize(RWMol mol) |
static RWMol |
normalize(RWMol mol,
CleanupParameters params) |
static void |
normalizeAngleDeg(SWIGTYPE_p_double angleDeg) |
static long |
numAtomStereoCenters(ROMol mol) |
static int |
NumBitsInCommon(ExplicitBitVect bv1,
ExplicitBitVect bv2) |
static int |
NumOnBitsInCommon(ExplicitBitVect bv1,
ExplicitBitVect bv2) |
static long |
numUnspecifiedAtomStereoCenters(ROMol mol) |
static Double_Vect |
OffBitProjSimilarity(ExplicitBitVect bv1,
ExplicitBitVect bv2) |
static Int_Vect |
OffBitsInCommon(ExplicitBitVect bv1,
ExplicitBitVect bv2) |
static Double_Vect |
OnBitProjSimilarity(ExplicitBitVect bv1,
ExplicitBitVect bv2) |
static double |
OnBitSimilarity(ExplicitBitVect bv1,
ExplicitBitVect bv2) |
static Int_Vect |
OnBitsInCommon(ExplicitBitVect bv1,
ExplicitBitVect bv2) |
static void |
parseAtomType(int val,
SWIGTYPE_p_int atomic_num,
SWIGTYPE_p_bool aromatic) |
static void |
parseMCSParametersJSON(java.lang.String json,
SWIGTYPE_p_RDKit__MCSParameters params) |
static void |
parseQueryDefFile(java.lang.String filename,
StringMolMap queryDefs) |
static void |
parseQueryDefFile(java.lang.String filename,
StringMolMap queryDefs,
boolean standardize) |
static void |
parseQueryDefFile(java.lang.String filename,
StringMolMap queryDefs,
boolean standardize,
java.lang.String delimiter) |
static void |
parseQueryDefFile(java.lang.String filename,
StringMolMap queryDefs,
boolean standardize,
java.lang.String delimiter,
java.lang.String comment) |
static void |
parseQueryDefFile(java.lang.String filename,
StringMolMap queryDefs,
boolean standardize,
java.lang.String delimiter,
java.lang.String comment,
long nameColumn) |
static void |
parseQueryDefFile(java.lang.String filename,
StringMolMap queryDefs,
boolean standardize,
java.lang.String delimiter,
java.lang.String comment,
long nameColumn,
long smartsColumn) |
static void |
parseQueryDefFile(SWIGTYPE_p_std__istream inStream,
StringMolMap queryDefs) |
static void |
parseQueryDefFile(SWIGTYPE_p_std__istream inStream,
StringMolMap queryDefs,
boolean standardize) |
static void |
parseQueryDefFile(SWIGTYPE_p_std__istream inStream,
StringMolMap queryDefs,
boolean standardize,
java.lang.String delimiter) |
static void |
parseQueryDefFile(SWIGTYPE_p_std__istream inStream,
StringMolMap queryDefs,
boolean standardize,
java.lang.String delimiter,
java.lang.String comment) |
static void |
parseQueryDefFile(SWIGTYPE_p_std__istream inStream,
StringMolMap queryDefs,
boolean standardize,
java.lang.String delimiter,
java.lang.String comment,
long nameColumn) |
static void |
parseQueryDefFile(SWIGTYPE_p_std__istream inStream,
StringMolMap queryDefs,
boolean standardize,
java.lang.String delimiter,
java.lang.String comment,
long nameColumn,
long smartsColumn) |
static void |
parseQueryDefText(java.lang.String queryDefText,
StringMolMap queryDefs) |
static void |
parseQueryDefText(java.lang.String queryDefText,
StringMolMap queryDefs,
boolean standardize) |
static void |
parseQueryDefText(java.lang.String queryDefText,
StringMolMap queryDefs,
boolean standardize,
java.lang.String delimiter) |
static void |
parseQueryDefText(java.lang.String queryDefText,
StringMolMap queryDefs,
boolean standardize,
java.lang.String delimiter,
java.lang.String comment) |
static void |
parseQueryDefText(java.lang.String queryDefText,
StringMolMap queryDefs,
boolean standardize,
java.lang.String delimiter,
java.lang.String comment,
long nameColumn) |
static void |
parseQueryDefText(java.lang.String queryDefText,
StringMolMap queryDefs,
boolean standardize,
java.lang.String delimiter,
java.lang.String comment,
long nameColumn,
long smartsColumn) |
static ROMol |
pathToSubmol(ROMol mol,
Int_Vect path) |
static ROMol |
pathToSubmol(ROMol mol,
Int_Vect path,
boolean useQuery) |
static ROMol |
pathToSubmol(ROMol mol,
Int_Vect path,
boolean useQuery,
Int_Int_Map atomIdxMap) |
static ExplicitBitVect |
PatternFingerprintMol(ROMol mol) |
static ExplicitBitVect |
PatternFingerprintMol(ROMol mol,
long fpSize) |
static ExplicitBitVect |
PatternFingerprintMol(ROMol mol,
long fpSize,
UInt_Vect atomCounts) |
static ExplicitBitVect |
PatternFingerprintMol(ROMol mol,
long fpSize,
UInt_Vect atomCounts,
ExplicitBitVect setOnlyBits) |
static RWMol |
PDBBlockToMol(java.lang.String str) |
static RWMol |
PDBBlockToMol(java.lang.String str,
boolean sanitize) |
static RWMol |
PDBBlockToMol(java.lang.String str,
boolean sanitize,
boolean removeHs) |
static RWMol |
PDBBlockToMol(java.lang.String str,
boolean sanitize,
boolean removeHs,
long flavor) |
static RWMol |
PDBBlockToMol(java.lang.String str,
boolean sanitize,
boolean removeHs,
long flavor,
boolean proximityBonding) |
static RWMol |
PDBDataStreamToMol(SWIGTYPE_p_std__istream inStream) |
static RWMol |
PDBDataStreamToMol(SWIGTYPE_p_std__istream inStream,
boolean sanitize) |
static RWMol |
PDBDataStreamToMol(SWIGTYPE_p_std__istream inStream,
boolean sanitize,
boolean removeHs) |
static RWMol |
PDBDataStreamToMol(SWIGTYPE_p_std__istream inStream,
boolean sanitize,
boolean removeHs,
long flavor) |
static RWMol |
PDBDataStreamToMol(SWIGTYPE_p_std__istream inStream,
boolean sanitize,
boolean removeHs,
long flavor,
boolean proximityBonding) |
static RWMol |
PDBFileToMol(java.lang.String fname) |
static RWMol |
PDBFileToMol(java.lang.String fname,
boolean sanitize) |
static RWMol |
PDBFileToMol(java.lang.String fname,
boolean sanitize,
boolean removeHs) |
static RWMol |
PDBFileToMol(java.lang.String fname,
boolean sanitize,
boolean removeHs,
long flavor) |
static RWMol |
PDBFileToMol(java.lang.String fname,
boolean sanitize,
boolean removeHs,
long flavor,
boolean proximityBonding) |
static void |
pickFusedRings(int curr,
Int_Int_Vect_Map neighMap,
Int_Vect res,
SWIGTYPE_p_boost__dynamic_bitsetT_t done) |
static void |
pickFusedRings(int curr,
Int_Int_Vect_Map neighMap,
Int_Vect res,
SWIGTYPE_p_boost__dynamic_bitsetT_t done,
int depth) |
static double |
pickRandomDistMat(BoundsMatrix mmat,
DoubleSymmMatrix distmat) |
static double |
pickRandomDistMat(BoundsMatrix mmat,
DoubleSymmMatrix distmat,
int seed) |
static double |
pickRandomDistMat(BoundsMatrix mmat,
DoubleSymmMatrix distmat,
SWIGTYPE_p_RDKit__double_source_type rng) |
static Int_Vect |
pickUsingFingerprints(EBV_Vect ebvs,
long nToPick) |
static Int_Vect |
pickUsingFingerprints(EBV_Vect ebvs,
long nToPick,
int seed) |
static Int_Vect |
pickUsingFingerprints(EBV_Vect ebvs,
long nToPick,
int seed,
Int_Vect firstPicks) |
static Int_Vect |
pickUsingFingerprints(EBV_Vect ebvs,
long nToPick,
int seed,
Int_Vect firstPicks,
boolean useCache) |
static void |
prepareAndDrawMolecule(MolDraw2D drawer,
ROMol mol) |
static void |
prepareAndDrawMolecule(MolDraw2D drawer,
ROMol mol,
java.lang.String legend) |
static void |
prepareAndDrawMolecule(MolDraw2D drawer,
ROMol mol,
java.lang.String legend,
Int_Vect highlight_atoms) |
static void |
prepareAndDrawMolecule(MolDraw2D drawer,
ROMol mol,
java.lang.String legend,
Int_Vect highlight_atoms,
Int_Vect highlight_bonds) |
static void |
prepareAndDrawMolecule(MolDraw2D drawer,
ROMol mol,
java.lang.String legend,
Int_Vect highlight_atoms,
Int_Vect highlight_bonds,
ColourPalette highlight_atom_map) |
static void |
prepareAndDrawMolecule(MolDraw2D drawer,
ROMol mol,
java.lang.String legend,
Int_Vect highlight_atoms,
Int_Vect highlight_bonds,
ColourPalette highlight_atom_map,
ColourPalette highlight_bond_map) |
static void |
prepareAndDrawMolecule(MolDraw2D drawer,
ROMol mol,
java.lang.String legend,
Int_Vect highlight_atoms,
Int_Vect highlight_bonds,
ColourPalette highlight_atom_map,
ColourPalette highlight_bond_map,
Int_Double_Map highlight_radii) |
static void |
prepareAndDrawMolecule(MolDraw2D drawer,
ROMol mol,
java.lang.String legend,
Int_Vect highlight_atoms,
Int_Vect highlight_bonds,
ColourPalette highlight_atom_map,
ColourPalette highlight_bond_map,
Int_Double_Map highlight_radii,
int confId) |
static void |
prepareMolForDrawing(RWMol mol) |
static void |
prepareMolForDrawing(RWMol mol,
boolean kekulize) |
static void |
prepareMolForDrawing(RWMol mol,
boolean kekulize,
boolean addChiralHs) |
static void |
prepareMolForDrawing(RWMol mol,
boolean kekulize,
boolean addChiralHs,
boolean wedgeBonds) |
static void |
prepareMolForDrawing(RWMol mol,
boolean kekulize,
boolean addChiralHs,
boolean wedgeBonds,
boolean forceCoords) |
static java.lang.String |
qhelper(SWIGTYPE_p_Queries__QueryT_int_RDKit__Atom_const_p_true_t q,
long depth) |
static java.lang.String |
qhelper(SWIGTYPE_p_Queries__QueryT_int_RDKit__Bond_const_p_true_t q,
long depth) |
static int |
queryAtomAliphatic(Atom at) |
static long |
queryAtomAllBondProduct(Atom at) |
static int |
queryAtomAromatic(Atom at) |
static long |
queryAtomBondProduct(Atom at) |
static int |
queryAtomExplicitDegree(Atom at) |
static int |
queryAtomExplicitValence(Atom at) |
static int |
queryAtomFormalCharge(Atom at) |
static int |
queryAtomHasAliphaticHeteroatomNbrs(Atom at) |
static int |
queryAtomHasChiralTag(Atom at) |
static int |
queryAtomHasHeteroatomNbrs(Atom at) |
static int |
queryAtomHasImplicitH(Atom at) |
static int |
queryAtomHasRingBond(Atom at) |
static int |
queryAtomHCount(Atom at) |
static int |
queryAtomHeavyAtomDegree(Atom at) |
static int |
queryAtomHybridization(Atom at) |
static int |
queryAtomImplicitHCount(Atom at) |
static int |
queryAtomImplicitValence(Atom at) |
static int |
queryAtomIsotope(Atom at) |
static int |
queryAtomMass(Atom at) |
static int |
queryAtomMinRingSize(Atom at) |
static int |
queryAtomMissingChiralTag(Atom at) |
static int |
queryAtomNegativeFormalCharge(Atom at) |
static int |
queryAtomNonHydrogenDegree(Atom at) |
static int |
queryAtomNum(Atom at) |
static int |
queryAtomNumAliphaticHeteroatomNbrs(Atom at) |
static int |
queryAtomNumHeteroatomNbrs(Atom at) |
static int |
queryAtomNumRadicalElectrons(Atom at) |
static int |
queryAtomRingBondCount(Atom at) |
static int |
queryAtomRingMembership(Atom at) |
static int |
queryAtomTotalDegree(Atom at) |
static int |
queryAtomTotalValence(Atom at) |
static int |
queryAtomType(Atom at) |
static int |
queryAtomUnsaturated(Atom at) |
static int |
queryBondDir(Bond bond) |
static int |
queryBondHasStereo(Bond bnd) |
static int |
queryBondIsSingleOrAromatic(Bond bond) |
static int |
queryBondMinRingSize(Bond bond) |
static int |
queryBondOrder(Bond bond) |
static int |
queryIsAtomInNRings(Atom at) |
static int |
queryIsAtomInRing(Atom at) |
static int |
queryIsBondInNRings(Bond at) |
static int |
queryIsBondInRing(Bond bond) |
static ExplicitBitVect |
RDKFingerprintMol(ROMol mol) |
static ExplicitBitVect |
RDKFingerprintMol(ROMol mol,
long minPath) |
static ExplicitBitVect |
RDKFingerprintMol(ROMol mol,
long minPath,
long maxPath) |
static ExplicitBitVect |
RDKFingerprintMol(ROMol mol,
long minPath,
long maxPath,
long fpSize) |
static ExplicitBitVect |
RDKFingerprintMol(ROMol mol,
long minPath,
long maxPath,
long fpSize,
long nBitsPerHash) |
static ExplicitBitVect |
RDKFingerprintMol(ROMol mol,
long minPath,
long maxPath,
long fpSize,
long nBitsPerHash,
boolean useHs) |
static ExplicitBitVect |
RDKFingerprintMol(ROMol mol,
long minPath,
long maxPath,
long fpSize,
long nBitsPerHash,
boolean useHs,
double tgtDensity) |
static ExplicitBitVect |
RDKFingerprintMol(ROMol mol,
long minPath,
long maxPath,
long fpSize,
long nBitsPerHash,
boolean useHs,
double tgtDensity,
long minSize) |
static ExplicitBitVect |
RDKFingerprintMol(ROMol mol,
long minPath,
long maxPath,
long fpSize,
long nBitsPerHash,
boolean useHs,
double tgtDensity,
long minSize,
boolean branchedPaths) |
static ExplicitBitVect |
RDKFingerprintMol(ROMol mol,
long minPath,
long maxPath,
long fpSize,
long nBitsPerHash,
boolean useHs,
double tgtDensity,
long minSize,
boolean branchedPaths,
boolean useBondOrder) |
static ExplicitBitVect |
RDKFingerprintMol(ROMol mol,
long minPath,
long maxPath,
long fpSize,
long nBitsPerHash,
boolean useHs,
double tgtDensity,
long minSize,
boolean branchedPaths,
boolean useBondOrder,
UInt_Vect atomInvariants) |
static ExplicitBitVect |
RDKFingerprintMol(ROMol mol,
long minPath,
long maxPath,
long fpSize,
long nBitsPerHash,
boolean useHs,
double tgtDensity,
long minSize,
boolean branchedPaths,
boolean useBondOrder,
UInt_Vect atomInvariants,
UInt_Vect fromAtoms) |
static ExplicitBitVect |
RDKFingerprintMol(ROMol mol,
long minPath,
long maxPath,
long fpSize,
long nBitsPerHash,
boolean useHs,
double tgtDensity,
long minSize,
boolean branchedPaths,
boolean useBondOrder,
UInt_Vect atomInvariants,
UInt_Vect fromAtoms,
SWIGTYPE_p_std__vectorT_std__vectorT_boost__uint32_t_t_t atomBits) |
static ExplicitBitVect |
RDKFingerprintMol(ROMol mol,
long minPath,
long maxPath,
long fpSize,
long nBitsPerHash,
boolean useHs,
double tgtDensity,
long minSize,
boolean branchedPaths,
boolean useBondOrder,
UInt_Vect atomInvariants,
UInt_Vect fromAtoms,
SWIGTYPE_p_std__vectorT_std__vectorT_boost__uint32_t_t_t atomBits,
SWIGTYPE_p_std__mapT_unsigned_int_std__vectorT_std__vectorT_int_t_t_t bitInfo) |
static RWMol |
RDKitSVGToMol(java.lang.String svg) |
static RWMol |
RDKitSVGToMol(java.lang.String svg,
boolean sanitize) |
static RWMol |
RDKitSVGToMol(java.lang.String svg,
boolean sanitize,
boolean removeHs) |
static RWMol |
RDKitSVGToMol(SWIGTYPE_p_std__istream instream) |
static RWMol |
RDKitSVGToMol(SWIGTYPE_p_std__istream instream,
boolean sanitize) |
static RWMol |
RDKitSVGToMol(SWIGTYPE_p_std__istream instream,
boolean sanitize,
boolean removeHs) |
static long |
readAmberTrajectory(java.lang.String fName,
Trajectory traj) |
static long |
readGromosTrajectory(java.lang.String fName,
Trajectory traj) |
static void |
registerDescriptors() |
static RWMol |
reionize(RWMol mol) |
static RWMol |
reionize(RWMol mol,
CleanupParameters params) |
static void |
removeGroupsWithAtom(Atom atom,
StereoGroup_Vect groups) |
static void |
removeGroupsWithAtoms(Atom_Vect atoms,
StereoGroup_Vect groups) |
static ROMol |
removeHs(ROMol mol)
returns a copy of a molecule with hydrogens removed
|
static ROMol |
removeHs(ROMol mol,
boolean implicitOnly)
returns a copy of a molecule with hydrogens removed
|
static ROMol |
removeHs(ROMol mol,
boolean implicitOnly,
boolean updateExplicitCount)
returns a copy of a molecule with hydrogens removed
|
static ROMol |
removeHs(ROMol mol,
boolean implicitOnly,
boolean updateExplicitCount,
boolean sanitize)
returns a copy of a molecule with hydrogens removed
|
static void |
removeHs(RWMol mol) |
static void |
removeHs(RWMol mol,
boolean implicitOnly) |
static void |
removeHs(RWMol mol,
boolean implicitOnly,
boolean updateExplicitCount) |
static void |
removeHs(RWMol mol,
boolean implicitOnly,
boolean updateExplicitCount,
boolean sanitize) |
static void |
removeStereochemistry(ROMol mol)
Removes all stereochemistry information from atoms (i.e.
