rdkit.Chem.rdMolDescriptors module
Module containing functions to compute molecular descriptors
class rdkit.Chem.rdMolDescriptors.
AtomPairsParameters
((object)arg1) → None :
Bases: Boost.Python.instance
C++ signature :
void __init__(_object*)
atomTypes
= <rdkit.rdBase._vectj object>
codeSize
= 9
numAtomPairFingerprintBits
= 23
numBranchBits
= 3
numChiralBits
= 2
numPathBits
= 5
numPiBits
= 2
numTypeBits
= 4
version
= '1.1.0'
rdkit.Chem.rdMolDescriptors.
CalcAUTOCORR2D
((Mol)mol[, (str)CustomAtomProperty='']) → list :
Returns 2D Autocorrelation descriptors vector
C++ signature :
boost::python::list CalcAUTOCORR2D(RDKit::ROMol [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’‘])
rdkit.Chem.rdMolDescriptors.
CalcAUTOCORR3D
((Mol)mol[, (int)confId=-1[, (str)CustomAtomProperty='']]) → list :
Returns 3D Autocorrelation descriptors vector
C++ signature :
boost::python::list CalcAUTOCORR3D(RDKit::ROMol [,int=-1 [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’‘]])
rdkit.Chem.rdMolDescriptors.
CalcAsphericity
((Mol)mol[, (int)confId=-1[, (bool)useAtomicMasses=True[, (bool)force=True]]]) → float :
C++ signature :
double CalcAsphericity(RDKit::ROMol [,int=-1 [,bool=True [,bool=True]]])
rdkit.Chem.rdMolDescriptors.
CalcChi0n
((Mol)mol[, (bool)force=False]) → float :
C++ signature :
double CalcChi0n(RDKit::ROMol [,bool=False])
rdkit.Chem.rdMolDescriptors.
CalcChi0v
((Mol)mol[, (bool)force=False]) → float :
C++ signature :
double CalcChi0v(RDKit::ROMol [,bool=False])
rdkit.Chem.rdMolDescriptors.
CalcChi1n
((Mol)mol[, (bool)force=False]) → float :
C++ signature :
double CalcChi1n(RDKit::ROMol [,bool=False])
rdkit.Chem.rdMolDescriptors.
CalcChi1v
((Mol)mol[, (bool)force=False]) → float :
C++ signature :
double CalcChi1v(RDKit::ROMol [,bool=False])
rdkit.Chem.rdMolDescriptors.
CalcChi2n
((Mol)mol[, (bool)force=False]) → float :
C++ signature :
double CalcChi2n(RDKit::ROMol [,bool=False])
rdkit.Chem.rdMolDescriptors.
CalcChi2v
((Mol)mol[, (bool)force=False]) → float :
C++ signature :
double CalcChi2v(RDKit::ROMol [,bool=False])
rdkit.Chem.rdMolDescriptors.
CalcChi3n
((Mol)mol[, (bool)force=False]) → float :
C++ signature :
double CalcChi3n(RDKit::ROMol [,bool=False])
rdkit.Chem.rdMolDescriptors.
CalcChi3v
((Mol)mol[, (bool)force=False]) → float :
C++ signature :
double CalcChi3v(RDKit::ROMol [,bool=False])
rdkit.Chem.rdMolDescriptors.
CalcChi4n
((Mol)mol[, (bool)force=False]) → float :
C++ signature :
double CalcChi4n(RDKit::ROMol [,bool=False])
rdkit.Chem.rdMolDescriptors.
CalcChi4v
((Mol)mol[, (bool)force=False]) → float :
C++ signature :
double CalcChi4v(RDKit::ROMol [,bool=False])
rdkit.Chem.rdMolDescriptors.
CalcChiNn
((Mol)mol, (int)n[, (bool)force=False]) → float :
C++ signature :
double CalcChiNn(RDKit::ROMol,unsigned int [,bool=False])
rdkit.Chem.rdMolDescriptors.