|
static ROMol |
renumberAtoms(ROMol mol,
UInt_Vect newOrder) |
static ROMol |
replaceCore(ROMol mol,
ROMol coreQuery) |
static ROMol |
replaceCore(ROMol mol,
ROMol coreQuery,
boolean replaceDummies) |
static ROMol |
replaceCore(ROMol mol,
ROMol coreQuery,
boolean replaceDummies,
boolean labelByIndex) |
static ROMol |
replaceCore(ROMol mol,
ROMol coreQuery,
boolean replaceDummies,
boolean labelByIndex,
boolean requireDummyMatch) |
static ROMol |
replaceCore(ROMol mol,
ROMol coreQuery,
boolean replaceDummies,
boolean labelByIndex,
boolean requireDummyMatch,
boolean useChirality) |
static ROMol |
replaceCore(ROMol mol,
ROMol core,
Match_Vect matchVect) |
static ROMol |
replaceCore(ROMol mol,
ROMol core,
Match_Vect matchVect,
boolean replaceDummies) |
static ROMol |
replaceCore(ROMol mol,
ROMol core,
Match_Vect matchVect,
boolean replaceDummies,
boolean labelByIndex) |
static ROMol |
replaceCore(ROMol mol,
ROMol core,
Match_Vect matchVect,
boolean replaceDummies,
boolean labelByIndex,
boolean requireDummyMatch) |
static ROMol |
replaceSidechains(ROMol mol,
ROMol coreQuery) |
static ROMol |
replaceSidechains(ROMol mol,
ROMol coreQuery,
boolean useChirality) |
static ROMol_Vect |
replaceSubstructs(ROMol mol,
ROMol query,
ROMol replacement) |
static ROMol_Vect |
replaceSubstructs(ROMol mol,
ROMol query,
ROMol replacement,
boolean replaceAll) |
static ROMol_Vect |
replaceSubstructs(ROMol mol,
ROMol query,
ROMol replacement,
boolean replaceAll,
long replacementConnectionPoint) |
static ROMol_Vect |
replaceSubstructs(ROMol mol,
ROMol query,
ROMol replacement,
boolean replaceAll,
long replacementConnectionPoint,
boolean useChirality) |
static long |
RGroupDecompose(ROMol_Vect cores,
ROMol_Vect mols,
StringMolMap_Vect rows) |
static long |
RGroupDecompose(ROMol_Vect cores,
ROMol_Vect mols,
StringMolMap_Vect rows,
UInt_Vect unmatched) |
static long |
RGroupDecompose(ROMol_Vect cores,
ROMol_Vect mols,
StringMolMap_Vect rows,
UInt_Vect unmatched,
RGroupDecompositionParameters options) |
static long |
RGroupDecompose(ROMol_Vect cores,
ROMol_Vect mols,
StringROMol_VectMap columns) |
static long |
RGroupDecompose(ROMol_Vect cores,
ROMol_Vect mols,
StringROMol_VectMap columns,
UInt_Vect unmatched) |
static long |
RGroupDecompose(ROMol_Vect cores,
ROMol_Vect mols,
StringROMol_VectMap columns,
UInt_Vect unmatched,
RGroupDecompositionParameters options) |
static double |
round(double v) |
static FilterCatalogEntry_VectVect |
RunFilterCatalog(FilterCatalog filterCatalog,
Str_Vect smiles) |
static FilterCatalogEntry_VectVect |
RunFilterCatalog(FilterCatalog filterCatalog,
Str_Vect smiles,
int numThreads) |
static double |
RusselSimilarity(ExplicitBitVect bv1,
ExplicitBitVect bv2) |
static ChemicalReaction |
RxnBlockToChemicalReaction(java.lang.String rxnBlock) |
static ChemicalReaction |
RxnDataStreamToChemicalReaction(SWIGTYPE_p_std__istream rxnStream,
SWIGTYPE_p_unsigned_int line) |
static ChemicalReaction |
RxnFileToChemicalReaction(java.lang.String fileName) |
static ChemicalReaction |
RxnMolToChemicalReaction(ROMol mol) |
static ChemicalReaction |
RxnSmartsToChemicalReaction(java.lang.String text) |
static ChemicalReaction |
RxnSmartsToChemicalReaction(java.lang.String text,
String_String_Map replacements) |
static ChemicalReaction |
RxnSmartsToChemicalReaction(java.lang.String text,
String_String_Map replacements,
boolean useSmiles) |
static void |
sanitizeMol(RWMol mol)
carries out a collection of tasks for cleaning up a molecule and ensuring that it makes 'chemical sense'
|
static int |
sanitizeMol(RWMol mol,
int sanitizeOps) |
static void |
sanitizeMol(RWMol mol,
SWIGTYPE_p_unsigned_int operationThatFailed) |
static void |
sanitizeMol(RWMol mol,
SWIGTYPE_p_unsigned_int operationThatFailed,
long sanitizeOps) |
static long |
set2DCoords(ROMol mol) |
static long |
set2DCoords(ROMol mol,
boolean clearConfs) |
static java.lang.String |
set2DCoords(java.lang.String data,
boolean isSmiles) |
static void |
setAngleDeg(Conformer conf,
long iAtomId,
long jAtomId,
long kAtomId,
double value) |
static void |
setAngleRad(Conformer conf,
long iAtomId,
long jAtomId,
long kAtomId,
double value) |
static int |
setAromaticity(RWMol mol)
Sets up the aromaticity for a molecule.
|
static int |
setAromaticity(RWMol mol,
AromaticityModel model) |
static int |
setAromaticity(RWMol mol,
AromaticityModel model,
SWIGTYPE_p_f_r_RDKit__RWMol__int func) |
static void |
setAtomAlias(Atom atom,
java.lang.String alias) |
static void |
setAtomRLabel(Atom atm,
int rlabel) |
static void |
setAtomValue(Atom atom,
java.lang.String value) |
static void |
setBondLength(Conformer conf,
long iAtomId,
long jAtomId,
double value) |
static void |
setBondStereoFromDirections(ROMol mol) |
static void |
setBoostVersion(java.lang.String value) |
static void |
setConjugation(ROMol mol) |
static void |
setDEFAULT_FILTERMATCHERBASE_NAME(java.lang.String value) |
static void |
setDefaultConfId(int value) |
static void |
setDefaultFeatureSmarts(Str_Vect value) |
static void |
setDihedralDeg(Conformer conf,
long iAtomId,
long jAtomId,
long kAtomId,
long lAtomId,
double value) |
static void |
setDihedralRad(Conformer conf,
long iAtomId,
long jAtomId,
long kAtomId,
long lAtomId,
double value) |
static void |
setDoubleBondNeighborDirections(ROMol mol) |
static void |
setDoubleBondNeighborDirections(ROMol mol,
Conformer conf) |
static void |
setHybridization(ROMol mol) |
static void |
setPreferCoordGen(boolean arg0) |
static void |
setRdkitBuild(java.lang.String value) |
static void |
setRdkitVersion(java.lang.String value) |
static void |
setSupplementalSmilesLabel(Atom atom,
java.lang.String label) |
static void |
setTopolBounds(ROMol mol,
SWIGTYPE_p_boost__shared_ptrT_DistGeom__BoundsMatrix_t mmat) |
static void |
setTopolBounds(ROMol mol,
SWIGTYPE_p_boost__shared_ptrT_DistGeom__BoundsMatrix_t mmat,
boolean set15bounds) |
static void |
setTopolBounds(ROMol mol,
SWIGTYPE_p_boost__shared_ptrT_DistGeom__BoundsMatrix_t mmat,
boolean set15bounds,
boolean scaleVDW) |
static void |
setTopolBounds(ROMol mol,
SWIGTYPE_p_boost__shared_ptrT_DistGeom__BoundsMatrix_t mmat,
Match_Vect bonds,
Int_Vect_Vect angles) |
static void |
setTopolBounds(ROMol mol,
SWIGTYPE_p_boost__shared_ptrT_DistGeom__BoundsMatrix_t mmat,
Match_Vect bonds,
Int_Vect_Vect angles,
boolean set15bounds) |
static void |
setTopolBounds(ROMol mol,
SWIGTYPE_p_boost__shared_ptrT_DistGeom__BoundsMatrix_t mmat,
Match_Vect bonds,
Int_Vect_Vect angles,
boolean set15bounds,
boolean scaleVDW) |
static Atom |
SmartsToAtom(java.lang.String sma) |
static Bond |
SmartsToBond(java.lang.String sma) |
static Atom |
SmilesToAtom(java.lang.String smi) |
static Bond |
SmilesToBond(java.lang.String smi) |
static double |
SokalSimilarity(ExplicitBitVect bv1,
ExplicitBitVect bv2) |
static void |
SplitMolecule(RWMol mol,
SWIGTYPE_p_std__vectorT_RDKit__RWMol_p_t molv) |
static java.lang.String |
standardizeSmiles(java.lang.String smiles) |
static void |
stereoParent(RWMol mol) |
static void |
stereoParent(RWMol mol,
CleanupParameters params) |
static void |
Strip(RWMol mol,
long striptype) |
static java.lang.String |
strip(java.lang.String orig) |
static ExplicitBitVect |
StructuralFingerprintChemReaction(ChemicalReaction rxn) |
static ExplicitBitVect |
StructuralFingerprintChemReaction(ChemicalReaction rxn,
ReactionFingerprintParams params) |
static boolean |
SubstructLibraryCanSerialize() |
static SubstructLibrary |
SubstructLibraryDeserialize(byte[] b) |
static void |
superParent(RWMol mol) |
static void |
superParent(RWMol mol,
CleanupParameters params) |
static int |
symmetrizeSSSR(ROMol mol)
This is an overloaded member function, provided for convenience.
|
static int |
symmetrizeSSSR(ROMol mol,
Int_Vect_Vect res) |
static double |
TanimotoSimilarity(ExplicitBitVect bv1,
ExplicitBitVect bv2) |
static double |
TanimotoSimilarityEBV(ExplicitBitVect bv1,
ExplicitBitVect bv2) |
static double |
TanimotoSimilaritySIVi32(SparseIntVect32 v1,
SparseIntVect32 v2) |
static double |
TanimotoSimilaritySIVi32(SparseIntVect32 v1,
SparseIntVect32 v2,
boolean returnDistance) |
static double |
TanimotoSimilaritySIVi32(SparseIntVect32 v1,
SparseIntVect32 v2,
boolean returnDistance,
double bounds) |
static double |
TanimotoSimilaritySIVi64(SparseIntVect64 v1,
SparseIntVect64 v2) |
static double |
TanimotoSimilaritySIVi64(SparseIntVect64 v1,
SparseIntVect64 v2,
boolean returnDistance) |
static double |
TanimotoSimilaritySIVi64(SparseIntVect64 v1,
SparseIntVect64 v2,
boolean returnDistance,
double bounds) |
static double |
TanimotoSimilaritySIVu32(SparseIntVectu32 v1,
SparseIntVectu32 v2) |
static double |
TanimotoSimilaritySIVu32(SparseIntVectu32 v1,
SparseIntVectu32 v2,
boolean returnDistance) |
static double |
TanimotoSimilaritySIVu32(SparseIntVectu32 v1,
SparseIntVectu32 v2,
boolean returnDistance,
double bounds) |
static void |
tautomerParent(RWMol mol) |
static void |
tautomerParent(RWMol mol,
CleanupParameters params) |
static RWMol |
TPLDataStreamToMol(SWIGTYPE_p_std__istream inStream,
SWIGTYPE_p_unsigned_int line) |
static RWMol |
TPLDataStreamToMol(SWIGTYPE_p_std__istream inStream,
SWIGTYPE_p_unsigned_int line,
boolean sanitize) |
static RWMol |
TPLDataStreamToMol(SWIGTYPE_p_std__istream inStream,
SWIGTYPE_p_unsigned_int line,
boolean sanitize,
boolean skipFirstConf) |
static RWMol |
TPLFileToMol(java.lang.String fName) |
static RWMol |
TPLFileToMol(java.lang.String fName,
boolean sanitize) |
static RWMol |
TPLFileToMol(java.lang.String fName,
boolean sanitize,
boolean skipFirstConf) |
static void |
transformAtom(Atom atom,
Transform3D tform) |
static void |
transformConformer(Conformer conf,
Transform3D trans) |
static void |
transformMolsAtoms(ROMol mol,
Transform3D tform) |
static boolean |
triangleSmoothBounds(BoundsMatrix boundsMat) |
static boolean |
triangleSmoothBounds(BoundsMatrix boundsMat,
double tol) |
static boolean |
triangleSmoothBounds(SWIGTYPE_p_boost__shared_ptrT_DistGeom__BoundsMatrix_t boundsMat) |
static boolean |
triangleSmoothBounds(SWIGTYPE_p_boost__shared_ptrT_DistGeom__BoundsMatrix_t boundsMat,
double tol) |
static double |
TverskySimilarity(ExplicitBitVect bv1,
ExplicitBitVect bv2,
double a,
double b) |
static double |
TverskySimilarity(SparseIntVect32 v1,
SparseIntVect32 v2,
double a,
double b) |
static double |
TverskySimilarity(SparseIntVect32 v1,
SparseIntVect32 v2,
double a,
double b,
boolean returnDistance) |
static double |
TverskySimilarity(SparseIntVect32 v1,
SparseIntVect32 v2,
double a,
double b,
boolean returnDistance,
double bounds) |
static double |
TverskySimilarity(SparseIntVect64 v1,
SparseIntVect64 v2,
double a,
double b) |
static double |
TverskySimilarity(SparseIntVect64 v1,
SparseIntVect64 v2,
double a,
double b,
boolean returnDistance) |
static double |
TverskySimilarity(SparseIntVect64 v1,
SparseIntVect64 v2,
double a,
double b,
boolean returnDistance,
double bounds) |
static double |
TverskySimilarity(SparseIntVectu32 v1,
SparseIntVectu32 v2,
double a,
double b) |
static double |
TverskySimilarity(SparseIntVectu32 v1,
SparseIntVectu32 v2,
double a,
double b,
boolean returnDistance) |
static double |
TverskySimilarity(SparseIntVectu32 v1,
SparseIntVectu32 v2,
double a,
double b,
boolean returnDistance,
double bounds) |
static void |
Union(Int_Vect_Vect rings,
Int_Vect res) |
static void |
Union(Int_Vect_Vect rings,
Int_Vect res,
Int_Vect exclude) |
static void |
Union(Int_Vect r1,
Int_Vect r2,
Int_Vect res) |
static Int_Vect_List |
uniquifyPaths(ROMol mol,
Int_Vect_List allPathsb) |
static Int_Vect_List |
uniquifyPaths(ROMol mol,
Int_Vect_List allPathsb,
boolean useBO) |
static void |
UpdateBitVectFromFPSText(ExplicitBitVect bv1,
java.lang.String fps) |
static void |
updateDrawerParamsFromJSON(MolDraw2D drawer,
java.lang.String json) |
public static double computeDihedralAngle(Point3D pt1, Point3D pt2, Point3D pt3, Point3D pt4)
public static double computeSignedDihedralAngle(Point3D pt1, Point3D pt2, Point3D pt3, Point3D pt4)
public static java.lang.String getComputedPropName()
public static java.lang.String get_Name()
public static java.lang.String getMolFileInfo()
public static java.lang.String getMolFileComments()
public static java.lang.String get_2DConf()
public static java.lang.String get_3DConf()
public static java.lang.String get_doIsoSmiles()
public static java.lang.String getExtraRings()
public static java.lang.String get_smilesAtomOutputOrder()
public static java.lang.String get_StereochemDone()
public static java.lang.String get_NeedsQueryScan()
public static java.lang.String get_fragSMARTS()
public static java.lang.String getMaxAttachIdx()
public static java.lang.String getOrigNoImplicit()
public static java.lang.String getRingMembership()
public static java.lang.String get_connectivityHKDeltas()
public static java.lang.String get_connectivityNVals()
public static java.lang.String get_crippenLogP()
public static java.lang.String get_crippenLogPContribs()
public static java.lang.String get_crippenMR()
public static java.lang.String get_crippenMRContribs()
public static java.lang.String get_labuteASA()
public static java.lang.String get_labuteAtomContribs()
public static java.lang.String get_labuteAtomHContrib()
public static java.lang.String get_tpsa()
public static java.lang.String get_tpsaAtomContribs()
public static java.lang.String getNumArom()
public static java.lang.String get_MMFFSanitized()
public static java.lang.String get_CrippenLogP()
public static java.lang.String get_CrippenMR()
public static java.lang.String get_GasteigerCharge()
public static java.lang.String get_GasteigerHCharge()
public static java.lang.String get_BondsPotentialStereo()
public static java.lang.String get_CIPCode()
public static java.lang.String get_CIPRank()
public static java.lang.String get_ChiralityPossible()
public static java.lang.String get_UnknownStereo()
public static java.lang.String get_ringStereoAtoms()
public static java.lang.String get_ringStereochemCand()
public static java.lang.String get_ringStereoWarning()
public static java.lang.String get_SmilesStart()
public static java.lang.String get_TraversalBondIndexOrder()
public static java.lang.String get_TraversalRingClosureBond()
public static java.lang.String get_TraversalStartPoint()
public static java.lang.String get_queryRootAtom()
public static java.lang.String get_hasMassQuery()
public static java.lang.String get_protected()
public static java.lang.String get_supplementalSmilesLabel()
public static java.lang.String get_unspecifiedOrder()
public static java.lang.String get_RingClosures()
public static java.lang.String getAtomLabel()
public static java.lang.String getMolAtomMapNumber()
public static java.lang.String getMolFileAlias()
public static java.lang.String getMolFileValue()
public static java.lang.String getMolInversionFlag()
public static java.lang.String getMolParity()
public static java.lang.String getMolRxnComponent()
public static java.lang.String getMolRxnRole()
public static java.lang.String getMolTotValence()
public static java.lang.String get_MolFileRLabel()
public static java.lang.String get_MolFileChiralFlag()
public static java.lang.String get_MolFileAtomQuery()
public static java.lang.String get_MolFileBondQuery()
public static java.lang.String get_MolFileBondEndPts()
public static java.lang.String get_MolFileBondAttach()
public static java.lang.String get_MolFileBondType()
public static java.lang.String get_MolFileBondStereo()
public static java.lang.String get_MolFileBondCfg()
public static java.lang.String getMRV_SMA()
public static java.lang.String getDummyLabel()
public static java.lang.String get_QueryFormalCharge()
public static java.lang.String get_QueryHCount()
public static java.lang.String get_QueryIsotope()
public static java.lang.String get_QueryMass()
public static java.lang.String get_ReactionDegreeChanged()
public static java.lang.String getNullBond()
public static java.lang.String get_rgroupAtomMaps()
public static java.lang.String get_rgroupBonds()
public static java.lang.String getReactantAtomIdx()
public static java.lang.String getReactionMapNum()
public static java.lang.String get_AtomID()
public static java.lang.String get_starred()
public static java.lang.String get_SLN_s()
public static java.lang.String get_Unfinished_SLN_()
public static java.lang.String get_brokenChirality()
public static java.lang.String getIsImplicit()
public static java.lang.String getSmilesSymbol()
public static java.lang.String get_TriposAtomType()
public static java.lang.String getTWOD()
public static java.lang.String getBalabanJ()
public static java.lang.String getBalanbanJ()
public static java.lang.String getDiscrims()
public static java.lang.String getDistanceMatrix_Paths()
public static java.lang.String getInternalRgroupSmiles()
public static double getMAX_DOUBLE()
public static double getEPS_DOUBLE()
public static double getSMALL_DOUBLE()
public static double getMAX_INT()
public static double getMAX_LONGINT()
public static void Union(Int_Vect_Vect rings, Int_Vect res, Int_Vect exclude)
public static void Union(Int_Vect_Vect rings, Int_Vect res)
public static int nextCombination(Int_Vect comb, int tot)
public static double round(double v)
public static boolean hasNonZeroZCoords(Conformer conf)
public static void removeGroupsWithAtom(Atom atom, StereoGroup_Vect groups)
public static void removeGroupsWithAtoms(Atom_Vect atoms, StereoGroup_Vect groups)
public static int getCi_RIGHTMOST_ATOM()
public static int getCi_LEADING_BOND()
public static int getCi_ATOM_HOLDER()
public static boolean getPreferCoordGen()
public static void setPreferCoordGen(boolean arg0)
public static int getMOLFILE_MAXLINE()
public static java.lang.String strip(java.lang.String orig)
public static RWMol MolDataStreamToMol(SWIGTYPE_p_std__istream inStream, SWIGTYPE_p_unsigned_int line, boolean sanitize, boolean removeHs, boolean strictParsing)
public static RWMol MolDataStreamToMol(SWIGTYPE_p_std__istream inStream, SWIGTYPE_p_unsigned_int line, boolean sanitize, boolean removeHs)
public static RWMol MolDataStreamToMol(SWIGTYPE_p_std__istream inStream, SWIGTYPE_p_unsigned_int line, boolean sanitize)
public static RWMol MolDataStreamToMol(SWIGTYPE_p_std__istream inStream, SWIGTYPE_p_unsigned_int line)
public static RWMol MolBlockToMol(java.lang.String molBlock, boolean sanitize, boolean removeHs, boolean strictParsing)
public static RWMol MolBlockToMol(java.lang.String molBlock, boolean sanitize, boolean removeHs)
public static RWMol MolBlockToMol(java.lang.String molBlock, boolean sanitize)
public static RWMol MolBlockToMol(java.lang.String molBlock)
public static RWMol MolFileToMol(java.lang.String fName, boolean sanitize, boolean removeHs, boolean strictParsing)
public static RWMol MolFileToMol(java.lang.String fName, boolean sanitize, boolean removeHs)
public static RWMol MolFileToMol(java.lang.String fName, boolean sanitize)
public static RWMol MolFileToMol(java.lang.String fName)
public static java.lang.String MolToMolBlock(ROMol mol, boolean includeStereo, int confId, boolean kekulize, boolean forceV3000)
public static java.lang.String MolToMolBlock(ROMol mol, boolean includeStereo, int confId, boolean kekulize)
public static java.lang.String MolToMolBlock(ROMol mol, boolean includeStereo, int confId)
public static java.lang.String MolToMolBlock(ROMol mol, boolean includeStereo)
public static java.lang.String MolToMolBlock(ROMol mol)
public static void MolToMolFile(ROMol mol, java.lang.String fName, boolean includeStereo, int confId, boolean kekulize, boolean forceV3000)
public static void MolToMolFile(ROMol mol, java.lang.String fName, boolean includeStereo, int confId, boolean kekulize)
public static void MolToMolFile(ROMol mol, java.lang.String fName, boolean includeStereo, int confId)
public static void MolToMolFile(ROMol mol, java.lang.String fName, boolean includeStereo)
public static void MolToMolFile(ROMol mol, java.lang.String fName)
public static java.lang.String MolToXYZBlock(ROMol mol, int confId)
public static java.lang.String MolToXYZBlock(ROMol mol)
public static void MolToXYZFile(ROMol mol, java.lang.String fName, int confId)
public static void MolToXYZFile(ROMol mol, java.lang.String fName)
public static RWMol TPLDataStreamToMol(SWIGTYPE_p_std__istream inStream, SWIGTYPE_p_unsigned_int line, boolean sanitize, boolean skipFirstConf)
public static RWMol TPLDataStreamToMol(SWIGTYPE_p_std__istream inStream, SWIGTYPE_p_unsigned_int line, boolean sanitize)
public static RWMol TPLDataStreamToMol(SWIGTYPE_p_std__istream inStream, SWIGTYPE_p_unsigned_int line)
public static RWMol TPLFileToMol(java.lang.String fName, boolean sanitize, boolean skipFirstConf)
public static RWMol TPLFileToMol(java.lang.String fName, boolean sanitize)
public static RWMol TPLFileToMol(java.lang.String fName)
public static java.lang.String MolToTPLText(ROMol mol, java.lang.String partialChargeProp, boolean writeFirstConfTwice)
public static java.lang.String MolToTPLText(ROMol mol, java.lang.String partialChargeProp)
public static java.lang.String MolToTPLText(ROMol mol)
public static void MolToTPLFile(ROMol mol, java.lang.String fName, java.lang.String partialChargeProp, boolean writeFirstConfTwice)
public static void MolToTPLFile(ROMol mol, java.lang.String fName, java.lang.String partialChargeProp)
public static void MolToTPLFile(ROMol mol, java.lang.String fName)
public static RWMol Mol2FileToMol(java.lang.String fName, boolean sanitize, boolean removeHs, Mol2Type variant, boolean cleanupSubstructures)
public static RWMol Mol2FileToMol(java.lang.String fName, boolean sanitize, boolean removeHs, Mol2Type variant)
public static RWMol Mol2FileToMol(java.lang.String fName, boolean sanitize, boolean removeHs)
public static RWMol Mol2FileToMol(java.lang.String fName, boolean sanitize)
public static RWMol Mol2FileToMol(java.lang.String fName)
public static RWMol Mol2DataStreamToMol(SWIGTYPE_p_std__istream inStream, boolean sanitize, boolean removeHs, Mol2Type variant, boolean cleanupSubstructures)
public static RWMol Mol2DataStreamToMol(SWIGTYPE_p_std__istream inStream, boolean sanitize, boolean removeHs, Mol2Type variant)
public static RWMol Mol2DataStreamToMol(SWIGTYPE_p_std__istream inStream, boolean sanitize, boolean removeHs)
public static RWMol Mol2DataStreamToMol(SWIGTYPE_p_std__istream inStream, boolean sanitize)
public static RWMol Mol2DataStreamToMol(SWIGTYPE_p_std__istream inStream)
public static RWMol Mol2BlockToMol(java.lang.String molBlock, boolean sanitize, boolean removeHs, Mol2Type variant, boolean cleanupSubstructures)
public static RWMol Mol2BlockToMol(java.lang.String molBlock, boolean sanitize, boolean removeHs, Mol2Type variant)
public static RWMol Mol2BlockToMol(java.lang.String molBlock, boolean sanitize, boolean removeHs)
public static RWMol Mol2BlockToMol(java.lang.String molBlock, boolean sanitize)
public static RWMol Mol2BlockToMol(java.lang.String molBlock)
public static RWMol PDBBlockToMol(java.lang.String str, boolean sanitize, boolean removeHs, long flavor, boolean proximityBonding)
public static RWMol PDBBlockToMol(java.lang.String str, boolean sanitize, boolean removeHs, long flavor)
public static RWMol PDBBlockToMol(java.lang.String str, boolean sanitize, boolean removeHs)
public static RWMol PDBBlockToMol(java.lang.String str, boolean sanitize)
public static RWMol PDBBlockToMol(java.lang.String str)
public static RWMol PDBDataStreamToMol(SWIGTYPE_p_std__istream inStream, boolean sanitize, boolean removeHs, long flavor, boolean proximityBonding)
public static RWMol PDBDataStreamToMol(SWIGTYPE_p_std__istream inStream, boolean sanitize, boolean removeHs, long flavor)
public static RWMol PDBDataStreamToMol(SWIGTYPE_p_std__istream inStream, boolean sanitize, boolean removeHs)
public static RWMol PDBDataStreamToMol(SWIGTYPE_p_std__istream inStream, boolean sanitize)
public static RWMol PDBDataStreamToMol(SWIGTYPE_p_std__istream inStream)
public static RWMol PDBFileToMol(java.lang.String fname, boolean sanitize, boolean removeHs, long flavor, boolean proximityBonding)
public static RWMol PDBFileToMol(java.lang.String fname, boolean sanitize, boolean removeHs, long flavor)
public static RWMol PDBFileToMol(java.lang.String fname, boolean sanitize, boolean removeHs)
public static RWMol PDBFileToMol(java.lang.String fname, boolean sanitize)
public static RWMol PDBFileToMol(java.lang.String fname)
public static java.lang.String MolToPDBBlock(ROMol mol, int confId, long flavor)
public static java.lang.String MolToPDBBlock(ROMol mol, int confId)
public static java.lang.String MolToPDBBlock(ROMol mol)
public static void MolToPDBFile(ROMol mol, java.lang.String fname, int confId, long flavor)
public static void MolToPDBFile(ROMol mol, java.lang.String fname, int confId)
public static void MolToPDBFile(ROMol mol, java.lang.String fname)
public static RWMol RDKitSVGToMol(java.lang.String svg, boolean sanitize, boolean removeHs)
public static RWMol RDKitSVGToMol(java.lang.String svg, boolean sanitize)
public static RWMol RDKitSVGToMol(java.lang.String svg)
public static RWMol RDKitSVGToMol(SWIGTYPE_p_std__istream instream, boolean sanitize, boolean removeHs)
public static RWMol RDKitSVGToMol(SWIGTYPE_p_std__istream instream, boolean sanitize)
public static RWMol RDKitSVGToMol(SWIGTYPE_p_std__istream instream)
public static void setAtomRLabel(Atom atm, int rlabel)
public static int getAtomRLabel(Atom atm)
public static void setAtomAlias(Atom atom, java.lang.String alias)
public static java.lang.String getAtomAlias(Atom atom)
public static void setAtomValue(Atom atom, java.lang.String value)
public static java.lang.String getAtomValue(Atom atom)
public static void setSupplementalSmilesLabel(Atom atom, java.lang.String label)
public static java.lang.String getSupplementalSmilesLabel(Atom atom)
public static boolean isEarlyAtom(int atomicNum)
public static int getCi_SPARSEINTVECT_VERSION()
public static java.lang.String getAtomPairsVersion()
public static SparseIntVect32 getAtomPairFingerprint(ROMol mol, long minLength, long maxLength, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants, boolean includeChirality, boolean use2D, int confId)
public static SparseIntVect32 getAtomPairFingerprint(ROMol mol, long minLength, long maxLength, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants, boolean includeChirality, boolean use2D)
public static SparseIntVect32 getAtomPairFingerprint(ROMol mol, long minLength, long maxLength, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants, boolean includeChirality)
public static SparseIntVect32 getAtomPairFingerprint(ROMol mol, long minLength, long maxLength, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants)
public static SparseIntVect32 getAtomPairFingerprint(ROMol mol, long minLength, long maxLength, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms)
public static SparseIntVect32 getAtomPairFingerprint(ROMol mol, long minLength, long maxLength, UInt_Vect fromAtoms)
public static SparseIntVect32 getAtomPairFingerprint(ROMol mol, long minLength, long maxLength)
public static SparseIntVect32 getAtomPairFingerprint(ROMol mol, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants, boolean includeChirality, boolean use2D, int confId)
public static SparseIntVect32 getAtomPairFingerprint(ROMol mol, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants, boolean includeChirality, boolean use2D)
public static SparseIntVect32 getAtomPairFingerprint(ROMol mol, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants, boolean includeChirality)
public static SparseIntVect32 getAtomPairFingerprint(ROMol mol, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants)
public static SparseIntVect32 getAtomPairFingerprint(ROMol mol, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms)
public static SparseIntVect32 getAtomPairFingerprint(ROMol mol, UInt_Vect fromAtoms)
public static SparseIntVect32 getAtomPairFingerprint(ROMol mol)
public static SparseIntVect32 getHashedAtomPairFingerprint(ROMol mol, long nBits, long minLength, long maxLength, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants, boolean includeChirality, boolean use2D, int confId)
public static SparseIntVect32 getHashedAtomPairFingerprint(ROMol mol, long nBits, long minLength, long maxLength, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants, boolean includeChirality, boolean use2D)
public static SparseIntVect32 getHashedAtomPairFingerprint(ROMol mol, long nBits, long minLength, long maxLength, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants, boolean includeChirality)
public static SparseIntVect32 getHashedAtomPairFingerprint(ROMol mol, long nBits, long minLength, long maxLength, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants)
public static SparseIntVect32 getHashedAtomPairFingerprint(ROMol mol, long nBits, long minLength, long maxLength, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms)
public static SparseIntVect32 getHashedAtomPairFingerprint(ROMol mol, long nBits, long minLength, long maxLength, UInt_Vect fromAtoms)
public static SparseIntVect32 getHashedAtomPairFingerprint(ROMol mol, long nBits, long minLength, long maxLength)
public static SparseIntVect32 getHashedAtomPairFingerprint(ROMol mol, long nBits, long minLength)
public static SparseIntVect32 getHashedAtomPairFingerprint(ROMol mol, long nBits)
public static SparseIntVect32 getHashedAtomPairFingerprint(ROMol mol)
public static ExplicitBitVect getHashedAtomPairFingerprintAsBitVect(ROMol mol, long nBits, long minLength, long maxLength, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants, long nBitsPerEntry, boolean includeChirality, boolean use2D, int confId)
public static ExplicitBitVect getHashedAtomPairFingerprintAsBitVect(ROMol mol, long nBits, long minLength, long maxLength, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants, long nBitsPerEntry, boolean includeChirality, boolean use2D)
public static ExplicitBitVect getHashedAtomPairFingerprintAsBitVect(ROMol mol, long nBits, long minLength, long maxLength, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants, long nBitsPerEntry, boolean includeChirality)
public static ExplicitBitVect getHashedAtomPairFingerprintAsBitVect(ROMol mol, long nBits, long minLength, long maxLength, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants, long nBitsPerEntry)
public static ExplicitBitVect getHashedAtomPairFingerprintAsBitVect(ROMol mol, long nBits, long minLength, long maxLength, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants)
public static ExplicitBitVect getHashedAtomPairFingerprintAsBitVect(ROMol mol, long nBits, long minLength, long maxLength, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms)
public static ExplicitBitVect getHashedAtomPairFingerprintAsBitVect(ROMol mol, long nBits, long minLength, long maxLength, UInt_Vect fromAtoms)
public static ExplicitBitVect getHashedAtomPairFingerprintAsBitVect(ROMol mol, long nBits, long minLength, long maxLength)
public static ExplicitBitVect getHashedAtomPairFingerprintAsBitVect(ROMol mol, long nBits, long minLength)
public static ExplicitBitVect getHashedAtomPairFingerprintAsBitVect(ROMol mol, long nBits)
public static ExplicitBitVect getHashedAtomPairFingerprintAsBitVect(ROMol mol)
public static SparseIntVect64 getTopologicalTorsionFingerprint(ROMol mol, long targetSize, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants, boolean includeChirality)
public static SparseIntVect64 getTopologicalTorsionFingerprint(ROMol mol, long targetSize, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants)
public static SparseIntVect64 getTopologicalTorsionFingerprint(ROMol mol, long targetSize, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms)
public static SparseIntVect64 getTopologicalTorsionFingerprint(ROMol mol, long targetSize, UInt_Vect fromAtoms)
public static SparseIntVect64 getTopologicalTorsionFingerprint(ROMol mol, long targetSize)
public static SparseIntVect64 getTopologicalTorsionFingerprint(ROMol mol)
public static SparseIntVect64 getHashedTopologicalTorsionFingerprint(ROMol mol, long nBits, long targetSize, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants, boolean includeChirality)
public static SparseIntVect64 getHashedTopologicalTorsionFingerprint(ROMol mol, long nBits, long targetSize, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants)
public static SparseIntVect64 getHashedTopologicalTorsionFingerprint(ROMol mol, long nBits, long targetSize, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms)
public static SparseIntVect64 getHashedTopologicalTorsionFingerprint(ROMol mol, long nBits, long targetSize, UInt_Vect fromAtoms)
public static SparseIntVect64 getHashedTopologicalTorsionFingerprint(ROMol mol, long nBits, long targetSize)
public static SparseIntVect64 getHashedTopologicalTorsionFingerprint(ROMol mol, long nBits)
public static SparseIntVect64 getHashedTopologicalTorsionFingerprint(ROMol mol)
public static ExplicitBitVect getHashedTopologicalTorsionFingerprintAsBitVect(ROMol mol, long nBits, long targetSize, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants, long nBitsPerEntry, boolean includeChirality)
public static ExplicitBitVect getHashedTopologicalTorsionFingerprintAsBitVect(ROMol mol, long nBits, long targetSize, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants, long nBitsPerEntry)
public static ExplicitBitVect getHashedTopologicalTorsionFingerprintAsBitVect(ROMol mol, long nBits, long targetSize, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms, UInt_Vect atomInvariants)
public static ExplicitBitVect getHashedTopologicalTorsionFingerprintAsBitVect(ROMol mol, long nBits, long targetSize, UInt_Vect fromAtoms, UInt_Vect ignoreAtoms)
public static ExplicitBitVect getHashedTopologicalTorsionFingerprintAsBitVect(ROMol mol, long nBits, long targetSize, UInt_Vect fromAtoms)
public static ExplicitBitVect getHashedTopologicalTorsionFingerprintAsBitVect(ROMol mol, long nBits, long targetSize)
public static ExplicitBitVect getHashedTopologicalTorsionFingerprintAsBitVect(ROMol mol, long nBits)
public static ExplicitBitVect getHashedTopologicalTorsionFingerprintAsBitVect(ROMol mol)
public static int getMAX_NATOMS()
public static int getMAX_CYCLES()
public static int getMAX_BONDTYPE()
public static void canonicalizeFragment(ROMol mol, int atomIdx, SWIGTYPE_p_std__vectorT_RDKit__Canon__AtomColors_t colors, UInt_Vect ranks, SWIGTYPE_p_std__vectorT_RDKit__Canon__MolStackElem_t molStack, SWIGTYPE_p_boost__dynamic_bitsetT_t bondsInPlay, Str_Vect bondSymbols, boolean doIsomericSmiles, boolean doRandom)
public static void canonicalizeFragment(ROMol mol, int atomIdx, SWIGTYPE_p_std__vectorT_RDKit__Canon__AtomColors_t colors, UInt_Vect ranks, SWIGTYPE_p_std__vectorT_RDKit__Canon__MolStackElem_t molStack, SWIGTYPE_p_boost__dynamic_bitsetT_t bondsInPlay, Str_Vect bondSymbols, boolean doIsomericSmiles)
public static void canonicalizeFragment(ROMol mol, int atomIdx, SWIGTYPE_p_std__vectorT_RDKit__Canon__AtomColors_t colors, UInt_Vect ranks, SWIGTYPE_p_std__vectorT_RDKit__Canon__MolStackElem_t molStack, SWIGTYPE_p_boost__dynamic_bitsetT_t bondsInPlay, Str_Vect bondSymbols)
public static void canonicalizeFragment(ROMol mol, int atomIdx, SWIGTYPE_p_std__vectorT_RDKit__Canon__AtomColors_t colors, UInt_Vect ranks, SWIGTYPE_p_std__vectorT_RDKit__Canon__MolStackElem_t molStack, SWIGTYPE_p_boost__dynamic_bitsetT_t bondsInPlay)
public static void canonicalizeFragment(ROMol mol, int atomIdx, SWIGTYPE_p_std__vectorT_RDKit__Canon__AtomColors_t colors, UInt_Vect ranks, SWIGTYPE_p_std__vectorT_RDKit__Canon__MolStackElem_t molStack)
public static boolean chiralAtomNeedsTagInversion(ROMol mol, Atom atom, boolean isAtomFirst, long numClosures)
public static java.lang.String qhelper(SWIGTYPE_p_Queries__QueryT_int_RDKit__Atom_const_p_true_t q, long depth)
public static java.lang.String describeQuery(Atom atom)
public static java.lang.String qhelper(SWIGTYPE_p_Queries__QueryT_int_RDKit__Bond_const_p_true_t q, long depth)
public static java.lang.String describeQuery(Bond bond)
public static int queryAtomAromatic(Atom at)
public static int queryAtomAliphatic(Atom at)
public static int queryAtomExplicitDegree(Atom at)
public static int queryAtomTotalDegree(Atom at)
public static int queryAtomNonHydrogenDegree(Atom at)
public static int queryAtomHeavyAtomDegree(Atom at)
public static int queryAtomHCount(Atom at)
public static int queryAtomImplicitHCount(Atom at)
public static int queryAtomHasImplicitH(Atom at)
public static int queryAtomImplicitValence(Atom at)
public static int queryAtomExplicitValence(Atom at)
public static int queryAtomTotalValence(Atom at)
public static int queryAtomUnsaturated(Atom at)
public static int queryAtomNum(Atom at)
public static int makeAtomType(int atomic_num, boolean aromatic)
public static void parseAtomType(int val, SWIGTYPE_p_int atomic_num, SWIGTYPE_p_bool aromatic)
public static boolean getAtomTypeIsAromatic(int val)
public static int getAtomTypeAtomicNum(int val)
public static int queryAtomType(Atom at)
public static int getMassIntegerConversionFactor()
public static int queryAtomMass(Atom at)
public static int queryAtomIsotope(Atom at)
public static int queryAtomFormalCharge(Atom at)
public static int queryAtomNegativeFormalCharge(Atom at)
public static int queryAtomHybridization(Atom at)
public static int queryAtomNumRadicalElectrons(Atom at)
public static int queryAtomHasChiralTag(Atom at)
public static int queryAtomMissingChiralTag(Atom at)
public static int queryAtomHasHeteroatomNbrs(Atom at)
public static int queryAtomNumHeteroatomNbrs(Atom at)
public static int queryAtomHasAliphaticHeteroatomNbrs(Atom at)
public static int queryAtomNumAliphaticHeteroatomNbrs(Atom at)
public static long queryAtomBondProduct(Atom at)
public static long queryAtomAllBondProduct(Atom at)
public static int queryBondOrder(Bond bond)
public static int queryBondIsSingleOrAromatic(Bond bond)
public static int queryBondDir(Bond bond)
public static int queryIsBondInNRings(Bond at)
public static int queryBondHasStereo(Bond bnd)
public static int queryIsAtomInNRings(Atom at)
public static int queryIsAtomInRing(Atom at)
public static int queryAtomHasRingBond(Atom at)
public static int queryIsBondInRing(Bond bond)
public static int queryAtomMinRingSize(Atom at)
public static int queryBondMinRingSize(Bond bond)
public static int queryAtomRingBondCount(Atom at)
public static SWIGTYPE_p_Queries__RangeQueryT_int_RDKit__Atom_const_p_true_t makeAtomRangeQuery(int lower, int upper, boolean lowerOpen, boolean upperOpen, SWIGTYPE_p_f_p_q_const__RDKit__Atom__int func, java.lang.String description)
public static SWIGTYPE_p_Queries__RangeQueryT_int_RDKit__Atom_const_p_true_t makeAtomRangeQuery(int lower, int upper, boolean lowerOpen, boolean upperOpen, SWIGTYPE_p_f_p_q_const__RDKit__Atom__int func)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomNumQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomTypeQuery(int num, int aromatic)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomImplicitValenceQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomExplicitValenceQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomTotalValenceQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomExplicitDegreeQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomTotalDegreeQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomHeavyAtomDegreeQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomHCountQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomHasImplicitHQuery()
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomImplicitHCountQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomAromaticQuery()
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomAliphaticQuery()
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomMassQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomIsotopeQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomFormalChargeQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomNegativeFormalChargeQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomHybridizationQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomNumRadicalElectronsQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomHasChiralTagQuery()
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomMissingChiralTagQuery()
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomUnsaturatedQuery()
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomInRingQuery()
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomInNRingsQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomInRingOfSizeQuery(int tgt)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomMinRingSizeQuery(int tgt)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomRingBondCountQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAAtomQuery()
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAHAtomQuery()
public static SWIGTYPE_p_Queries__OrQueryT_int_RDKit__Atom_const_p_true_t makeQAtomQuery()
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeQHAtomQuery()
public static SWIGTYPE_p_Queries__OrQueryT_int_RDKit__Atom_const_p_true_t makeXAtomQuery()
public static SWIGTYPE_p_Queries__OrQueryT_int_RDKit__Atom_const_p_true_t makeXHAtomQuery()
public static SWIGTYPE_p_Queries__OrQueryT_int_RDKit__Atom_const_p_true_t makeMAtomQuery()
public static SWIGTYPE_p_Queries__OrQueryT_int_RDKit__Atom_const_p_true_t makeMHAtomQuery()
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomHasRingBondQuery()
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomNumHeteroatomNbrsQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomHasHeteroatomNbrsQuery()
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomNumAliphaticHeteroatomNbrsQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Atom_const_p_true_t makeAtomHasAliphaticHeteroatomNbrsQuery()
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Bond_const_p_true_t makeBondOrderEqualsQuery(Bond.BondType what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Bond_const_p_true_t makeSingleOrAromaticBondQuery()
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Bond_const_p_true_t makeBondDirEqualsQuery(Bond.BondDir what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Bond_const_p_true_t makeBondHasStereoQuery()
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Bond_const_p_true_t makeBondIsInRingQuery()
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Bond_const_p_true_t makeBondInRingOfSizeQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Bond_const_p_true_t makeBondMinRingSizeQuery(int what)
public static SWIGTYPE_p_Queries__EqualityQueryT_int_RDKit__Bond_const_p_true_t makeBondInNRingsQuery(int tgt)
public static SWIGTYPE_p_Queries__QueryT_int_RDKit__Bond_const_p_true_t makeBondNullQuery()
public static SWIGTYPE_p_Queries__QueryT_int_RDKit__Atom_const_p_true_t makeAtomNullQuery()
public static int queryAtomRingMembership(Atom at)
public static boolean isComplexQuery(Bond b)
public static boolean isComplexQuery(Atom a)
public static boolean isAtomAromatic(Atom a)
public static java.lang.String getPeriodicTableAtomData()
public static SWIGTYPE_p_std__string getIsotopesAtomData()
public static double getElectronMass()
public static Atom SmilesToAtom(java.lang.String smi)
public static Bond SmilesToBond(java.lang.String smi)
public static Atom SmartsToAtom(java.lang.String sma)
public static Bond SmartsToBond(java.lang.String sma)
public static java.lang.String getCXExtensions(ROMol mol)
public static boolean inOrganicSubset(int atomicNumber)
public static java.lang.String GetAtomSmiles(Atom atom, boolean doKekule, Bond bondIn, boolean allHsExplicit, boolean isomericSmiles)
public static java.lang.String GetAtomSmiles(Atom atom, boolean doKekule, Bond bondIn, boolean allHsExplicit)
public static java.lang.String GetAtomSmiles(Atom atom, boolean doKekule, Bond bondIn)
public static java.lang.String GetAtomSmiles(Atom atom, boolean doKekule)
public static java.lang.String GetAtomSmiles(Atom atom)
public static java.lang.String GetBondSmiles(Bond bond, int atomToLeftIdx, boolean doKekule, boolean allBondsExplicit)
public static java.lang.String GetBondSmiles(Bond bond, int atomToLeftIdx, boolean doKekule)
public static java.lang.String GetBondSmiles(Bond bond, int atomToLeftIdx)