CalcChiNv
((Mol)mol, (int)n[, (bool)force=False]) → float :
C++ signature :
double CalcChiNv(RDKit::ROMol,unsigned int [,bool=False])
rdkit.Chem.rdMolDescriptors.
CalcCrippenDescriptors
((Mol)mol[, (bool)includeHs=True[, (bool)force=False]]) → tuple :
returns a 2-tuple with the Wildman-Crippen logp,mr values
C++ signature :
boost::python::tuple CalcCrippenDescriptors(RDKit::ROMol [,bool=True [,bool=False]])
rdkit.Chem.rdMolDescriptors.
CalcEEMcharges
((Mol)mol[, (int)confId=-1]) → list :
Returns EEM atomic partial charges
C++ signature :
boost::python::list CalcEEMcharges(RDKit::ROMol {lvalue} [,int=-1])
rdkit.Chem.rdMolDescriptors.
CalcEccentricity
((Mol)mol[, (int)confId=-1[, (bool)useAtomicMasses=True[, (bool)force=True]]]) → float :
C++ signature :
double CalcEccentricity(RDKit::ROMol [,int=-1 [,bool=True [,bool=True]]])
rdkit.Chem.rdMolDescriptors.
CalcExactMolWt
((Mol)mol[, (bool)onlyHeavy=False]) → float :
returns the molecule’s exact molecular weight
C++ signature :
double CalcExactMolWt(RDKit::ROMol [,bool=False])
rdkit.Chem.rdMolDescriptors.
CalcFractionCSP3
((Mol)mol) → float :
returns the fraction of C atoms that are SP3 hybridized
C++ signature :
double CalcFractionCSP3(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcGETAWAY
((Mol)mol[, (int)confId=-1[, (float)precision=2[, (str)CustomAtomProperty='']]]) → list :
Returns the GETAWAY descriptors vector
C++ signature :
boost::python::list CalcGETAWAY(RDKit::ROMol [,int=-1 [,double=2 [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’‘]]])
rdkit.Chem.rdMolDescriptors.
CalcHallKierAlpha
((Mol)mol[, (AtomPairsParameters)atomContribs=None]) → float :
C++ signature :
double CalcHallKierAlpha(RDKit::ROMol [,boost::python::api::object=None])
rdkit.Chem.rdMolDescriptors.
CalcInertialShapeFactor
((Mol)mol[, (int)confId=-1[, (bool)useAtomicMasses=True[, (bool)force=True]]]) → float :
C++ signature :
double CalcInertialShapeFactor(RDKit::ROMol [,int=-1 [,bool=True [,bool=True]]])
rdkit.Chem.rdMolDescriptors.
CalcKappa1
((Mol)mol) → float :
C++ signature :
double CalcKappa1(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcKappa2
((Mol)mol) → float :
C++ signature :
double CalcKappa2(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcKappa3
((Mol)mol) → float :
C++ signature :
double CalcKappa3(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcLabuteASA
((Mol)mol[, (bool)includeHs=True[, (bool)force=False]]) → float :
returns the Labute ASA value for a molecule
C++ signature :
double CalcLabuteASA(RDKit::ROMol [,bool=True [,bool=False]])
rdkit.Chem.rdMolDescriptors.
CalcMORSE
((Mol)mol[, (int)confId=-1[, (str)CustomAtomProperty='']]) → list :
Returns Molecule Representation of Structures based on Electron diffraction descriptors
C++ signature :
boost::python::list CalcMORSE(RDKit::ROMol [,int=-1 [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’‘]])
rdkit.Chem.rdMolDescriptors.
CalcMolFormula
((Mol)mol[, (bool)separateIsotopes=False[, (bool)abbreviateHIsotopes=True]]) → str :
returns the molecule’s formula
C++ signature :
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > CalcMolFormula(RDKit::ROMol [,bool=False [,bool=True]])
rdkit.Chem.rdMolDescriptors.
CalcNPR1
((Mol)mol[, (int)confId=-1[, (bool)useAtomicMasses=True[, (bool)force=True]]]) → float :
C++ signature :
double CalcNPR1(RDKit::ROMol [,int=-1 [,bool=True [,bool=True]]])
rdkit.Chem.rdMolDescriptors.