public static java.lang.String GetBondSmiles(Bond bond)
public static java.lang.String MolToSmiles(ROMol mol, boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom, boolean canonical, boolean allBondsExplicit, boolean allHsExplicit, boolean doRandom)
public static java.lang.String MolToSmiles(ROMol mol, boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom, boolean canonical, boolean allBondsExplicit, boolean allHsExplicit)
public static java.lang.String MolToSmiles(ROMol mol, boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom, boolean canonical, boolean allBondsExplicit)
public static java.lang.String MolToSmiles(ROMol mol, boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom, boolean canonical)
public static java.lang.String MolToSmiles(ROMol mol, boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom)
public static java.lang.String MolToSmiles(ROMol mol, boolean doIsomericSmiles, boolean doKekule)
public static java.lang.String MolToSmiles(ROMol mol, boolean doIsomericSmiles)
public static java.lang.String MolToSmiles(ROMol mol)
public static java.lang.String MolFragmentToSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse, Str_Vect atomSymbols, Str_Vect bondSymbols, boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom, boolean canonical, boolean allBondsExplicit, boolean allHsExplicit)
public static java.lang.String MolFragmentToSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse, Str_Vect atomSymbols, Str_Vect bondSymbols, boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom, boolean canonical, boolean allBondsExplicit)
public static java.lang.String MolFragmentToSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse, Str_Vect atomSymbols, Str_Vect bondSymbols, boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom, boolean canonical)
public static java.lang.String MolFragmentToSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse, Str_Vect atomSymbols, Str_Vect bondSymbols, boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom)
public static java.lang.String MolFragmentToSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse, Str_Vect atomSymbols, Str_Vect bondSymbols, boolean doIsomericSmiles, boolean doKekule)
public static java.lang.String MolFragmentToSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse, Str_Vect atomSymbols, Str_Vect bondSymbols, boolean doIsomericSmiles)
public static java.lang.String MolFragmentToSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse, Str_Vect atomSymbols, Str_Vect bondSymbols)
public static java.lang.String MolFragmentToSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse, Str_Vect atomSymbols)
public static java.lang.String MolFragmentToSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse)
public static java.lang.String MolFragmentToSmiles(ROMol mol, Int_Vect atomsToUse)
public static java.lang.String MolToCXSmiles(ROMol mol, boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom, boolean canonical, boolean allBondsExplicit, boolean allHsExplicit, boolean doRandom)
public static java.lang.String MolToCXSmiles(ROMol mol, boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom, boolean canonical, boolean allBondsExplicit, boolean allHsExplicit)
public static java.lang.String MolToCXSmiles(ROMol mol, boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom, boolean canonical, boolean allBondsExplicit)
public static java.lang.String MolToCXSmiles(ROMol mol, boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom, boolean canonical)
public static java.lang.String MolToCXSmiles(ROMol mol, boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom)
public static java.lang.String MolToCXSmiles(ROMol mol, boolean doIsomericSmiles, boolean doKekule)
public static java.lang.String MolToCXSmiles(ROMol mol, boolean doIsomericSmiles)
public static java.lang.String MolToCXSmiles(ROMol mol)
public static java.lang.String MolFragmentToCXSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse, Str_Vect atomSymbols, Str_Vect bondSymbols, boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom, boolean canonical, boolean allBondsExplicit, boolean allHsExplicit)
public static java.lang.String MolFragmentToCXSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse, Str_Vect atomSymbols, Str_Vect bondSymbols, boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom, boolean canonical, boolean allBondsExplicit)
public static java.lang.String MolFragmentToCXSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse, Str_Vect atomSymbols, Str_Vect bondSymbols, boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom, boolean canonical)
public static java.lang.String MolFragmentToCXSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse, Str_Vect atomSymbols, Str_Vect bondSymbols, boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom)
public static java.lang.String MolFragmentToCXSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse, Str_Vect atomSymbols, Str_Vect bondSymbols, boolean doIsomericSmiles, boolean doKekule)
public static java.lang.String MolFragmentToCXSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse, Str_Vect atomSymbols, Str_Vect bondSymbols, boolean doIsomericSmiles)
public static java.lang.String MolFragmentToCXSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse, Str_Vect atomSymbols, Str_Vect bondSymbols)
public static java.lang.String MolFragmentToCXSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse, Str_Vect atomSymbols)
public static java.lang.String MolFragmentToCXSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse)
public static java.lang.String MolFragmentToCXSmiles(ROMol mol, Int_Vect atomsToUse)
public static java.lang.String GetAtomSmarts(QueryAtom qatom)
public static java.lang.String GetBondSmarts(QueryBond qbond, int atomToLeftIdx)
public static java.lang.String GetBondSmarts(QueryBond qbond)
public static java.lang.String MolToSmarts(ROMol mol, boolean doIsomericSmarts)
public static java.lang.String MolToSmarts(ROMol mol)
public static java.lang.String MolFragmentToSmarts(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse, boolean doIsomericSmarts)
public static java.lang.String MolFragmentToSmarts(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse)
public static java.lang.String MolFragmentToSmarts(ROMol mol, Int_Vect atomsToUse)
public static int getCi_LOCAL_INF()
public static int countAtomElec(Atom at)
return the number of electrons available on an atom to donate for aromaticity
The result is determined using the default valency, number of lone pairs, number of bonds and the formal charge. Note that the atom may not donate all of these electrons to a ring for aromaticity (also used in Conjugation and hybridization code).
at
- the atom of interest
public static int getFormalCharge(ROMol mol)
public static boolean atomHasConjugatedBond(Atom at)
public static long getMolFrags(ROMol mol, Int_Vect_Vect frags)
public static ROMol_Vect getMolFrags(ROMol mol, boolean sanitizeFrags, Int_Vect frags, Int_Vect_Vect fragsMolAtomMapping, boolean copyConformers)
public static ROMol_Vect getMolFrags(ROMol mol, boolean sanitizeFrags, Int_Vect frags, Int_Vect_Vect fragsMolAtomMapping)
public static ROMol_Vect getMolFrags(ROMol mol, boolean sanitizeFrags, Int_Vect frags)
public static ROMol_Vect getMolFrags(ROMol mol, boolean sanitizeFrags)
splits a molecule into its component fragments
mol
- the molecule of interest
sanitizeFrags toggles sanitization of the fragments after they are built
frags used to return the mapping of Atoms->fragments. if provided, frags will be mol->getNumAtoms() long on return and will contain the fragment assignment for each Atom
public static ROMol_Vect getMolFrags(ROMol mol)
splits a molecule into its component fragments
mol
- the molecule of interest
sanitizeFrags toggles sanitization of the fragments after they are built
frags used to return the mapping of Atoms->fragments. if provided, frags will be mol->getNumAtoms() long on return and will contain the fragment assignment for each Atom
public static double computeBalabanJ(ROMol mol, boolean useBO, boolean force, Int_Vect bondPath, boolean cacheIt)
calculates Balaban's J index for the molecule
mol
- the molecule of interest
useBO toggles inclusion of the bond order in the calculation (when false, we're not really calculating the J value)
force forces the calculation (instead of using cached results)
bondPath when included, only paths using bonds whose indices occur in this vector will be included in the calculation
cacheIt If this is true, the calculated value will be cached as a property on the molecule
public static double computeBalabanJ(ROMol mol, boolean useBO, boolean force, Int_Vect bondPath)
calculates Balaban's J index for the molecule
mol
- the molecule of interest
useBO toggles inclusion of the bond order in the calculation (when false, we're not really calculating the J value)
force forces the calculation (instead of using cached results)
bondPath when included, only paths using bonds whose indices occur in this vector will be included in the calculation
cacheIt If this is true, the calculated value will be cached as a property on the molecule
public static double computeBalabanJ(ROMol mol, boolean useBO, boolean force)
calculates Balaban's J index for the molecule
mol
- the molecule of interest
useBO toggles inclusion of the bond order in the calculation (when false, we're not really calculating the J value)
force forces the calculation (instead of using cached results)
bondPath when included, only paths using bonds whose indices occur in this vector will be included in the calculation
cacheIt If this is true, the calculated value will be cached as a property on the molecule
public static double computeBalabanJ(ROMol mol, boolean useBO)
calculates Balaban's J index for the molecule
mol
- the molecule of interest
useBO toggles inclusion of the bond order in the calculation (when false, we're not really calculating the J value)
force forces the calculation (instead of using cached results)
bondPath when included, only paths using bonds whose indices occur in this vector will be included in the calculation
cacheIt If this is true, the calculated value will be cached as a property on the molecule
public static double computeBalabanJ(ROMol mol)
calculates Balaban's J index for the molecule
mol
- the molecule of interest
useBO toggles inclusion of the bond order in the calculation (when false, we're not really calculating the J value)
force forces the calculation (instead of using cached results)
bondPath when included, only paths using bonds whose indices occur in this vector will be included in the calculation
cacheIt If this is true, the calculated value will be cached as a property on the molecule
public static double computeBalabanJ(SWIGTYPE_p_double distMat, int nb, int nAts)
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
public static ROMol addHs(ROMol mol, boolean explicitOnly, boolean addCoords, UInt_Vect onlyOnAtoms, boolean addResidueInfo)
public static ROMol addHs(ROMol mol, boolean explicitOnly, boolean addCoords, UInt_Vect onlyOnAtoms)
public static ROMol addHs(ROMol mol, boolean explicitOnly, boolean addCoords)
returns a copy of a molecule with hydrogens added in as explicit Atoms
mol
- the molecule to add Hs to
explicitOnly (optional) if this true, only explicit Hs will be added
addCoords (optional) If this is true, estimates for the atomic coordinates of the added Hs will be used.
public static ROMol addHs(ROMol mol, boolean explicitOnly)
returns a copy of a molecule with hydrogens added in as explicit Atoms
mol
- the molecule to add Hs to
explicitOnly (optional) if this true, only explicit Hs will be added
addCoords (optional) If this is true, estimates for the atomic coordinates of the added Hs will be used.
public static ROMol addHs(ROMol mol)
returns a copy of a molecule with hydrogens added in as explicit Atoms
mol
- the molecule to add Hs to
explicitOnly (optional) if this true, only explicit Hs will be added
addCoords (optional) If this is true, estimates for the atomic coordinates of the added Hs will be used.
public static void addHs(RWMol mol, boolean explicitOnly, boolean addCoords, UInt_Vect onlyOnAtoms, boolean addResidueInfo)
public static void addHs(RWMol mol, boolean explicitOnly, boolean addCoords, UInt_Vect onlyOnAtoms)
public static void addHs(RWMol mol, boolean explicitOnly, boolean addCoords)
public static void addHs(RWMol mol, boolean explicitOnly)
public static void addHs(RWMol mol)
public static ROMol removeHs(ROMol mol, boolean implicitOnly, boolean updateExplicitCount, boolean sanitize)
returns a copy of a molecule with hydrogens removed
mol
- the molecule to remove Hs from
implicitOnly (optional) if this true, only implicit Hs will be removed
updateExplicitCount (optional) If this is true, when explicit Hs are removed from the graph, the heavy atom to which they are bound will have its counter of explicit Hs increased.
sanitize,: (optional) If this is true, the final molecule will be sanitized
public static ROMol removeHs(ROMol mol, boolean implicitOnly, boolean updateExplicitCount)
returns a copy of a molecule with hydrogens removed
mol
- the molecule to remove Hs from
implicitOnly (optional) if this true, only implicit Hs will be removed
updateExplicitCount (optional) If this is true, when explicit Hs are removed from the graph, the heavy atom to which they are bound will have its counter of explicit Hs increased.
sanitize,: (optional) If this is true, the final molecule will be sanitized
public static ROMol removeHs(ROMol mol, boolean implicitOnly)
returns a copy of a molecule with hydrogens removed
mol
- the molecule to remove Hs from
implicitOnly (optional) if this true, only implicit Hs will be removed
updateExplicitCount (optional) If this is true, when explicit Hs are removed from the graph, the heavy atom to which they are bound will have its counter of explicit Hs increased.
sanitize,: (optional) If this is true, the final molecule will be sanitized
public static ROMol removeHs(ROMol mol)
returns a copy of a molecule with hydrogens removed
mol
- the molecule to remove Hs from
implicitOnly (optional) if this true, only implicit Hs will be removed
updateExplicitCount (optional) If this is true, when explicit Hs are removed from the graph, the heavy atom to which they are bound will have its counter of explicit Hs increased.
sanitize,: (optional) If this is true, the final molecule will be sanitized
public static void removeHs(RWMol mol, boolean implicitOnly, boolean updateExplicitCount, boolean sanitize)
public static void removeHs(RWMol mol, boolean implicitOnly, boolean updateExplicitCount)
public static void removeHs(RWMol mol, boolean implicitOnly)
public static void removeHs(RWMol mol)
public static ROMol mergeQueryHs(ROMol mol)
returns a copy of a molecule with hydrogens removed and added as queries to the heavy atoms to which they are bound.
This is really intended to be used with molecules that contain QueryAtoms
mol
- the molecule to remove Hs from
public static void mergeQueryHs(RWMol mol, boolean mergeUnmappedOnly)
public static void mergeQueryHs(RWMol mol)
public static ROMol adjustQueryProperties(ROMol mol, AdjustQueryParameters params)
public static void adjustQueryProperties(RWMol mol, AdjustQueryParameters params)
public static void adjustQueryProperties(RWMol mol)
public static void sanitizeMol(RWMol mol, SWIGTYPE_p_unsigned_int operationThatFailed, long sanitizeOps)
public static void sanitizeMol(RWMol mol, SWIGTYPE_p_unsigned_int operationThatFailed)
public static void sanitizeMol(RWMol mol)
carries out a collection of tasks for cleaning up a molecule and ensuring that it makes 'chemical sense'
This functions calls the following in sequence
1. MolOps::cleanUp() 2. MolOps::Kekulize() 3. MolOps::setAromaticity() 4. MolOps::setConjugation() 5. MolOps::setHybridization() 6. MolOps::cleanupChirality() 7. MolOps::adjustHs()
mol
- the RWMol to be cleaned
public static int setAromaticity(RWMol mol, AromaticityModel model, SWIGTYPE_p_f_r_RDKit__RWMol__int func)
public static int setAromaticity(RWMol mol, AromaticityModel model)
public static int setAromaticity(RWMol mol)
Sets up the aromaticity for a molecule.
This is what happens here:
1. find all the simple rings by calling the findSSSR function 2. loop over all the Atoms in each ring and mark them if they are candidates for aromaticity. A ring atom is a candidate if it can spare electrons to the ring and if it's from the first two rows of the periodic table. 3. ased on the candidate atoms, mark the rings to be either candidates or non-candidates. A ring is a candidate only if all its atoms are candidates 4. apply Hueckel rule to each of the candidate rings to check if the ring can be aromatic
mol
- the RWMol of interest
Kekulization has been done (i.e. MolOps::Kekulize() has already been called)
public static void cleanUp(RWMol mol)
Designed to be called by the sanitizer to handle special cases before anything is done.
Currently this:
modifies nitro groups, so that the nitrogen does not have a unreasonable valence of 5, as follows: o the nitrogen gets a positve charge o one of the oxygens gets a negative chage and the double bond to this oxygen is changed to a single bond The net result is that nitro groups can be counted on to be: '[N+](=O)[O-]'
mol
- the molecule of interestpublic static void assignRadicals(RWMol mol)
public static void adjustHs(RWMol mol)
adjust the number of implicit and explicit Hs for special cases
Currently this:
modifies aromatic nitrogens so that, when appropriate, they have an explicit H marked (e.g. so that we get things like 'c1cc[nH]cc1'
mol
- the molecule of interest
Assumptions
this is called after the molecule has been sanitized, aromaticity has been perceived, and the implicit valence of everything has been calculated.
public static void Kekulize(RWMol mol, boolean markAtomsBonds, long maxBackTracks)
Kekulizes the molecule.
mol
- the molecule of interest
markAtomsBonds if this is set to true, isAromatic boolean settings on both the Bonds and Atoms are turned to false following the Kekulization, otherwise they are left alone in their original state.
maxBackTracks the maximum number of attempts at back-tracking. The algorithm uses a back-tracking procedure to revist a previous setting of double bond if we hit a wall in the kekulization process
public static void Kekulize(RWMol mol, boolean markAtomsBonds)
Kekulizes the molecule.
mol
- the molecule of interest
markAtomsBonds if this is set to true, isAromatic boolean settings on both the Bonds and Atoms are turned to false following the Kekulization, otherwise they are left alone in their original state.
maxBackTracks the maximum number of attempts at back-tracking. The algorithm uses a back-tracking procedure to revist a previous setting of double bond if we hit a wall in the kekulization process
public static void Kekulize(RWMol mol)
Kekulizes the molecule.
mol
- the molecule of interest
markAtomsBonds if this is set to true, isAromatic boolean settings on both the Bonds and Atoms are turned to false following the Kekulization, otherwise they are left alone in their original state.
maxBackTracks the maximum number of attempts at back-tracking. The algorithm uses a back-tracking procedure to revist a previous setting of double bond if we hit a wall in the kekulization process
public static void setConjugation(ROMol mol)
public static void setHybridization(ROMol mol)
public static int findSSSR(ROMol mol, Int_Vect_Vect res)
public static int findSSSR(ROMol mol)
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
public static void fastFindRings(ROMol mol)
public static int symmetrizeSSSR(ROMol mol, Int_Vect_Vect res)
public static int symmetrizeSSSR(ROMol mol)
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
public static SWIGTYPE_p_double getAdjacencyMatrix(ROMol mol, boolean useBO, int emptyVal, boolean force, java.lang.String propNamePrefix, SWIGTYPE_p_boost__dynamic_bitsetT_t bondsToUse)
public static SWIGTYPE_p_double getAdjacencyMatrix(ROMol mol, boolean useBO, int emptyVal, boolean force, java.lang.String propNamePrefix)
returns a molecule's adjacency matrix
mol
- the molecule of interest
useBO toggles use of bond orders in the matrix
emptyVal sets the empty value (for non-adjacent atoms)
force forces calculation of the matrix, even if already computed
propNamePrefix used to set the cached property name
public static SWIGTYPE_p_double getAdjacencyMatrix(ROMol mol, boolean useBO, int emptyVal, boolean force)
returns a molecule's adjacency matrix
mol
- the molecule of interest
useBO toggles use of bond orders in the matrix
emptyVal sets the empty value (for non-adjacent atoms)
force forces calculation of the matrix, even if already computed
propNamePrefix used to set the cached property name
public static SWIGTYPE_p_double getAdjacencyMatrix(ROMol mol, boolean useBO, int emptyVal)
returns a molecule's adjacency matrix
mol
- the molecule of interest
useBO toggles use of bond orders in the matrix
emptyVal sets the empty value (for non-adjacent atoms)
force forces calculation of the matrix, even if already computed
propNamePrefix used to set the cached property name
public static SWIGTYPE_p_double getAdjacencyMatrix(ROMol mol, boolean useBO)
returns a molecule's adjacency matrix
mol
- the molecule of interest
useBO toggles use of bond orders in the matrix
emptyVal sets the empty value (for non-adjacent atoms)
force forces calculation of the matrix, even if already computed
propNamePrefix used to set the cached property name
public static SWIGTYPE_p_double getAdjacencyMatrix(ROMol mol)
returns a molecule's adjacency matrix
mol
- the molecule of interest
useBO toggles use of bond orders in the matrix
emptyVal sets the empty value (for non-adjacent atoms)
force forces calculation of the matrix, even if already computed
propNamePrefix used to set the cached property name
public static SWIGTYPE_p_double getDistanceMat(ROMol mol, boolean useBO, boolean useAtomWts, boolean force, java.lang.String propNamePrefix)
Computes the molecule's topological distance matrix.
Uses the Floyd-Warshall all-pairs-shortest-paths algorithm.
mol
- the molecule of interest
useBO toggles use of bond orders in the matrix
useAtomWts sets the diagonal elements of the result to 6.0/(atomic number) so that the matrix can be used to calculate Balaban J values. This does not affect the bond weights.
force forces calculation of the matrix, even if already computed
propNamePrefix used to set the cached property name
public static SWIGTYPE_p_double getDistanceMat(ROMol mol, boolean useBO, boolean useAtomWts, boolean force)
Computes the molecule's topological distance matrix.
Uses the Floyd-Warshall all-pairs-shortest-paths algorithm.
mol
- the molecule of interest
useBO toggles use of bond orders in the matrix
useAtomWts sets the diagonal elements of the result to 6.0/(atomic number) so that the matrix can be used to calculate Balaban J values. This does not affect the bond weights.
force forces calculation of the matrix, even if already computed
propNamePrefix used to set the cached property name
public static SWIGTYPE_p_double getDistanceMat(ROMol mol, boolean useBO, boolean useAtomWts)
Computes the molecule's topological distance matrix.
Uses the Floyd-Warshall all-pairs-shortest-paths algorithm.
mol
- the molecule of interest
useBO toggles use of bond orders in the matrix
useAtomWts sets the diagonal elements of the result to 6.0/(atomic number) so that the matrix can be used to calculate Balaban J values. This does not affect the bond weights.
force forces calculation of the matrix, even if already computed
propNamePrefix used to set the cached property name
public static SWIGTYPE_p_double getDistanceMat(ROMol mol, boolean useBO)
Computes the molecule's topological distance matrix.
Uses the Floyd-Warshall all-pairs-shortest-paths algorithm.
mol
- the molecule of interest
useBO toggles use of bond orders in the matrix
useAtomWts sets the diagonal elements of the result to 6.0/(atomic number) so that the matrix can be used to calculate Balaban J values. This does not affect the bond weights.
force forces calculation of the matrix, even if already computed
propNamePrefix used to set the cached property name
public static SWIGTYPE_p_double getDistanceMat(ROMol mol)
Computes the molecule's topological distance matrix.
Uses the Floyd-Warshall all-pairs-shortest-paths algorithm.
mol
- the molecule of interest
useBO toggles use of bond orders in the matrix
useAtomWts sets the diagonal elements of the result to 6.0/(atomic number) so that the matrix can be used to calculate Balaban J values. This does not affect the bond weights.
force forces calculation of the matrix, even if already computed
propNamePrefix used to set the cached property name
public static SWIGTYPE_p_double getDistanceMat(ROMol mol, Int_Vect activeAtoms, SWIGTYPE_p_std__vectorT_RDKit__Bond_const_p_t bonds, boolean useBO, boolean useAtomWts)
Computes the molecule's topological distance matrix.
Uses the Floyd-Warshall all-pairs-shortest-paths algorithm.
mol
- the molecule of interest
activeAtoms only elements corresponding to these atom indices will be included in the calculation
bonds only bonds found in this list will be included in the calculation
useBO toggles use of bond orders in the matrix
useAtomWts sets the diagonal elements of the result to 6.0/(atomic number) so that the matrix can be used to calculate Balaban J values. This does not affect the bond weights.
public static SWIGTYPE_p_double getDistanceMat(ROMol mol, Int_Vect activeAtoms, SWIGTYPE_p_std__vectorT_RDKit__Bond_const_p_t bonds, boolean useBO)
Computes the molecule's topological distance matrix.
Uses the Floyd-Warshall all-pairs-shortest-paths algorithm.
mol
- the molecule of interest
activeAtoms only elements corresponding to these atom indices will be included in the calculation
bonds only bonds found in this list will be included in the calculation
useBO toggles use of bond orders in the matrix
useAtomWts sets the diagonal elements of the result to 6.0/(atomic number) so that the matrix can be used to calculate Balaban J values. This does not affect the bond weights.
public static SWIGTYPE_p_double getDistanceMat(ROMol mol, Int_Vect activeAtoms, SWIGTYPE_p_std__vectorT_RDKit__Bond_const_p_t bonds)
Computes the molecule's topological distance matrix.
Uses the Floyd-Warshall all-pairs-shortest-paths algorithm.
mol
- the molecule of interest
activeAtoms only elements corresponding to these atom indices will be included in the calculation
bonds only bonds found in this list will be included in the calculation
useBO toggles use of bond orders in the matrix
useAtomWts sets the diagonal elements of the result to 6.0/(atomic number) so that the matrix can be used to calculate Balaban J values. This does not affect the bond weights.
public static SWIGTYPE_p_double get3DDistanceMat(ROMol mol, int confId, boolean useAtomWts, boolean force, java.lang.String propNamePrefix)
public static SWIGTYPE_p_double get3DDistanceMat(ROMol mol, int confId, boolean useAtomWts, boolean force)
public static SWIGTYPE_p_double get3DDistanceMat(ROMol mol, int confId, boolean useAtomWts)
public static SWIGTYPE_p_double get3DDistanceMat(ROMol mol, int confId)
public static SWIGTYPE_p_double get3DDistanceMat(ROMol mol)
public static Int_List getShortestPath(ROMol mol, int aid1, int aid2)
Find the shortest path between two atoms.
Uses the Bellman-Ford algorithm
mol
- molecule of interest
aid1 index of the first atom
aid2 index of the second atom
public static void cleanupChirality(RWMol mol)
public static void assignChiralTypesFrom3D(ROMol mol, int confId, boolean replaceExistingTags)
Uses a conformer to assign ChiralType to a molecule's atoms.
mol
- the molecule of interest
confId the conformer to use
replaceExistingTags if this flag is true, any existing atomic chiral tags will be replaced
If the conformer provided is not a 3D conformer, nothing will be done.public static void assignChiralTypesFrom3D(ROMol mol, int confId)
Uses a conformer to assign ChiralType to a molecule's atoms.
mol
- the molecule of interest
confId the conformer to use
replaceExistingTags if this flag is true, any existing atomic chiral tags will be replaced
If the conformer provided is not a 3D conformer, nothing will be done.public static void assignChiralTypesFrom3D(ROMol mol)
Uses a conformer to assign ChiralType to a molecule's atoms.
mol
- the molecule of interest
confId the conformer to use
replaceExistingTags if this flag is true, any existing atomic chiral tags will be replaced
If the conformer provided is not a 3D conformer, nothing will be done.public static void assignStereochemistryFrom3D(ROMol mol, int confId, boolean replaceExistingTags)
public static void assignStereochemistryFrom3D(ROMol mol, int confId)
public static void assignStereochemistryFrom3D(ROMol mol)
public static void assignChiralTypesFromBondDirs(ROMol mol, int confId, boolean replaceExistingTags)
public static void assignChiralTypesFromBondDirs(ROMol mol, int confId)
public static void assignChiralTypesFromBondDirs(ROMol mol)
public static void detectBondStereochemistry(ROMol mol, int confId)
public static void detectBondStereochemistry(ROMol mol)
public static void setDoubleBondNeighborDirections(ROMol mol, Conformer conf)
public static void setDoubleBondNeighborDirections(ROMol mol)
public static void setBondStereoFromDirections(ROMol mol)
public static void assignStereochemistry(ROMol mol, boolean cleanIt, boolean force, boolean flagPossibleStereoCenters)
public static void assignStereochemistry(ROMol mol, boolean cleanIt, boolean force)
Assign stereochemistry tags to atoms (i.e. R/S) and bonds (i.e. Z/E).
Does the CIP stereochemistry assignment for the molecule's atoms (R/S) and double bond (Z/E). Chiral atoms will have a property '_CIPCode' indicating their chiral code.
mol
- the molecule to use
cleanIt whether atoms with a chiral specifier that aren't
actually chiral (e.g. atoms with duplicate
substituents or only 2 substituents, etc.) will have
their chiral code set to CHI_UNSPECIFIED. Bonds with
STEREOCIS/STEREOTRANS specified that have duplicate
substituents based upon the CIP atom ranks will be
marked STEREONONE.
force causes the calculation to be repeated even if it has
already been done
public static void assignStereochemistry(ROMol mol, boolean cleanIt)
Assign stereochemistry tags to atoms (i.e. R/S) and bonds (i.e. Z/E).
Does the CIP stereochemistry assignment for the molecule's atoms (R/S) and double bond (Z/E). Chiral atoms will have a property '_CIPCode' indicating their chiral code.
mol
- the molecule to use
cleanIt whether atoms with a chiral specifier that aren't
actually chiral (e.g. atoms with duplicate
substituents or only 2 substituents, etc.) will have
their chiral code set to CHI_UNSPECIFIED. Bonds with
STEREOCIS/STEREOTRANS specified that have duplicate
substituents based upon the CIP atom ranks will be
marked STEREONONE.
force causes the calculation to be repeated even if it has
already been done
public static void assignStereochemistry(ROMol mol)
Assign stereochemistry tags to atoms (i.e. R/S) and bonds (i.e. Z/E).
Does the CIP stereochemistry assignment for the molecule's atoms (R/S) and double bond (Z/E). Chiral atoms will have a property '_CIPCode' indicating their chiral code.
mol
- the molecule to use
cleanIt whether atoms with a chiral specifier that aren't
actually chiral (e.g. atoms with duplicate
substituents or only 2 substituents, etc.) will have
their chiral code set to CHI_UNSPECIFIED. Bonds with
STEREOCIS/STEREOTRANS specified that have duplicate
substituents based upon the CIP atom ranks will be
marked STEREONONE.
force causes the calculation to be repeated even if it has
already been done
public static void removeStereochemistry(ROMol mol)
Removes all stereochemistry information from atoms (i.e. R/S) and bonds (i.e. Z/E).
mol
- the molecule of interestpublic static void findPotentialStereoBonds(ROMol mol, boolean cleanIt)
finds bonds that could be cis/trans in a molecule and mark them as Bond::STEREOANY
mol
- the molecule of interest
cleanIt toggles removal of stereo flags from double bonds that can not have stereochemistry
public static void findPotentialStereoBonds(ROMol mol)
finds bonds that could be cis/trans in a molecule and mark them as Bond::STEREOANY
mol
- the molecule of interest
cleanIt toggles removal of stereo flags from double bonds that can not have stereochemistry
public static long getNumAtomsWithDistinctProperty(ROMol mol, java.lang.String prop)
public static int sanitizeMol(RWMol mol, int sanitizeOps)
public static MolSanitizeException_Vect detectChemistryProblems(ROMol mol, int sanitizeOps)
public static MolSanitizeException_Vect detectChemistryProblems(ROMol mol)
public static void setDefaultConfId(int value)
public static int getDefaultConfId()
public static boolean isMoleculeReactantOfReaction(ChemicalReaction rxn, ROMol mol, SWIGTYPE_p_unsigned_int which)
public static boolean isMoleculeReactantOfReaction(ChemicalReaction rxn, ROMol mol)
public static boolean isMoleculeProductOfReaction(ChemicalReaction rxn, ROMol mol, SWIGTYPE_p_unsigned_int which)
public static boolean isMoleculeProductOfReaction(ChemicalReaction rxn, ROMol mol)
public static boolean isMoleculeAgentOfReaction(ChemicalReaction rxn, ROMol mol, SWIGTYPE_p_unsigned_int which)
public static boolean isMoleculeAgentOfReaction(ChemicalReaction rxn, ROMol mol)
public static Int_Vect_Vect getReactingAtoms(ChemicalReaction rxn, boolean mappedAtomsOnly)
public static Int_Vect_Vect getReactingAtoms(ChemicalReaction rxn)
public static void addRecursiveQueriesToReaction(ChemicalReaction rxn, StringMolMap queries, java.lang.String propName, SWIGTYPE_p_std__vectorT_std__vectorT_std__pairT_unsigned_int_std__string_t_t_t reactantLabels)
public static void addRecursiveQueriesToReaction(ChemicalReaction rxn, StringMolMap queries, java.lang.String propName)
public static void compute2DCoordsForReaction(ChemicalReaction rxn, double spacing, boolean updateProps, boolean canonOrient, long nFlipsPerSample, long nSamples, int sampleSeed, boolean permuteDeg4Nodes)
public static void compute2DCoordsForReaction(ChemicalReaction rxn, double spacing, boolean updateProps, boolean canonOrient, long nFlipsPerSample, long nSamples, int sampleSeed)
public static void compute2DCoordsForReaction(ChemicalReaction rxn, double spacing, boolean updateProps, boolean canonOrient, long nFlipsPerSample, long nSamples)
public static void compute2DCoordsForReaction(ChemicalReaction rxn, double spacing, boolean updateProps, boolean canonOrient, long nFlipsPerSample)
public static void compute2DCoordsForReaction(ChemicalReaction rxn, double spacing, boolean updateProps, boolean canonOrient)
public static void compute2DCoordsForReaction(ChemicalReaction rxn, double spacing, boolean updateProps)
public static void compute2DCoordsForReaction(ChemicalReaction rxn, double spacing)
public static void compute2DCoordsForReaction(ChemicalReaction rxn)
public static ChemicalReaction RxnBlockToChemicalReaction(java.lang.String rxnBlock)
public static ChemicalReaction RxnFileToChemicalReaction(java.lang.String fileName)
public static ChemicalReaction RxnDataStreamToChemicalReaction(SWIGTYPE_p_std__istream rxnStream, SWIGTYPE_p_unsigned_int line)
public static ChemicalReaction RxnSmartsToChemicalReaction(java.lang.String text, String_String_Map replacements, boolean useSmiles)
public static ChemicalReaction RxnSmartsToChemicalReaction(java.lang.String text, String_String_Map replacements)
public static ChemicalReaction RxnSmartsToChemicalReaction(java.lang.String text)
public static ChemicalReaction RxnMolToChemicalReaction(ROMol mol)
public static java.lang.String ChemicalReactionToRxnSmarts(ChemicalReaction rxn)
public static java.lang.String ChemicalReactionToRxnSmiles(ChemicalReaction rxn, boolean canonical)
public static java.lang.String ChemicalReactionToRxnSmiles(ChemicalReaction rxn)
public static java.lang.String ChemicalReactionToRxnBlock(ChemicalReaction rxn, boolean separateAgents)
public static java.lang.String ChemicalReactionToRxnBlock(ChemicalReaction rxn)
public static ROMol ChemicalReactionToRxnMol(ChemicalReaction rxn)
public static int getCi_BITVECT_VERSION()
public static boolean AllProbeBitsMatch(java.lang.String probe, java.lang.String ref)
public static boolean AllProbeBitsMatch(ExplicitBitVect probe, ExplicitBitVect ref)
public static int NumOnBitsInCommon(ExplicitBitVect bv1, ExplicitBitVect bv2)
public static int NumBitsInCommon(ExplicitBitVect bv1, ExplicitBitVect bv2)
public static long CalcBitmapPopcount(SWIGTYPE_p_unsigned_char bv1, long nBytes)
public static double CalcBitmapTanimoto(SWIGTYPE_p_unsigned_char bv1, SWIGTYPE_p_unsigned_char bv2, long nBytes)
public static double CalcBitmapDice(SWIGTYPE_p_unsigned_char bv1, SWIGTYPE_p_unsigned_char bv2, long nBytes)
public static double CalcBitmapTversky(SWIGTYPE_p_unsigned_char bv1, SWIGTYPE_p_unsigned_char bv2, long nBytes, double ca, double cb)
public static boolean CalcBitmapAllProbeBitsMatch(SWIGTYPE_p_unsigned_char probe, SWIGTYPE_p_unsigned_char ref, long nBytes)
public static ExplicitBitVect convertToExplicit(SWIGTYPE_p_SparseBitVect sbv)
public static Double_Vect OnBitProjSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2)
public static ExplicitBitVect FoldFingerprint(ExplicitBitVect bv1, long factor)
public static ExplicitBitVect FoldFingerprint(ExplicitBitVect bv1)
public static boolean AllProbeBitsMatch(ExplicitBitVect probe, java.lang.String pkl)
public static double TanimotoSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2)
public static double CosineSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2)
public static double KulczynskiSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2)
public static double DiceSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2)
public static double TverskySimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2, double a, double b)
public static double SokalSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2)
public static double McConnaugheySimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2)
public static double AsymmetricSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2)
public static double BraunBlanquetSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2)
public static double RusselSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2)
public static double OnBitSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2)
public static double AllBitSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2)
public static Int_Vect OnBitsInCommon(ExplicitBitVect bv1, ExplicitBitVect bv2)
public static Int_Vect OffBitsInCommon(ExplicitBitVect bv1, ExplicitBitVect bv2)
public static Double_Vect OffBitProjSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2)
public static java.lang.String BitVectToText(ExplicitBitVect bv1)
public static void FromBitString(ExplicitBitVect sbv, java.lang.String s)
public static void FromDaylightString(ExplicitBitVect sbv, java.lang.String s)
public static java.lang.String BitVectToFPSText(ExplicitBitVect bv1)
public static void UpdateBitVectFromFPSText(ExplicitBitVect bv1, java.lang.String fps)
public static ExplicitBitVect RDKFingerprintMol(ROMol mol, long minPath, long maxPath, long fpSize, long nBitsPerHash, boolean useHs, double tgtDensity, long minSize, boolean branchedPaths, boolean useBondOrder, UInt_Vect atomInvariants, UInt_Vect fromAtoms, SWIGTYPE_p_std__vectorT_std__vectorT_boost__uint32_t_t_t atomBits, SWIGTYPE_p_std__mapT_unsigned_int_std__vectorT_std__vectorT_int_t_t_t bitInfo)
public static ExplicitBitVect RDKFingerprintMol(ROMol mol, long minPath, long maxPath, long fpSize, long nBitsPerHash, boolean useHs, double tgtDensity, long minSize, boolean branchedPaths, boolean useBondOrder, UInt_Vect atomInvariants, UInt_Vect fromAtoms, SWIGTYPE_p_std__vectorT_std__vectorT_boost__uint32_t_t_t atomBits)
public static ExplicitBitVect RDKFingerprintMol(ROMol mol, long minPath, long maxPath, long fpSize, long nBitsPerHash, boolean useHs, double tgtDensity, long minSize, boolean branchedPaths, boolean useBondOrder, UInt_Vect atomInvariants, UInt_Vect fromAtoms)
public static ExplicitBitVect RDKFingerprintMol(ROMol mol, long minPath, long maxPath, long fpSize, long nBitsPerHash, boolean useHs, double tgtDensity, long minSize, boolean branchedPaths, boolean useBondOrder, UInt_Vect atomInvariants)
public static ExplicitBitVect RDKFingerprintMol(ROMol mol, long minPath, long maxPath, long fpSize, long nBitsPerHash, boolean useHs, double tgtDensity, long minSize, boolean branchedPaths, boolean useBondOrder)