CalcNPR2
((Mol)mol[, (int)confId=-1[, (bool)useAtomicMasses=True[, (bool)force=True]]]) → float :
C++ signature :
double CalcNPR2(RDKit::ROMol [,int=-1 [,bool=True [,bool=True]]])
rdkit.Chem.rdMolDescriptors.
CalcNumAliphaticCarbocycles
((Mol)mol) → int :
returns the number of aliphatic (containing at least one non-aromatic bond) carbocycles for a molecule
C++ signature :
unsigned int CalcNumAliphaticCarbocycles(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcNumAliphaticHeterocycles
((Mol)mol) → int :
returns the number of aliphatic (containing at least one non-aromatic bond) heterocycles for a molecule
C++ signature :
unsigned int CalcNumAliphaticHeterocycles(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcNumAliphaticRings
((Mol)mol) → int :
returns the number of aliphatic (containing at least one non-aromatic bond) rings for a molecule
C++ signature :
unsigned int CalcNumAliphaticRings(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcNumAmideBonds
((Mol)mol) → int :
returns the number of amide bonds in a molecule
C++ signature :
unsigned int CalcNumAmideBonds(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcNumAromaticCarbocycles
((Mol)mol) → int :
returns the number of aromatic carbocycles for a molecule
C++ signature :
unsigned int CalcNumAromaticCarbocycles(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcNumAromaticHeterocycles
((Mol)mol) → int :
returns the number of aromatic heterocycles for a molecule
C++ signature :
unsigned int CalcNumAromaticHeterocycles(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcNumAromaticRings
((Mol)mol) → int :
returns the number of aromatic rings for a molecule
C++ signature :
unsigned int CalcNumAromaticRings(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcNumAtomStereoCenters
((Mol)mol) → int :
Returns the total number of atomic stereocenters (specified and unspecified)
C++ signature :
unsigned int CalcNumAtomStereoCenters(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcNumBridgeheadAtoms
((Mol)mol[, (AtomPairsParameters)atoms=None]) → int :
Returns the number of bridgehead atoms (atoms shared between rings that share at least two bonds)
C++ signature :
unsigned int CalcNumBridgeheadAtoms(RDKit::ROMol [,boost::python::api::object=None])
rdkit.Chem.rdMolDescriptors.
CalcNumHBA
((Mol)mol) → int :
returns the number of H-bond acceptors for a molecule
C++ signature :
unsigned int CalcNumHBA(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcNumHBD
((Mol)mol) → int :
returns the number of H-bond donors for a molecule
C++ signature :
unsigned int CalcNumHBD(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcNumHeteroatoms
((Mol)mol) → int :
returns the number of heteroatoms for a molecule
C++ signature :
unsigned int CalcNumHeteroatoms(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcNumHeterocycles
((Mol)mol) → int :
returns the number of heterocycles for a molecule
C++ signature :
unsigned int CalcNumHeterocycles(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcNumLipinskiHBA
((Mol)mol) → int :
returns the number of Lipinski H-bond acceptors for a molecule
C++ signature :
unsigned int CalcNumLipinskiHBA(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcNumLipinskiHBD
((Mol)mol) → int :
returns the number of Lipinski H-bond donors for a molecule
C++ signature :
unsigned int CalcNumLipinskiHBD(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcNumRings
((Mol)mol) → int :
returns the number of rings for a molecule
C++ signature :
unsigned int CalcNumRings(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcNumRotatableBonds
((Mol)mol, (bool)strict) → int :
returns the number of rotatable bonds for a molecule.