public static ExplicitBitVect RDKFingerprintMol(ROMol mol, long minPath, long maxPath, long fpSize, long nBitsPerHash, boolean useHs, double tgtDensity, long minSize, boolean branchedPaths)
public static ExplicitBitVect RDKFingerprintMol(ROMol mol, long minPath, long maxPath, long fpSize, long nBitsPerHash, boolean useHs, double tgtDensity, long minSize)
public static ExplicitBitVect RDKFingerprintMol(ROMol mol, long minPath, long maxPath, long fpSize, long nBitsPerHash, boolean useHs, double tgtDensity)
public static ExplicitBitVect RDKFingerprintMol(ROMol mol, long minPath, long maxPath, long fpSize, long nBitsPerHash, boolean useHs)
public static ExplicitBitVect RDKFingerprintMol(ROMol mol, long minPath, long maxPath, long fpSize, long nBitsPerHash)
public static ExplicitBitVect RDKFingerprintMol(ROMol mol, long minPath, long maxPath, long fpSize)
public static ExplicitBitVect RDKFingerprintMol(ROMol mol, long minPath, long maxPath)
public static ExplicitBitVect RDKFingerprintMol(ROMol mol, long minPath)
public static ExplicitBitVect RDKFingerprintMol(ROMol mol)
public static java.lang.String getRDKFingerprintMolVersion()
public static ExplicitBitVect LayeredFingerprintMol(ROMol mol, long layerFlags, long minPath, long maxPath, long fpSize, UInt_Vect atomCounts, ExplicitBitVect setOnlyBits, boolean branchedPaths, UInt_Vect fromAtoms)
public static ExplicitBitVect LayeredFingerprintMol(ROMol mol, long layerFlags, long minPath, long maxPath, long fpSize, UInt_Vect atomCounts, ExplicitBitVect setOnlyBits, boolean branchedPaths)
public static ExplicitBitVect LayeredFingerprintMol(ROMol mol, long layerFlags, long minPath, long maxPath, long fpSize, UInt_Vect atomCounts, ExplicitBitVect setOnlyBits)
public static ExplicitBitVect LayeredFingerprintMol(ROMol mol, long layerFlags, long minPath, long maxPath, long fpSize, UInt_Vect atomCounts)
public static ExplicitBitVect LayeredFingerprintMol(ROMol mol, long layerFlags, long minPath, long maxPath, long fpSize)
public static ExplicitBitVect LayeredFingerprintMol(ROMol mol, long layerFlags, long minPath, long maxPath)
public static ExplicitBitVect LayeredFingerprintMol(ROMol mol, long layerFlags, long minPath)
public static ExplicitBitVect LayeredFingerprintMol(ROMol mol, long layerFlags)
public static ExplicitBitVect LayeredFingerprintMol(ROMol mol)
public static long getMaxFingerprintLayers()
public static java.lang.String getLayeredFingerprintMolVersion()
public static long getSubstructLayers()
public static ExplicitBitVect PatternFingerprintMol(ROMol mol, long fpSize, UInt_Vect atomCounts, ExplicitBitVect setOnlyBits)
public static ExplicitBitVect PatternFingerprintMol(ROMol mol, long fpSize, UInt_Vect atomCounts)
public static ExplicitBitVect PatternFingerprintMol(ROMol mol, long fpSize)
public static ExplicitBitVect PatternFingerprintMol(ROMol mol)
public static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t getUnfoldedRDKFingerprintMol(ROMol mol, long minPath, long maxPath, boolean useHs, boolean branchedPaths, boolean useBondOrder, UInt_Vect atomInvariants, UInt_Vect fromAtoms, SWIGTYPE_p_std__vectorT_std__vectorT_unsigned_long_long_t_t atomBits, SWIGTYPE_p_std__mapT_unsigned_long_long_std__vectorT_std__vectorT_int_t_t_t bitInfo)
public static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t getUnfoldedRDKFingerprintMol(ROMol mol, long minPath, long maxPath, boolean useHs, boolean branchedPaths, boolean useBondOrder, UInt_Vect atomInvariants, UInt_Vect fromAtoms, SWIGTYPE_p_std__vectorT_std__vectorT_unsigned_long_long_t_t atomBits)
public static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t getUnfoldedRDKFingerprintMol(ROMol mol, long minPath, long maxPath, boolean useHs, boolean branchedPaths, boolean useBondOrder, UInt_Vect atomInvariants, UInt_Vect fromAtoms)
public static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t getUnfoldedRDKFingerprintMol(ROMol mol, long minPath, long maxPath, boolean useHs, boolean branchedPaths, boolean useBondOrder, UInt_Vect atomInvariants)
public static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t getUnfoldedRDKFingerprintMol(ROMol mol, long minPath, long maxPath, boolean useHs, boolean branchedPaths, boolean useBondOrder)
public static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t getUnfoldedRDKFingerprintMol(ROMol mol, long minPath, long maxPath, boolean useHs, boolean branchedPaths)
public static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t getUnfoldedRDKFingerprintMol(ROMol mol, long minPath, long maxPath, boolean useHs)
public static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t getUnfoldedRDKFingerprintMol(ROMol mol, long minPath, long maxPath)
public static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t getUnfoldedRDKFingerprintMol(ROMol mol, long minPath)
public static SWIGTYPE_p_RDKit__SparseIntVectT_unsigned_long_long_t getUnfoldedRDKFingerprintMol(ROMol mol)
public static java.lang.String getMaccsFingerprintVersion()
public static ExplicitBitVect MACCSFingerprintMol(ROMol mol)
public static long getNumTypeBits()
public static SWIGTYPE_p_unsigned_int getAtomNumberTypes()
public static long getNumPiBits()
public static long getMaxNumPi()
public static long getNumBranchBits()
public static long getMaxNumBranches()
public static long getNumChiralBits()
public static long getCodeSize()
public static long getNumPathBits()
public static long getMaxPathLen()
public static long getNumAtomPairFingerprintBits()
public static long getAtomCode(Atom atom, long branchSubtract, boolean includeChirality)
public static long getAtomCode(Atom atom, long branchSubtract)
public static long getAtomCode(Atom atom)
public static long getAtomPairCode(long codeI, long codeJ, long dist, boolean includeChirality)
public static long getAtomPairCode(long codeI, long codeJ, long dist)
public static java.math.BigInteger getTopologicalTorsionCode(UInt_Vect atomCodes, boolean includeChirality)
public static java.math.BigInteger getTopologicalTorsionCode(UInt_Vect atomCodes)
public static long getTopologicalTorsionHash(UInt_Vect pathCodes)
public static void setDefaultFeatureSmarts(Str_Vect value)
public static Str_Vect getDefaultFeatureSmarts()
public static void getConnectivityInvariants(ROMol mol, UInt_Vect invars, boolean includeRingMembership)
public static java.lang.String getMorganConnectivityInvariantVersion()
public static void getFeatureInvariants(ROMol mol, UInt_Vect invars, SWIGTYPE_p_std__vectorT_RDKit__ROMol_const_p_t patterns)
public static java.lang.String getMorganFeatureInvariantVersion()
public static void buildDefaultRDKitFingerprintAtomInvariants(ROMol mol, UInt_Vect lAtomInvariants)
public static void identifyQueryBonds(ROMol mol, SWIGTYPE_p_std__vectorT_RDKit__Bond_const_p_t bondCache, SWIGTYPE_p_std__vectorT_short_t isQueryBond)
public static UInt_Vect generateBondHashes(ROMol mol, SWIGTYPE_p_boost__dynamic_bitsetT_t atomsInPath, SWIGTYPE_p_std__vectorT_RDKit__Bond_const_p_t bondCache, SWIGTYPE_p_std__vectorT_short_t isQueryBond, Int_Vect path, boolean useBondOrder, UInt_Vect atomInvariants)
public static java.lang.String getMorganFingerprintVersion()
public static SparseIntVectu32 MorganFingerprintMol(ROMol mol, long radius, UInt_Vect invariants, UInt_Vect fromAtoms, boolean useChirality, boolean useBondTypes, boolean useCounts, boolean onlyNonzeroInvariants, BitInfoMap atomsSettingBits)
public static SparseIntVectu32 MorganFingerprintMol(ROMol mol, long radius, UInt_Vect invariants, UInt_Vect fromAtoms, boolean useChirality, boolean useBondTypes, boolean useCounts, boolean onlyNonzeroInvariants)
public static SparseIntVectu32 MorganFingerprintMol(ROMol mol, long radius, UInt_Vect invariants, UInt_Vect fromAtoms, boolean useChirality, boolean useBondTypes, boolean useCounts)
public static SparseIntVectu32 MorganFingerprintMol(ROMol mol, long radius, UInt_Vect invariants, UInt_Vect fromAtoms, boolean useChirality, boolean useBondTypes)
public static SparseIntVectu32 MorganFingerprintMol(ROMol mol, long radius, UInt_Vect invariants, UInt_Vect fromAtoms, boolean useChirality)
public static SparseIntVectu32 MorganFingerprintMol(ROMol mol, long radius, UInt_Vect invariants, UInt_Vect fromAtoms)
public static SparseIntVectu32 MorganFingerprintMol(ROMol mol, long radius, UInt_Vect invariants)
public static SparseIntVectu32 MorganFingerprintMol(ROMol mol, long radius)
public static SparseIntVectu32 getHashedFingerprint(ROMol mol, long radius, long nBits, UInt_Vect invariants, UInt_Vect fromAtoms, boolean useChirality, boolean useBondTypes, boolean onlyNonzeroInvariants, BitInfoMap atomsSettingBits)
public static SparseIntVectu32 getHashedFingerprint(ROMol mol, long radius, long nBits, UInt_Vect invariants, UInt_Vect fromAtoms, boolean useChirality, boolean useBondTypes, boolean onlyNonzeroInvariants)
public static SparseIntVectu32 getHashedFingerprint(ROMol mol, long radius, long nBits, UInt_Vect invariants, UInt_Vect fromAtoms, boolean useChirality, boolean useBondTypes)
public static SparseIntVectu32 getHashedFingerprint(ROMol mol, long radius, long nBits, UInt_Vect invariants, UInt_Vect fromAtoms, boolean useChirality)
public static SparseIntVectu32 getHashedFingerprint(ROMol mol, long radius, long nBits, UInt_Vect invariants, UInt_Vect fromAtoms)
public static SparseIntVectu32 getHashedFingerprint(ROMol mol, long radius, long nBits, UInt_Vect invariants)
public static SparseIntVectu32 getHashedFingerprint(ROMol mol, long radius, long nBits)
public static SparseIntVectu32 getHashedFingerprint(ROMol mol, long radius)
public static ExplicitBitVect getMorganFingerprintAsBitVect(ROMol mol, long radius, long nBits, UInt_Vect invariants, UInt_Vect fromAtoms, boolean useChirality, boolean useBondTypes, boolean onlyNonzeroInvariants, BitInfoMap atomsSettingBits)
public static ExplicitBitVect getMorganFingerprintAsBitVect(ROMol mol, long radius, long nBits, UInt_Vect invariants, UInt_Vect fromAtoms, boolean useChirality, boolean useBondTypes, boolean onlyNonzeroInvariants)
public static ExplicitBitVect getMorganFingerprintAsBitVect(ROMol mol, long radius, long nBits, UInt_Vect invariants, UInt_Vect fromAtoms, boolean useChirality, boolean useBondTypes)
public static ExplicitBitVect getMorganFingerprintAsBitVect(ROMol mol, long radius, long nBits, UInt_Vect invariants, UInt_Vect fromAtoms, boolean useChirality)
public static ExplicitBitVect getMorganFingerprintAsBitVect(ROMol mol, long radius, long nBits, UInt_Vect invariants, UInt_Vect fromAtoms)
public static ExplicitBitVect getMorganFingerprintAsBitVect(ROMol mol, long radius, long nBits, UInt_Vect invariants)
public static ExplicitBitVect getMorganFingerprintAsBitVect(ROMol mol, long radius, long nBits)
public static double TanimotoSimilarityEBV(ExplicitBitVect bv1, ExplicitBitVect bv2)
public static double DiceSimilarity(SparseIntVectu32 v1, SparseIntVectu32 v2, boolean returnDistance, double bounds)
public static double DiceSimilarity(SparseIntVectu32 v1, SparseIntVectu32 v2, boolean returnDistance)
public static double DiceSimilarity(SparseIntVectu32 v1, SparseIntVectu32 v2)
public static double DiceSimilarity(SparseIntVect32 v1, SparseIntVect32 v2, boolean returnDistance, double bounds)
public static double DiceSimilarity(SparseIntVect32 v1, SparseIntVect32 v2, boolean returnDistance)
public static double DiceSimilarity(SparseIntVect32 v1, SparseIntVect32 v2)
public static double DiceSimilarity(SparseIntVect64 v1, SparseIntVect64 v2, boolean returnDistance, double bounds)
public static double DiceSimilarity(SparseIntVect64 v1, SparseIntVect64 v2, boolean returnDistance)
public static double DiceSimilarity(SparseIntVect64 v1, SparseIntVect64 v2)
public static double TanimotoSimilaritySIVu32(SparseIntVectu32 v1, SparseIntVectu32 v2, boolean returnDistance, double bounds)
public static double TanimotoSimilaritySIVu32(SparseIntVectu32 v1, SparseIntVectu32 v2, boolean returnDistance)
public static double TanimotoSimilaritySIVu32(SparseIntVectu32 v1, SparseIntVectu32 v2)
public static double TanimotoSimilaritySIVi32(SparseIntVect32 v1, SparseIntVect32 v2, boolean returnDistance, double bounds)
public static double TanimotoSimilaritySIVi32(SparseIntVect32 v1, SparseIntVect32 v2, boolean returnDistance)
public static double TanimotoSimilaritySIVi32(SparseIntVect32 v1, SparseIntVect32 v2)
public static double TanimotoSimilaritySIVi64(SparseIntVect64 v1, SparseIntVect64 v2, boolean returnDistance, double bounds)
public static double TanimotoSimilaritySIVi64(SparseIntVect64 v1, SparseIntVect64 v2, boolean returnDistance)
public static double TanimotoSimilaritySIVi64(SparseIntVect64 v1, SparseIntVect64 v2)
public static double TverskySimilarity(SparseIntVectu32 v1, SparseIntVectu32 v2, double a, double b, boolean returnDistance, double bounds)
public static double TverskySimilarity(SparseIntVectu32 v1, SparseIntVectu32 v2, double a, double b, boolean returnDistance)
public static double TverskySimilarity(SparseIntVectu32 v1, SparseIntVectu32 v2, double a, double b)
public static double TverskySimilarity(SparseIntVect32 v1, SparseIntVect32 v2, double a, double b, boolean returnDistance, double bounds)
public static double TverskySimilarity(SparseIntVect32 v1, SparseIntVect32 v2, double a, double b, boolean returnDistance)
public static double TverskySimilarity(SparseIntVect32 v1, SparseIntVect32 v2, double a, double b)
public static double TverskySimilarity(SparseIntVect64 v1, SparseIntVect64 v2, double a, double b, boolean returnDistance, double bounds)
public static double TverskySimilarity(SparseIntVect64 v1, SparseIntVect64 v2, double a, double b, boolean returnDistance)
public static double TverskySimilarity(SparseIntVect64 v1, SparseIntVect64 v2, double a, double b)
public static SparseIntVectu32 getFeatureFingerprint(ROMol mol, long radius, boolean useChirality, boolean useBondTypes, boolean useCounts)
public static SparseIntVectu32 getFeatureFingerprint(ROMol mol, long radius, boolean useChirality, boolean useBondTypes)
public static SparseIntVectu32 getFeatureFingerprint(ROMol mol, long radius, boolean useChirality)
public static SparseIntVectu32 getFeatureFingerprint(ROMol mol, long radius)
public static ReactionFingerprintParams getDefaultStructuralFPParams()
public static ReactionFingerprintParams getDefaultDifferenceFPParams()
public static ExplicitBitVect StructuralFingerprintChemReaction(ChemicalReaction rxn, ReactionFingerprintParams params)
public static ExplicitBitVect StructuralFingerprintChemReaction(ChemicalReaction rxn)
public static SparseIntVectu32 DifferenceFingerprintChemReaction(ChemicalReaction rxn, ReactionFingerprintParams params)
public static SparseIntVectu32 DifferenceFingerprintChemReaction(ChemicalReaction rxn)
public static void pickFusedRings(int curr, Int_Int_Vect_Map neighMap, Int_Vect res, SWIGTYPE_p_boost__dynamic_bitsetT_t done, int depth)
public static void pickFusedRings(int curr, Int_Int_Vect_Map neighMap, Int_Vect res, SWIGTYPE_p_boost__dynamic_bitsetT_t done)
public static void makeRingNeighborMap(Int_Vect_Vect brings, Int_Int_Vect_Map neighMap, long maxSize, long maxOverlapSize)
public static void makeRingNeighborMap(Int_Vect_Vect brings, Int_Int_Vect_Map neighMap, long maxSize)
public static void makeRingNeighborMap(Int_Vect_Vect brings, Int_Int_Vect_Map neighMap)
public static void convertToBonds(Int_Vect_Vect res, Int_Vect_Vect brings, ROMol mol)
public static long getDIM_2D()
public static long getDIM_3D()
public static void initBoundsMat(BoundsMatrix mmat, double defaultMin, double defaultMax)
public static void initBoundsMat(BoundsMatrix mmat, double defaultMin)
public static void initBoundsMat(BoundsMatrix mmat)
public static void setTopolBounds(ROMol mol, SWIGTYPE_p_boost__shared_ptrT_DistGeom__BoundsMatrix_t mmat, boolean set15bounds, boolean scaleVDW)
public static void setTopolBounds(ROMol mol, SWIGTYPE_p_boost__shared_ptrT_DistGeom__BoundsMatrix_t mmat, boolean set15bounds)
public static void setTopolBounds(ROMol mol, SWIGTYPE_p_boost__shared_ptrT_DistGeom__BoundsMatrix_t mmat)
public static void setTopolBounds(ROMol mol, SWIGTYPE_p_boost__shared_ptrT_DistGeom__BoundsMatrix_t mmat, Match_Vect bonds, Int_Vect_Vect angles, boolean set15bounds, boolean scaleVDW)
public static void setTopolBounds(ROMol mol, SWIGTYPE_p_boost__shared_ptrT_DistGeom__BoundsMatrix_t mmat, Match_Vect bonds, Int_Vect_Vect angles, boolean set15bounds)
public static void setTopolBounds(ROMol mol, SWIGTYPE_p_boost__shared_ptrT_DistGeom__BoundsMatrix_t mmat, Match_Vect bonds, Int_Vect_Vect angles)
public static void collectBondsAndAngles(ROMol mol, Match_Vect bonds, Int_Vect_Vect angles)
public static double pickRandomDistMat(BoundsMatrix mmat, DoubleSymmMatrix distmat, int seed)
public static double pickRandomDistMat(BoundsMatrix mmat, DoubleSymmMatrix distmat)
public static double pickRandomDistMat(BoundsMatrix mmat, DoubleSymmMatrix distmat, SWIGTYPE_p_RDKit__double_source_type rng)
public static boolean computeInitialCoords(DoubleSymmMatrix distmat, Point_Vect positions, boolean randNegEig, long numZeroFail, int seed)
public static boolean computeInitialCoords(DoubleSymmMatrix distmat, Point_Vect positions, boolean randNegEig, long numZeroFail)
public static boolean computeInitialCoords(DoubleSymmMatrix distmat, Point_Vect positions, boolean randNegEig)
public static boolean computeInitialCoords(DoubleSymmMatrix distmat, Point_Vect positions)
public static boolean computeInitialCoords(DoubleSymmMatrix distmat, Point_Vect positions, SWIGTYPE_p_RDKit__double_source_type rng, boolean randNegEig, long numZeroFail)
public static boolean computeInitialCoords(DoubleSymmMatrix distmat, Point_Vect positions, SWIGTYPE_p_RDKit__double_source_type rng, boolean randNegEig)
public static boolean computeInitialCoords(DoubleSymmMatrix distmat, Point_Vect positions, SWIGTYPE_p_RDKit__double_source_type rng)
public static boolean computeRandomCoords(Point_Vect positions, double boxSize, int seed)
public static boolean computeRandomCoords(Point_Vect positions, double boxSize)
public static boolean computeRandomCoords(Point_Vect positions, double boxSize, SWIGTYPE_p_RDKit__double_source_type rng)
public static ForceField construct3DForceField(BoundsMatrix mmat, Point3D_Vect positions, SWIGTYPE_p_ForceFields__CrystalFF__CrystalFFDetails etkdgDetails)
public static ForceField constructPlain3DForceField(BoundsMatrix mmat, Point3D_Vect positions, SWIGTYPE_p_ForceFields__CrystalFF__CrystalFFDetails etkdgDetails)
public static ForceField construct3DImproperForceField(BoundsMatrix mmat, Point3D_Vect positions, Int_Vect_Vect improperAtoms, Int_Vect atomNums)
public static boolean triangleSmoothBounds(BoundsMatrix boundsMat, double tol)
public static boolean triangleSmoothBounds(BoundsMatrix boundsMat)
public static boolean triangleSmoothBounds(SWIGTYPE_p_boost__shared_ptrT_DistGeom__BoundsMatrix_t boundsMat, double tol)
public static boolean triangleSmoothBounds(SWIGTYPE_p_boost__shared_ptrT_DistGeom__BoundsMatrix_t boundsMat)
public static EmbedParameters getKDG()
public static EmbedParameters getETDG()
public static EmbedParameters getETKDG()
public static EmbedParameters getETKDGv2()
public static void normalizeAngleDeg(SWIGTYPE_p_double angleDeg)
public static void computeDihedral(Point_Vect pos, long idx1, long idx2, long idx3, long idx4, SWIGTYPE_p_double dihedral, SWIGTYPE_p_double cosPhi, Point3D r, Point3D t, SWIGTYPE_p_double d)
public static void computeDihedral(Point_Vect pos, long idx1, long idx2, long idx3, long idx4, SWIGTYPE_p_double dihedral, SWIGTYPE_p_double cosPhi, Point3D r, Point3D t)
public static void computeDihedral(Point_Vect pos, long idx1, long idx2, long idx3, long idx4, SWIGTYPE_p_double dihedral, SWIGTYPE_p_double cosPhi, Point3D r)
public static void computeDihedral(Point_Vect pos, long idx1, long idx2, long idx3, long idx4, SWIGTYPE_p_double dihedral, SWIGTYPE_p_double cosPhi)
public static void computeDihedral(Point_Vect pos, long idx1, long idx2, long idx3, long idx4, SWIGTYPE_p_double dihedral)
public static void computeDihedral(Point_Vect pos, long idx1, long idx2, long idx3, long idx4)
public static void computeDihedral(SWIGTYPE_p_double pos, long idx1, long idx2, long idx3, long idx4, SWIGTYPE_p_double dihedral, SWIGTYPE_p_double cosPhi, Point3D r, Point3D t, SWIGTYPE_p_double d)
public static void computeDihedral(SWIGTYPE_p_double pos, long idx1, long idx2, long idx3, long idx4, SWIGTYPE_p_double dihedral, SWIGTYPE_p_double cosPhi, Point3D r, Point3D t)
public static void computeDihedral(SWIGTYPE_p_double pos, long idx1, long idx2, long idx3, long idx4, SWIGTYPE_p_double dihedral, SWIGTYPE_p_double cosPhi, Point3D r)
public static void computeDihedral(SWIGTYPE_p_double pos, long idx1, long idx2, long idx3, long idx4, SWIGTYPE_p_double dihedral, SWIGTYPE_p_double cosPhi)
public static void computeDihedral(SWIGTYPE_p_double pos, long idx1, long idx2, long idx3, long idx4, SWIGTYPE_p_double dihedral)
public static void computeDihedral(SWIGTYPE_p_double pos, long idx1, long idx2, long idx3, long idx4)
public static void computeDihedral(Point3D p1, Point3D p2, Point3D p3, Point3D p4, SWIGTYPE_p_double dihedral, SWIGTYPE_p_double cosPhi, Point3D r, Point3D t, SWIGTYPE_p_double d)
public static void computeDihedral(Point3D p1, Point3D p2, Point3D p3, Point3D p4, SWIGTYPE_p_double dihedral, SWIGTYPE_p_double cosPhi, Point3D r, Point3D t)
public static void computeDihedral(Point3D p1, Point3D p2, Point3D p3, Point3D p4, SWIGTYPE_p_double dihedral, SWIGTYPE_p_double cosPhi, Point3D r)
public static void computeDihedral(Point3D p1, Point3D p2, Point3D p3, Point3D p4, SWIGTYPE_p_double dihedral, SWIGTYPE_p_double cosPhi)
public static void computeDihedral(Point3D p1, Point3D p2, Point3D p3, Point3D p4, SWIGTYPE_p_double dihedral)
public static double getDEG2RAD()
public static double getRAD2DEG()
public static boolean isDoubleZero(double x)
public static void clipToOne(SWIGTYPE_p_double x)
public static double getLambda()
public static double getG()
public static double getAmideBondOrder()
public static double calcAngleForceConstant(double theta0, double bondOrder12, double bondOrder23, AtomicParams at1Params, AtomicParams at2Params, AtomicParams at3Params)
public static void calcAngleBendGrad(Point3D r, SWIGTYPE_p_double dist, SWIGTYPE_p_p_double g, SWIGTYPE_p_double dE_dTheta, SWIGTYPE_p_double cosTheta, SWIGTYPE_p_double sinTheta)
public static double calcBondRestLength(double bondOrder, AtomicParams end1Params, AtomicParams end2Params)
public static double calcBondForceConstant(double restLength, AtomicParams end1Params, AtomicParams end2Params)
public static double calcNonbondedMinimum(AtomicParams at1Params, AtomicParams at2Params)
public static double calcNonbondedDepth(AtomicParams at1Params, AtomicParams at2Params)
public static double calculateCosTorsion(Point3D p1, Point3D p2, Point3D p3, Point3D p4)
public static void calcTorsionGrad(Point3D r, Point3D t, SWIGTYPE_p_double d, SWIGTYPE_p_p_double g, SWIGTYPE_p_double sinTerm, SWIGTYPE_p_double cosPhi)
public static double equation17(double bondOrder23, AtomicParams at2Params, AtomicParams at3Params)
public static boolean isInGroup6(int num)
public static double calculateCosY(Point3D iPoint, Point3D jPoint, Point3D kPoint, Point3D lPoint)
public static SWIGTYPE_p_boost__tupleT_double_double_double_double_t calcInversionCoefficientsAndForceConstant(int at2AtomicNum, boolean isCBoundToO)
public static ROMol deleteSubstructs(ROMol mol, ROMol query, boolean onlyFrags, boolean useChirality)
public static ROMol_Vect replaceSubstructs(ROMol mol, ROMol query, ROMol replacement, boolean replaceAll, long replacementConnectionPoint, boolean useChirality)
public static ROMol_Vect replaceSubstructs(ROMol mol, ROMol query, ROMol replacement, boolean replaceAll, long replacementConnectionPoint)
public static ROMol_Vect replaceSubstructs(ROMol mol, ROMol query, ROMol replacement, boolean replaceAll)
public static ROMol_Vect replaceSubstructs(ROMol mol, ROMol query, ROMol replacement)
public static ROMol replaceSidechains(ROMol mol, ROMol coreQuery, boolean useChirality)
public static ROMol replaceCore(ROMol mol, ROMol core, Match_Vect matchVect, boolean replaceDummies, boolean labelByIndex, boolean requireDummyMatch)
public static ROMol replaceCore(ROMol mol, ROMol core, Match_Vect matchVect, boolean replaceDummies, boolean labelByIndex)
public static ROMol replaceCore(ROMol mol, ROMol core, Match_Vect matchVect, boolean replaceDummies)
public static ROMol replaceCore(ROMol mol, ROMol core, Match_Vect matchVect)
public static ROMol replaceCore(ROMol mol, ROMol coreQuery, boolean replaceDummies, boolean labelByIndex, boolean requireDummyMatch, boolean useChirality)
public static ROMol replaceCore(ROMol mol, ROMol coreQuery, boolean replaceDummies, boolean labelByIndex, boolean requireDummyMatch)
public static ROMol replaceCore(ROMol mol, ROMol coreQuery, boolean replaceDummies, boolean labelByIndex)
public static void addRecursiveQueries(ROMol mol, StringMolMap queries, java.lang.String propName, SWIGTYPE_p_std__vectorT_std__pairT_unsigned_int_std__string_t_t reactantLabels)
public static void addRecursiveQueries(ROMol mol, StringMolMap queries, java.lang.String propName)
public static void parseQueryDefFile(java.lang.String filename, StringMolMap queryDefs, boolean standardize, java.lang.String delimiter, java.lang.String comment, long nameColumn, long smartsColumn)
public static void parseQueryDefFile(java.lang.String filename, StringMolMap queryDefs, boolean standardize, java.lang.String delimiter, java.lang.String comment, long nameColumn)
public static void parseQueryDefFile(java.lang.String filename, StringMolMap queryDefs, boolean standardize, java.lang.String delimiter, java.lang.String comment)
public static void parseQueryDefFile(java.lang.String filename, StringMolMap queryDefs, boolean standardize, java.lang.String delimiter)
public static void parseQueryDefFile(java.lang.String filename, StringMolMap queryDefs, boolean standardize)
public static void parseQueryDefFile(java.lang.String filename, StringMolMap queryDefs)
public static void parseQueryDefFile(SWIGTYPE_p_std__istream inStream, StringMolMap queryDefs, boolean standardize, java.lang.String delimiter, java.lang.String comment, long nameColumn, long smartsColumn)
public static void parseQueryDefFile(SWIGTYPE_p_std__istream inStream, StringMolMap queryDefs, boolean standardize, java.lang.String delimiter, java.lang.String comment, long nameColumn)
public static void parseQueryDefFile(SWIGTYPE_p_std__istream inStream, StringMolMap queryDefs, boolean standardize, java.lang.String delimiter, java.lang.String comment)
public static void parseQueryDefFile(SWIGTYPE_p_std__istream inStream, StringMolMap queryDefs, boolean standardize, java.lang.String delimiter)
public static void parseQueryDefFile(SWIGTYPE_p_std__istream inStream, StringMolMap queryDefs, boolean standardize)
public static void parseQueryDefFile(SWIGTYPE_p_std__istream inStream, StringMolMap queryDefs)
public static void parseQueryDefText(java.lang.String queryDefText, StringMolMap queryDefs, boolean standardize, java.lang.String delimiter, java.lang.String comment, long nameColumn, long smartsColumn)
public static void parseQueryDefText(java.lang.String queryDefText, StringMolMap queryDefs, boolean standardize, java.lang.String delimiter, java.lang.String comment, long nameColumn)
public static void parseQueryDefText(java.lang.String queryDefText, StringMolMap queryDefs, boolean standardize, java.lang.String delimiter, java.lang.String comment)
public static void parseQueryDefText(java.lang.String queryDefText, StringMolMap queryDefs, boolean standardize, java.lang.String delimiter)
public static void parseQueryDefText(java.lang.String queryDefText, StringMolMap queryDefs, boolean standardize)
public static void parseQueryDefText(java.lang.String queryDefText, StringMolMap queryDefs)
public static Int_Int_Vect_List_Map findAllSubgraphsOfLengthsMtoN(ROMol mol, long lowerLen, long upperLen, boolean useHs, int rootedAtAtom)
public static Int_Int_Vect_List_Map findAllSubgraphsOfLengthsMtoN(ROMol mol, long lowerLen, long upperLen, boolean useHs)
public static Int_Int_Vect_List_Map findAllSubgraphsOfLengthsMtoN(ROMol mol, long lowerLen, long upperLen)
public static Int_Vect_List findAllSubgraphsOfLengthN(ROMol mol, long targetLen, boolean useHs, int rootedAtAtom)
public static Int_Vect_List findAllSubgraphsOfLengthN(ROMol mol, long targetLen, boolean useHs)
public static Int_Vect_List findAllSubgraphsOfLengthN(ROMol mol, long targetLen)
public static Int_Vect_List findUniqueSubgraphsOfLengthN(ROMol mol, long targetLen, boolean useHs, boolean useBO, int rootedAtAtom)
public static Int_Vect_List findUniqueSubgraphsOfLengthN(ROMol mol, long targetLen, boolean useHs, boolean useBO)
public static Int_Vect_List findUniqueSubgraphsOfLengthN(ROMol mol, long targetLen, boolean useHs)
public static Int_Vect_List findUniqueSubgraphsOfLengthN(ROMol mol, long targetLen)
public static Int_Vect_List findAllPathsOfLengthN(ROMol mol, long targetLen, boolean useBonds, boolean useHs, int rootedAtAtom)
public static Int_Vect_List findAllPathsOfLengthN(ROMol mol, long targetLen, boolean useBonds, boolean useHs)
public static Int_Vect_List findAllPathsOfLengthN(ROMol mol, long targetLen, boolean useBonds)
public static Int_Vect_List findAllPathsOfLengthN(ROMol mol, long targetLen)
public static Int_Int_Vect_List_Map findAllPathsOfLengthsMtoN(ROMol mol, long lowerLen, long upperLen, boolean useBonds, boolean useHs, int rootedAtAtom)
public static Int_Int_Vect_List_Map findAllPathsOfLengthsMtoN(ROMol mol, long lowerLen, long upperLen, boolean useBonds, boolean useHs)
public static Int_Int_Vect_List_Map findAllPathsOfLengthsMtoN(ROMol mol, long lowerLen, long upperLen, boolean useBonds)
public static Int_Int_Vect_List_Map findAllPathsOfLengthsMtoN(ROMol mol, long lowerLen, long upperLen)
public static Int_Vect findAtomEnvironmentOfRadiusN(ROMol mol, long radius, long rootedAtAtom, boolean useHs)
public static Int_Vect findAtomEnvironmentOfRadiusN(ROMol mol, long radius, long rootedAtAtom)
public static Int_Vect_List uniquifyPaths(ROMol mol, Int_Vect_List allPathsb, boolean useBO)
public static Int_Vect_List uniquifyPaths(ROMol mol, Int_Vect_List allPathsb)
public static ROMol pathToSubmol(ROMol mol, Int_Vect path, boolean useQuery, Int_Int_Map atomIdxMap)
public static void transformMolsAtoms(ROMol mol, Transform3D tform)
public static void transformAtom(Atom atom, Transform3D tform)
public static Transform3D computeCanonicalTransform(Conformer conf, Point3D center, boolean normalizeCovar, boolean ignoreHs)
public static Transform3D computeCanonicalTransform(Conformer conf, Point3D center, boolean normalizeCovar)
public static Transform3D computeCanonicalTransform(Conformer conf, Point3D center)
public static Transform3D computeCanonicalTransform(Conformer conf)
public static void transformConformer(Conformer conf, Transform3D trans)
public static void canonicalizeConformer(Conformer conf, Point3D center, boolean normalizeCovar, boolean ignoreHs)
public static void canonicalizeConformer(Conformer conf, Point3D center, boolean normalizeCovar)
public static void canonicalizeConformer(Conformer conf)
public static void canonicalizeMol(ROMol mol, boolean normalizeCovar, boolean ignoreHs)
public static void canonicalizeMol(ROMol mol, boolean normalizeCovar)
public static void canonicalizeMol(ROMol mol)
public static double getBondLength(Conformer conf, long iAtomId, long jAtomId)
public static void setBondLength(Conformer conf, long iAtomId, long jAtomId, double value)
public static double getAngleRad(Conformer conf, long iAtomId, long jAtomId, long kAtomId)
public static double getAngleDeg(Conformer conf, long iAtomId, long jAtomId, long kAtomId)
public static void setAngleRad(Conformer conf, long iAtomId, long jAtomId, long kAtomId, double value)
public static void setAngleDeg(Conformer conf, long iAtomId, long jAtomId, long kAtomId, double value)
public static double getDihedralRad(Conformer conf, long iAtomId, long jAtomId, long kAtomId, long lAtomId)
public static double getDihedralDeg(Conformer conf, long iAtomId, long jAtomId, long kAtomId, long lAtomId)
public static void setDihedralRad(Conformer conf, long iAtomId, long jAtomId, long kAtomId, long lAtomId, double value)
public static void setDihedralDeg(Conformer conf, long iAtomId, long jAtomId, long kAtomId, long lAtomId, double value)
public static boolean MCSAtomCompareAny(MCSAtomCompareParameters p, ROMol mol1, long atom1, ROMol mol2, long atom2, SWIGTYPE_p_void userData)
public static boolean MCSAtomCompareAnyHeavyAtom(MCSAtomCompareParameters p, ROMol mol1, long atom1, ROMol mol2, long atom2, SWIGTYPE_p_void userData)
public static boolean MCSAtomCompareElements(MCSAtomCompareParameters p, ROMol mol1, long atom1, ROMol mol2, long atom2, SWIGTYPE_p_void userData)
public static boolean MCSAtomCompareIsotopes(MCSAtomCompareParameters p, ROMol mol1, long atom1, ROMol mol2, long atom2, SWIGTYPE_p_void userData)
public static boolean MCSBondCompareAny(MCSBondCompareParameters p, ROMol mol1, long bond1, ROMol mol2, long bond2, SWIGTYPE_p_void userData)
public static boolean MCSBondCompareOrder(MCSBondCompareParameters p, ROMol mol1, long bond1, ROMol mol2, long bond2, SWIGTYPE_p_void userData)
public static boolean MCSBondCompareOrderExact(MCSBondCompareParameters p, ROMol mol1, long bond1, ROMol mol2, long bond2, SWIGTYPE_p_void userData)
public static boolean MCSProgressCallbackTimeout(MCSProgressData stat, SWIGTYPE_p_RDKit__MCSParameters params, SWIGTYPE_p_void userData)
public static void parseMCSParametersJSON(java.lang.String json, SWIGTYPE_p_RDKit__MCSParameters params)
public static MCSResult findMCS(ROMol_Vect mols)
public static MCSResult findMCS_P(ROMol_Vect mols, java.lang.String params_json)
public static MCSResult findMCS(ROMol_Vect mols, boolean maximizeBonds, double threshold, long timeout, boolean verbose, boolean matchValences, boolean ringMatchesRingOnly, boolean completeRingsOnly, boolean matchChiralTag, AtomComparator atomComp, BondComparator bondComp, RingComparator ringComp)
public static MCSResult findMCS(ROMol_Vect mols, boolean maximizeBonds, double threshold, long timeout, boolean verbose, boolean matchValences, boolean ringMatchesRingOnly, boolean completeRingsOnly, boolean matchChiralTag, AtomComparator atomComp, BondComparator bondComp)
public static MCSResult findMCS(ROMol_Vect mols, boolean maximizeBonds, double threshold, long timeout, boolean verbose, boolean matchValences, boolean ringMatchesRingOnly, boolean completeRingsOnly, boolean matchChiralTag, AtomComparator atomComp)
public static MCSResult findMCS(ROMol_Vect mols, boolean maximizeBonds, double threshold, long timeout, boolean verbose, boolean matchValences, boolean ringMatchesRingOnly, boolean completeRingsOnly, boolean matchChiralTag)
public static MCSResult findMCS(ROMol_Vect mols, boolean maximizeBonds, double threshold, long timeout, boolean verbose, boolean matchValences, boolean ringMatchesRingOnly, boolean completeRingsOnly)
public static MCSResult findMCS(ROMol_Vect mols, boolean maximizeBonds, double threshold, long timeout, boolean verbose, boolean matchValences, boolean ringMatchesRingOnly)
public static MCSResult findMCS(ROMol_Vect mols, boolean maximizeBonds, double threshold, long timeout, boolean verbose, boolean matchValences)
public static MCSResult findMCS(ROMol_Vect mols, boolean maximizeBonds, double threshold, long timeout, boolean verbose)
public static MCSResult findMCS(ROMol_Vect mols, boolean maximizeBonds, double threshold, long timeout)
public static MCSResult findMCS(ROMol_Vect mols, boolean maximizeBonds, double threshold)
public static MCSResult findMCS(ROMol_Vect mols, boolean maximizeBonds)
public static void assignDefaultPalette(ColourPalette palette)
public static void assignBWPalette(ColourPalette palette)
public static void prepareMolForDrawing(RWMol mol, boolean kekulize, boolean addChiralHs, boolean wedgeBonds, boolean forceCoords)
public static void prepareMolForDrawing(RWMol mol, boolean kekulize, boolean addChiralHs, boolean wedgeBonds)
public static void prepareMolForDrawing(RWMol mol, boolean kekulize, boolean addChiralHs)
public static void prepareMolForDrawing(RWMol mol, boolean kekulize)
public static void prepareMolForDrawing(RWMol mol)
public static void prepareAndDrawMolecule(MolDraw2D drawer, ROMol mol, java.lang.String legend, Int_Vect highlight_atoms, Int_Vect highlight_bonds, ColourPalette highlight_atom_map, ColourPalette highlight_bond_map, Int_Double_Map highlight_radii, int confId)
public static void prepareAndDrawMolecule(MolDraw2D drawer, ROMol mol, java.lang.String legend, Int_Vect highlight_atoms, Int_Vect highlight_bonds, ColourPalette highlight_atom_map, ColourPalette highlight_bond_map, Int_Double_Map highlight_radii)
public static void prepareAndDrawMolecule(MolDraw2D drawer, ROMol mol, java.lang.String legend, Int_Vect highlight_atoms, Int_Vect highlight_bonds, ColourPalette highlight_atom_map, ColourPalette highlight_bond_map)
public static void prepareAndDrawMolecule(MolDraw2D drawer, ROMol mol, java.lang.String legend, Int_Vect highlight_atoms, Int_Vect highlight_bonds, ColourPalette highlight_atom_map)