strict = NumRotatableBondsOptions.NonStrict - Simple rotatable bond definition. strict = NumRotatableBondsOptions.Strict - (default) does not count things like
amide or ester bonds
strict = NumRotatableBondsOptions.StrictLinkages - handles linkages between ring
systems. - Single bonds between aliphatic ring Cs are always rotatable. This
means that the central bond in CC1CCCC(C)C1-C1C(C)CCCC1C is now considered rotatable; it was not before
- Heteroatoms in the linked rings no longer affect whether or not the linking bond is rotatable
the linking bond in systems like Cc1cccc(C)c1-c1c(C)cccc1 is now
considered non-rotatable
C++ signature :
unsigned int CalcNumRotatableBonds(RDKit::ROMol,bool)
CalcNumRotatableBonds( (Mol)mol [, (NumRotatableBondsOptions)strict=rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions.Default]) -> int :
returns the number of rotatable bonds for a molecule.
strict = NumRotatableBondsOptions.NonStrict - Simple rotatable bond definition. strict = NumRotatableBondsOptions.Strict - (default) does not count things like
amide or ester bonds
strict = NumRotatableBondsOptions.StrictLinkages - handles linkages between ring
systems. - Single bonds between aliphatic ring Cs are always rotatable. This
means that the central bond in CC1CCCC(C)C1-C1C(C)CCCC1C is now considered rotatable; it was not before
- Heteroatoms in the linked rings no longer affect whether or not the linking bond is rotatable
-
the linking bond in systems like Cc1cccc(C)c1-c1c(C)cccc1 is now
considered non-rotatable
C++ signature :
unsigned int CalcNumRotatableBonds(RDKit::ROMol [,RDKit::Descriptors::NumRotatableBondsOptions=rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions.Default])
rdkit.Chem.rdMolDescriptors.
CalcNumSaturatedCarbocycles
((Mol)mol) → int :
returns the number of saturated carbocycles for a molecule
C++ signature :
unsigned int CalcNumSaturatedCarbocycles(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcNumSaturatedHeterocycles
((Mol)mol) → int :
returns the number of saturated heterocycles for a molecule
C++ signature :
unsigned int CalcNumSaturatedHeterocycles(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcNumSaturatedRings
((Mol)mol) → int :
returns the number of saturated rings for a molecule
C++ signature :
unsigned int CalcNumSaturatedRings(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcNumSpiroAtoms
((Mol)mol[, (AtomPairsParameters)atoms=None]) → int :
Returns the number of spiro atoms (atoms shared between rings that share exactly one atom)
C++ signature :
unsigned int CalcNumSpiroAtoms(RDKit::ROMol [,boost::python::api::object=None])
rdkit.Chem.rdMolDescriptors.
CalcNumUnspecifiedAtomStereoCenters
((Mol)mol) → int :
Returns the number of unspecified atomic stereocenters
C++ signature :
unsigned int CalcNumUnspecifiedAtomStereoCenters(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
CalcPBF
((Mol)mol[, (int)confId=-1]) → float :
Returns the PBF (plane of best fit) descriptor (https://doi.org/10.1021/ci300293f)
C++ signature :
double CalcPBF(RDKit::ROMol [,int=-1])
rdkit.Chem.rdMolDescriptors.
CalcPMI1
((Mol)mol[, (int)confId=-1[, (bool)useAtomicMasses=True[, (bool)force=True]]]) → float :
C++ signature :
double CalcPMI1(RDKit::ROMol [,int=-1 [,bool=True [,bool=True]]])
rdkit.Chem.rdMolDescriptors.
CalcPMI2
((Mol)mol[, (int)confId=-1[, (bool)useAtomicMasses=True[, (bool)force=True]]]) → float :
C++ signature :
double CalcPMI2(RDKit::ROMol [,int=-1 [,bool=True [,bool=True]]])
rdkit.Chem.rdMolDescriptors.
CalcPMI3
((Mol)mol[, (int)confId=-1[, (bool)useAtomicMasses=True[, (bool)force=True]]]) → float :
C++ signature :
double CalcPMI3(RDKit::ROMol [,int=-1 [,bool=True [,bool=True]]])
rdkit.Chem.rdMolDescriptors.
CalcRDF
((Mol)mol[, (int)confId=-1[, (str)CustomAtomProperty='']]) → list :
Returns radial distribution fonction descriptors (RDF)
C++ signature :
boost::python::list CalcRDF(RDKit::ROMol [,int=-1 [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’‘]])
rdkit.Chem.rdMolDescriptors.
CalcRadiusOfGyration
((Mol)mol[, (int)confId=-1[, (bool)useAtomicMasses=True[, (bool)force=True]]]) → float :
C++ signature :
double CalcRadiusOfGyration(RDKit::ROMol [,int=-1 [,bool=True [,bool=True]]])
rdkit.Chem.rdMolDescriptors.
CalcSpherocityIndex
((Mol)mol[, (int)confId=-1[, (bool)force=True]]) → float :
C++ signature :
double CalcSpherocityIndex(RDKit::ROMol [,int=-1 [,bool=True]])
rdkit.Chem.rdMolDescriptors.
CalcTPSA
((Mol)mol[, (bool)force=False[, (bool)includeSandP=False]]) → float :
returns the TPSA value for a molecule
C++ signature :
double CalcTPSA(RDKit::ROMol [,bool=False [,bool=False]])
rdkit.Chem.rdMolDescriptors.
CalcWHIM
((Mol)mol[, (int)confId=-1[, (float)thresh=0.001[, (str)CustomAtomProperty='']]]) → list :
Returns the WHIM descriptors vector
C++ signature :
boost::python::list CalcWHIM(RDKit::ROMol [,int=-1 [,double=0.001 [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’‘]]])
rdkit.Chem.rdMolDescriptors.
CustomProp_VSA_
((Mol)mol, (str)customPropName, (AtomPairsParameters)bins[, (bool)force=False]) → list :
C++ signature :
boost::python::list CustomProp_VSA_(RDKit::ROMol,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,boost::python::api::object [,bool=False])
rdkit.Chem.rdMolDescriptors.
GetAtomPairAtomCode
((Atom)atom[, (int)branchSubtract=0[, (bool)includeChirality=False]]) → int :
Returns the atom code (hash) for an atom
C++ signature :
unsigned int GetAtomPairAtomCode(RDKit::Atom const* [,unsigned int=0 [,bool=False]])
rdkit.Chem.rdMolDescriptors.
GetAtomPairCode
((int)atom1Code, (int)atom2Code, (int)distance[, (bool)includeChirality=False]) → int :
Returns the atom-pair code (hash) for a pair of atoms separated by a certain number of bonds
C++ signature :
unsigned int GetAtomPairCode(unsigned int,unsigned int,unsigned int [,bool=False])
rdkit.Chem.rdMolDescriptors.
GetAtomPairFingerprint
((Mol)mol[, (int)minLength=1[, (int)maxLength=30[, (AtomPairsParameters)fromAtoms=0[, (AtomPairsParameters)ignoreAtoms=0[, (AtomPairsParameters)atomInvariants=0[, (bool)includeChirality=False[, (bool)use2D=True[, (int)confId=-1]]]]]]]]) → IntSparseIntVect :
Returns the atom-pair fingerprint for a molecule as an IntSparseIntVect
C++ signature :
RDKit::SparseIntVect<int>* GetAtomPairFingerprint(RDKit::ROMol [,unsigned int=1 [,unsigned int=30 [,boost::python::api::object=0 [,boost::python::api::object=0 [,boost::python::api::object=0 [,bool=False [,bool=True [,int=-1]]]]]]]])
rdkit.Chem.rdMolDescriptors.
GetConnectivityInvariants
((Mol)mol[, (bool)includeRingMembership=True]) → list :
Returns connectivity invariants (ECFP-like) for a molecule.
C++ signature :
boost::python::list GetConnectivityInvariants(RDKit::ROMol [,bool=True])
rdkit.Chem.rdMolDescriptors.
GetFeatureInvariants
((Mol)mol) → list :
Returns feature invariants (FCFP-like) for a molecule.