public static void prepareAndDrawMolecule(MolDraw2D drawer, ROMol mol, java.lang.String legend, Int_Vect highlight_atoms, Int_Vect highlight_bonds)
public static void prepareAndDrawMolecule(MolDraw2D drawer, ROMol mol, java.lang.String legend, Int_Vect highlight_atoms)
public static void prepareAndDrawMolecule(MolDraw2D drawer, ROMol mol, java.lang.String legend)
public static void updateDrawerParamsFromJSON(MolDraw2D drawer, java.lang.String json)
public static void contourAndDrawGrid(MolDraw2D drawer, SWIGTYPE_p_double grid, Double_Vect xcoords, Double_Vect ycoords, long nContours, Double_Vect levels, ContourParams ps)
public static void contourAndDrawGrid(MolDraw2D drawer, SWIGTYPE_p_double grid, Double_Vect xcoords, Double_Vect ycoords, long nContours, Double_Vect levels)
public static void contourAndDrawGrid(MolDraw2D drawer, SWIGTYPE_p_double grid, Double_Vect xcoords, Double_Vect ycoords, long nContours, ContourParams ps)
public static void contourAndDrawGrid(MolDraw2D drawer, SWIGTYPE_p_double grid, Double_Vect xcoords, Double_Vect ycoords, long nContours)
public static void contourAndDrawGrid(MolDraw2D drawer, SWIGTYPE_p_double grid, Double_Vect xcoords, Double_Vect ycoords)
public static void contourAndDrawGaussians(MolDraw2D drawer, SWIGTYPE_p_std__vectorT_RDGeom__Point2D_t locs, Double_Vect heights, Double_Vect widths, long nContours, Double_Vect levels, ContourParams ps)
public static void contourAndDrawGaussians(MolDraw2D drawer, SWIGTYPE_p_std__vectorT_RDGeom__Point2D_t locs, Double_Vect heights, Double_Vect widths, long nContours, Double_Vect levels)
public static void contourAndDrawGaussians(MolDraw2D drawer, SWIGTYPE_p_std__vectorT_RDGeom__Point2D_t locs, Double_Vect heights, Double_Vect widths, long nContours, ContourParams ps)
public static void contourAndDrawGaussians(MolDraw2D drawer, SWIGTYPE_p_std__vectorT_RDGeom__Point2D_t locs, Double_Vect heights, Double_Vect widths, long nContours)
public static void contourAndDrawGaussians(MolDraw2D drawer, SWIGTYPE_p_std__vectorT_RDGeom__Point2D_t locs, Double_Vect heights, Double_Vect widths)
public static int getVersionMajor()
public static int getVersionMinor()
public static int getVersionPatch()
public static int getEndianId()
public static void setDEFAULT_FILTERMATCHERBASE_NAME(java.lang.String value)
public static java.lang.String getDEFAULT_FILTERMATCHERBASE_NAME()
public static boolean FilterCatalogCanSerialize()
public static FilterCatalogEntry_VectVect RunFilterCatalog(FilterCatalog filterCatalog, Str_Vect smiles, int numThreads)
public static FilterCatalogEntry_VectVect RunFilterCatalog(FilterCatalog filterCatalog, Str_Vect smiles)
public static FilterCatalog FilterCatalogDeserialize(byte[] b)
public static long readAmberTrajectory(java.lang.String fName, Trajectory traj)
public static long readGromosTrajectory(java.lang.String fName, Trajectory traj)
public static CleanupParameters getDefaultCleanupParameters()
public static RWMol cleanup(RWMol mol, CleanupParameters params)
public static void tautomerParent(RWMol mol, CleanupParameters params)
public static void tautomerParent(RWMol mol)
public static RWMol fragmentParent(RWMol mol, CleanupParameters params, boolean skip_standardize)
public static RWMol fragmentParent(RWMol mol, CleanupParameters params)
public static void stereoParent(RWMol mol, CleanupParameters params)
public static void stereoParent(RWMol mol)
public static void isotopeParent(RWMol mol, CleanupParameters params)
public static void isotopeParent(RWMol mol)
public static RWMol chargeParent(RWMol mol, CleanupParameters params, boolean skip_standardize)
public static RWMol chargeParent(RWMol mol, CleanupParameters params)
public static void superParent(RWMol mol, CleanupParameters params)
public static void superParent(RWMol mol)
public static RWMol normalize(RWMol mol, CleanupParameters params)
public static RWMol reionize(RWMol mol, CleanupParameters params)
public static java.lang.String standardizeSmiles(java.lang.String smiles)
public static Str_Vect enumerateTautomerSmiles(java.lang.String smiles, CleanupParameters params)
public static Str_Vect enumerateTautomerSmiles(java.lang.String smiles)
public static boolean SubstructLibraryCanSerialize()
public static SubstructLibrary SubstructLibraryDeserialize(byte[] b)
public static long RGroupDecompose(ROMol_Vect cores, ROMol_Vect mols, StringMolMap_Vect rows, UInt_Vect unmatched, RGroupDecompositionParameters options)
public static long RGroupDecompose(ROMol_Vect cores, ROMol_Vect mols, StringMolMap_Vect rows, UInt_Vect unmatched)
public static long RGroupDecompose(ROMol_Vect cores, ROMol_Vect mols, StringMolMap_Vect rows)
public static long RGroupDecompose(ROMol_Vect cores, ROMol_Vect mols, StringROMol_VectMap columns, UInt_Vect unmatched, RGroupDecompositionParameters options)
public static long RGroupDecompose(ROMol_Vect cores, ROMol_Vect mols, StringROMol_VectMap columns, UInt_Vect unmatched)
public static long RGroupDecompose(ROMol_Vect cores, ROMol_Vect mols, StringROMol_VectMap columns)
public static java.lang.String MolHash(RWMol mol, HashFunction func)
public static void Strip(RWMol mol, long striptype)
public static void SplitMolecule(RWMol mol, SWIGTYPE_p_std__vectorT_RDKit__RWMol_p_t molv)
public static java.lang.String getAmwVersion()
public static double calcAMW(ROMol mol, boolean onlyHeavy)
public static double calcAMW(ROMol mol)
public static java.lang.String getExactmwVersion()
public static double calcExactMW(ROMol mol, boolean onlyHeavy)
public static double calcExactMW(ROMol mol)
public static java.lang.String calcMolFormula(ROMol mol, boolean separateIsotopes, boolean abbreviateHIsotopes)
public static java.lang.String calcMolFormula(ROMol mol, boolean separateIsotopes)
public static java.lang.String calcMolFormula(ROMol mol)
public static java.lang.String getLipinskiHBAVersion()
public static long calcLipinskiHBA(ROMol mol)
public static java.lang.String getLipinskiHBDVersion()
public static long calcLipinskiHBD(ROMol mol)
public static java.lang.String getNumRotatableBondsVersion()
public static long calcNumRotatableBonds(ROMol mol, NumRotatableBondsOptions useStrictDefinition)
public static long calcNumRotatableBonds(ROMol mol)
public static long calcNumRotatableBonds(ROMol mol, boolean strict)
public static java.lang.String getNumHBDVersion()
public static long calcNumHBD(ROMol mol)
public static java.lang.String getNumHBAVersion()
public static long calcNumHBA(ROMol mol)
public static java.lang.String getNumHeteroatomsVersion()
public static long calcNumHeteroatoms(ROMol mol)
public static java.lang.String getNumAmideBondsVersion()
public static long calcNumAmideBonds(ROMol mol)
public static java.lang.String getFractionCSP3Version()
public static double calcFractionCSP3(ROMol mol)
public static java.lang.String getNumRingsVersion()
public static long calcNumRings(ROMol mol)
public static java.lang.String getNumAromaticRingsVersion()
public static long calcNumAromaticRings(ROMol mol)
public static java.lang.String getNumAliphaticRingsVersion()
public static long calcNumAliphaticRings(ROMol mol)
public static java.lang.String getNumSaturatedRingsVersion()
public static long calcNumSaturatedRings(ROMol mol)
public static java.lang.String getNumHeterocyclesVersion()
public static long calcNumHeterocycles(ROMol mol)
public static java.lang.String getNumAromaticHeterocyclesVersion()
public static long calcNumAromaticHeterocycles(ROMol mol)
public static java.lang.String getNumAromaticCarbocyclesVersion()
public static long calcNumAromaticCarbocycles(ROMol mol)
public static java.lang.String getNumSaturatedHeterocyclesVersion()
public static long calcNumSaturatedHeterocycles(ROMol mol)
public static java.lang.String getNumSaturatedCarbocyclesVersion()
public static long calcNumSaturatedCarbocycles(ROMol mol)
public static java.lang.String getNumAliphaticHeterocyclesVersion()
public static long calcNumAliphaticHeterocycles(ROMol mol)
public static java.lang.String getNumAliphaticCarbocyclesVersion()
public static long calcNumAliphaticCarbocycles(ROMol mol)
public static java.lang.String getNumSpiroAtomsVersion()
public static long calcNumSpiroAtoms(ROMol mol)
public static java.lang.String getNumBridgeheadAtomsVersion()
public static long calcNumBridgeheadAtoms(ROMol mol)
public static java.lang.String getNumAtomStereoCentersVersion()
public static long numAtomStereoCenters(ROMol mol)
public static java.lang.String getNumUnspecifiedAtomStereoCentersVersion()
public static long numUnspecifiedAtomStereoCenters(ROMol mol)
public static void registerDescriptors()
public static java.lang.String getLabuteASAVersion()
public static double getLabuteAtomContribs(ROMol mol, Double_Vect Vi, SWIGTYPE_p_double hContrib, boolean includeHs, boolean force)
public static double getLabuteAtomContribs(ROMol mol, Double_Vect Vi, SWIGTYPE_p_double hContrib, boolean includeHs)
public static double getLabuteAtomContribs(ROMol mol, Double_Vect Vi, SWIGTYPE_p_double hContrib)
public static double calcLabuteASA(ROMol mol, boolean includeHs, boolean force)
public static double calcLabuteASA(ROMol mol, boolean includeHs)
public static double calcLabuteASA(ROMol mol)
public static java.lang.String getTpsaVersion()
public static double getTPSAAtomContribs(ROMol mol, Double_Vect Vi, boolean force, boolean includeSandP)
public static double getTPSAAtomContribs(ROMol mol, Double_Vect Vi, boolean force)
public static double getTPSAAtomContribs(ROMol mol, Double_Vect Vi)
public static double calcTPSA(ROMol mol, boolean force, boolean includeSandP)
public static double calcTPSA(ROMol mol, boolean force)
public static double calcTPSA(ROMol mol)
public static Double_Vect calcSlogP_VSA(ROMol mol, Double_Vect bins, boolean force)
public static Double_Vect calcSlogP_VSA(ROMol mol, Double_Vect bins)
public static Double_Vect calcSlogP_VSA(ROMol mol)
public static Double_Vect calcSMR_VSA(ROMol mol, Double_Vect bins, boolean force)
public static Double_Vect calcSMR_VSA(ROMol mol, Double_Vect bins)
public static Double_Vect calcSMR_VSA(ROMol mol)
public static Double_Vect calcPEOE_VSA(ROMol mol, Double_Vect bins, boolean force)
public static Double_Vect calcPEOE_VSA(ROMol mol, Double_Vect bins)
public static Double_Vect calcPEOE_VSA(ROMol mol)
public static Double_Vect calcCustomProp_VSA(ROMol mol, java.lang.String customPropName, Double_Vect bins, boolean force)
public static Double_Vect calcCustomProp_VSA(ROMol mol, java.lang.String customPropName, Double_Vect bins)
public static double calcChi0v(ROMol mol, boolean force)
public static double calcChi0v(ROMol mol)
public static java.lang.String getChi0vVersion()
public static double calcChi1v(ROMol mol, boolean force)
public static double calcChi1v(ROMol mol)
public static java.lang.String getChi1vVersion()
public static double calcChi2v(ROMol mol, boolean force)
public static double calcChi2v(ROMol mol)
public static java.lang.String getChi2vVersion()
public static double calcChi3v(ROMol mol, boolean force)
public static double calcChi3v(ROMol mol)
public static java.lang.String getChi3vVersion()
public static double calcChi4v(ROMol mol, boolean force)
public static double calcChi4v(ROMol mol)
public static java.lang.String getChi4vVersion()
public static double calcChiNv(ROMol mol, long n, boolean force)
public static double calcChiNv(ROMol mol, long n)
public static java.lang.String getChiNvVersion()
public static double calcChi0n(ROMol mol, boolean force)
public static double calcChi0n(ROMol mol)
public static java.lang.String getChi0nVersion()
public static double calcChi1n(ROMol mol, boolean force)
public static double calcChi1n(ROMol mol)
public static java.lang.String getChi1nVersion()
public static double calcChi2n(ROMol mol, boolean force)
public static double calcChi2n(ROMol mol)
public static java.lang.String getChi2nVersion()
public static double calcChi3n(ROMol mol, boolean force)
public static double calcChi3n(ROMol mol)
public static java.lang.String getChi3nVersion()
public static double calcChi4n(ROMol mol, boolean force)
public static double calcChi4n(ROMol mol)
public static java.lang.String getChi4nVersion()
public static double calcChiNn(ROMol mol, long n, boolean force)
public static double calcChiNn(ROMol mol, long n)
public static java.lang.String getChiNnVersion()
public static double calcHallKierAlpha(ROMol mol, Double_Vect atomContribs)
public static double calcHallKierAlpha(ROMol mol)
public static java.lang.String getHallKierAlphaVersion()
public static double calcKappa1(ROMol mol)
public static java.lang.String getKappa1Version()
public static double calcKappa2(ROMol mol)
public static java.lang.String getKappa2Version()
public static double calcKappa3(ROMol mol)
public static java.lang.String getKappa3Version()
public static void hkDeltas(ROMol mol, Double_Vect deltas, boolean force)
public static java.lang.String getMQNVersion()
public static Double_Pair calcCrippenDescriptors(ROMol mol, boolean includeHs, boolean force)
public static Double_Pair calcCrippenDescriptors(ROMol mol, boolean includeHs)
public static Double_Pair calcCrippenDescriptors(ROMol mol)
public static double calcMolLogP(ROMol mol)
public static double calcMolMR(ROMol mol)
public static int getAvalonSSSBits()
public static int getAvalonSimilarityBits()
public static java.lang.String getCanonSmiles(ROMol mol, int flags)
public static java.lang.String getCanonSmiles(ROMol mol)
public static void getAvalonCountFP(ROMol mol, SparseIntVectu32 res, long nBits, boolean isQuery, boolean resetVect, long bitFlags)
public static void getAvalonCountFP(ROMol mol, SparseIntVectu32 res, long nBits, boolean isQuery, boolean resetVect)
public static void getAvalonCountFP(ROMol mol, SparseIntVectu32 res, long nBits, boolean isQuery)
public static void getAvalonCountFP(ROMol mol, SparseIntVectu32 res, long nBits)
public static void getAvalonCountFP(ROMol mol, SparseIntVectu32 res)
public static void getAvalonFP(ROMol mol, ExplicitBitVect res, long nBits, boolean isQuery, boolean resetVect, long bitFlags)
public static void getAvalonFP(ROMol mol, ExplicitBitVect res, long nBits, boolean isQuery, boolean resetVect)
public static void getAvalonFP(ROMol mol, ExplicitBitVect res, long nBits, boolean isQuery)
public static void getAvalonFP(ROMol mol, ExplicitBitVect res, long nBits)
public static void getAvalonFP(ROMol mol, ExplicitBitVect res)
public static void getAvalonFP(ROMol mol, UInt_Vect res, long nBits, boolean isQuery, boolean resetVect, long bitFlags)
public static void getAvalonFP(ROMol mol, UInt_Vect res, long nBits, boolean isQuery, boolean resetVect)
public static long set2DCoords(ROMol mol, boolean clearConfs)
public static long set2DCoords(ROMol mol)
public static java.lang.String getCanonSmiles(java.lang.String data, boolean isSmiles, int flags)
public static java.lang.String getCanonSmiles(java.lang.String data, boolean isSmiles)
public static void getAvalonCountFP(java.lang.String data, boolean isSmiles, SparseIntVectu32 res, long nBits, boolean isQuery, long bitFlags)
public static void getAvalonCountFP(java.lang.String data, boolean isSmiles, SparseIntVectu32 res, long nBits, boolean isQuery)
public static void getAvalonCountFP(java.lang.String data, boolean isSmiles, SparseIntVectu32 res, long nBits)
public static void getAvalonCountFP(java.lang.String data, boolean isSmiles, SparseIntVectu32 res)
public static void getAvalonFP(java.lang.String data, boolean isSmiles, ExplicitBitVect res, long nBits, boolean isQuery, boolean resetVect, long bitFlags)
public static void getAvalonFP(java.lang.String data, boolean isSmiles, ExplicitBitVect res, long nBits, boolean isQuery, boolean resetVect)
public static void getAvalonFP(java.lang.String data, boolean isSmiles, ExplicitBitVect res, long nBits, boolean isQuery)
public static void getAvalonFP(java.lang.String data, boolean isSmiles, ExplicitBitVect res, long nBits)
public static void getAvalonFP(java.lang.String data, boolean isSmiles, ExplicitBitVect res)
public static void getAvalonFP(java.lang.String data, boolean isSmiles, UInt_Vect res, long nBits, boolean isQuery, boolean resetVect, long bitFlags)
public static void getAvalonFP(java.lang.String data, boolean isSmiles, UInt_Vect res, long nBits, boolean isQuery, boolean resetVect)
public static void getAvalonFP(java.lang.String data, boolean isSmiles, UInt_Vect res, long nBits, boolean isQuery)
public static void getAvalonFP(java.lang.String data, boolean isSmiles, UInt_Vect res, long nBits)
public static void getAvalonFP(java.lang.String data, boolean isSmiles, UInt_Vect res)
public static java.lang.String set2DCoords(java.lang.String data, boolean isSmiles)
public static int initCheckMol(java.lang.String optString)
public static ROMol checkMol(SWIGTYPE_p_int errors, ROMol inMol)
public static ROMol checkMol(SWIGTYPE_p_int errors, java.lang.String data, boolean isSmiles)
public static StringInt_Pair checkMolString(java.lang.String data, boolean isSmiles)
public static java.lang.String getCheckMolLog()
public static void closeCheckMolFiles()
public static RWMol InchiToMol(java.lang.String inchi, ExtraInchiReturnValues rv, boolean sanitize, boolean removeHs)
public static RWMol InchiToMol(java.lang.String inchi, ExtraInchiReturnValues rv, boolean sanitize)
public static RWMol InchiToMol(java.lang.String inchi, ExtraInchiReturnValues rv)
public static java.lang.String MolToInchi(ROMol mol, ExtraInchiReturnValues rv, java.lang.String options)
public static java.lang.String MolToInchi(ROMol mol, ExtraInchiReturnValues rv)
public static java.lang.String MolBlockToInchi(java.lang.String mol, ExtraInchiReturnValues rv, java.lang.String options)
public static java.lang.String MolBlockToInchi(java.lang.String mol, ExtraInchiReturnValues rv)
public static java.lang.String InchiToInchiKey(java.lang.String inchi)
public static java.lang.String MolToInchiKey(ROMol mol, java.lang.String options)
public static java.lang.String MolToInchiKey(ROMol mol)
public static Int_Vect pickUsingFingerprints(EBV_Vect ebvs, long nToPick, int seed, Int_Vect firstPicks, boolean useCache)
public static Int_Vect pickUsingFingerprints(EBV_Vect ebvs, long nToPick, int seed, Int_Vect firstPicks)
public static Int_Vect pickUsingFingerprints(EBV_Vect ebvs, long nToPick, int seed)
public static void setRdkitVersion(java.lang.String value)
public static java.lang.String getRdkitVersion()
public static void setBoostVersion(java.lang.String value)
public static java.lang.String getBoostVersion()
public static void setRdkitBuild(java.lang.String value)
public static java.lang.String getRdkitBuild()