C++ signature :
boost::python::list GetFeatureInvariants(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
GetHashedAtomPairFingerprint
((Mol)mol[, (int)nBits=2048[, (int)minLength=1[, (int)maxLength=30[, (AtomPairsParameters)fromAtoms=0[, (AtomPairsParameters)ignoreAtoms=0[, (AtomPairsParameters)atomInvariants=0[, (bool)includeChirality=False[, (bool)use2D=True[, (int)confId=-1]]]]]]]]]) → IntSparseIntVect :
Returns the hashed atom-pair fingerprint for a molecule as an IntSparseIntVect
C++ signature :
RDKit::SparseIntVect<int>* GetHashedAtomPairFingerprint(RDKit::ROMol [,unsigned int=2048 [,unsigned int=1 [,unsigned int=30 [,boost::python::api::object=0 [,boost::python::api::object=0 [,boost::python::api::object=0 [,bool=False [,bool=True [,int=-1]]]]]]]]])
rdkit.Chem.rdMolDescriptors.
GetHashedAtomPairFingerprintAsBitVect
((Mol)mol[, (int)nBits=2048[, (int)minLength=1[, (int)maxLength=30[, (AtomPairsParameters)fromAtoms=0[, (AtomPairsParameters)ignoreAtoms=0[, (AtomPairsParameters)atomInvariants=0[, (int)nBitsPerEntry=4[, (bool)includeChirality=False[, (bool)use2D=True[, (int)confId=-1]]]]]]]]]]) → ExplicitBitVect :
Returns the atom-pair fingerprint for a molecule as an ExplicitBitVect
C++ signature :
ExplicitBitVect* GetHashedAtomPairFingerprintAsBitVect(RDKit::ROMol [,unsigned int=2048 [,unsigned int=1 [,unsigned int=30 [,boost::python::api::object=0 [,boost::python::api::object=0 [,boost::python::api::object=0 [,unsigned int=4 [,bool=False [,bool=True [,int=-1]]]]]]]]]])
rdkit.Chem.rdMolDescriptors.
GetHashedMorganFingerprint
((Mol)mol, (int)radius[, (int)nBits=2048[, (AtomPairsParameters)invariants=[][, (AtomPairsParameters)fromAtoms=[][, (bool)useChirality=False[, (bool)useBondTypes=True[, (bool)useFeatures=False[, (AtomPairsParameters)bitInfo=None]]]]]]]) → UIntSparseIntVect :
Returns a hashed Morgan fingerprint for a molecule
C++ signature :
RDKit::SparseIntVect<unsigned int>* GetHashedMorganFingerprint(RDKit::ROMol,int [,int=2048 [,boost::python::api::object=[] [,boost::python::api::object=[] [,bool=False [,bool=True [,bool=False [,boost::python::api::object=None]]]]]]])
rdkit.Chem.rdMolDescriptors.
GetHashedTopologicalTorsionFingerprint
((Mol)mol[, (int)nBits=2048[, (int)targetSize=4[, (AtomPairsParameters)fromAtoms=0[, (AtomPairsParameters)ignoreAtoms=0[, (AtomPairsParameters)atomInvariants=0[, (bool)includeChirality=False]]]]]]) → LongSparseIntVect :
Returns the hashed topological-torsion fingerprint for a molecule as a LongIntSparseIntVect
C++ signature :
RDKit::SparseIntVect<long>* GetHashedTopologicalTorsionFingerprint(RDKit::ROMol [,unsigned int=2048 [,unsigned int=4 [,boost::python::api::object=0 [,boost::python::api::object=0 [,boost::python::api::object=0 [,bool=False]]]]]])
rdkit.Chem.rdMolDescriptors.
GetHashedTopologicalTorsionFingerprintAsBitVect
((Mol)mol[, (int)nBits=2048[, (int)targetSize=4[, (AtomPairsParameters)fromAtoms=0[, (AtomPairsParameters)ignoreAtoms=0[, (AtomPairsParameters)atomInvariants=0[, (int)nBitsPerEntry=4[, (bool)includeChirality=False]]]]]]]) → ExplicitBitVect :
Returns the topological-torsion fingerprint for a molecule as an ExplicitBitVect
C++ signature :
ExplicitBitVect* GetHashedTopologicalTorsionFingerprintAsBitVect(RDKit::ROMol [,unsigned int=2048 [,unsigned int=4 [,boost::python::api::object=0 [,boost::python::api::object=0 [,boost::python::api::object=0 [,unsigned int=4 [,bool=False]]]]]]])
rdkit.Chem.rdMolDescriptors.
GetMACCSKeysFingerprint
((Mol)mol) → ExplicitBitVect :
Returns the MACCS keys for a molecule as an ExplicitBitVect
C++ signature :
ExplicitBitVect* GetMACCSKeysFingerprint(RDKit::ROMol)
rdkit.Chem.rdMolDescriptors.
GetMorganFingerprint
((Mol)mol, (int)radius[, (AtomPairsParameters)invariants=[][, (AtomPairsParameters)fromAtoms=[][, (bool)useChirality=False[, (bool)useBondTypes=True[, (bool)useFeatures=False[, (bool)useCounts=True[, (AtomPairsParameters)bitInfo=None]]]]]]]) → UIntSparseIntVect :
Returns a Morgan fingerprint for a molecule
C++ signature :
RDKit::SparseIntVect<unsigned int>* GetMorganFingerprint(RDKit::ROMol,int [,boost::python::api::object=[] [,boost::python::api::object=[] [,bool=False [,bool=True [,bool=False [,bool=True [,boost::python::api::object=None]]]]]]])
rdkit.Chem.rdMolDescriptors.
GetMorganFingerprintAsBitVect
((Mol)mol, (int)radius[, (int)nBits=2048[, (AtomPairsParameters)invariants=[][, (AtomPairsParameters)fromAtoms=[][, (bool)useChirality=False[, (bool)useBondTypes=True[, (bool)useFeatures=False[, (AtomPairsParameters)bitInfo=None]]]]]]]) → ExplicitBitVect :
Returns a Morgan fingerprint for a molecule as a bit vector
C++ signature :
ExplicitBitVect* GetMorganFingerprintAsBitVect(RDKit::ROMol,int [,unsigned int=2048 [,boost::python::api::object=[] [,boost::python::api::object=[] [,bool=False [,bool=True [,bool=False [,boost::python::api::object=None]]]]]]])
rdkit.Chem.rdMolDescriptors.
GetTopologicalTorsionFingerprint
((Mol)mol[, (int)targetSize=4[, (AtomPairsParameters)fromAtoms=0[, (AtomPairsParameters)ignoreAtoms=0[, (AtomPairsParameters)atomInvariants=0[, (bool)includeChirality=False]]]]]) → LongSparseIntVect :
Returns the topological-torsion fingerprint for a molecule as a LongIntSparseIntVect
C++ signature :
RDKit::SparseIntVect<long>* GetTopologicalTorsionFingerprint(RDKit::ROMol [,unsigned int=4 [,boost::python::api::object=0 [,boost::python::api::object=0 [,boost::python::api::object=0 [,bool=False]]]]])
rdkit.Chem.rdMolDescriptors.
GetUSR
((Mol)mol[, (int)confId=-1]) → list :
Returns a USR descriptor for one conformer of a molecule
C++ signature :
boost::python::list GetUSR(RDKit::ROMol [,int=-1])
rdkit.Chem.rdMolDescriptors.
GetUSRCAT
((Mol)mol[, (AtomPairsParameters)atomSelections=None[, (int)confId=-1]]) → list :
Returns a USRCAT descriptor for one conformer of a molecule
C++ signature :
boost::python::list GetUSRCAT(RDKit::ROMol [,boost::python::api::object=None [,int=-1]])
rdkit.Chem.rdMolDescriptors.
GetUSRDistributions
((AtomPairsParameters)coords[, (AtomPairsParameters)points=None]) → list :
Returns the four USR distance distributions for a set of coordinates
C++ signature :
boost::python::list GetUSRDistributions(boost::python::api::object [,boost::python::api::object=None])
rdkit.Chem.rdMolDescriptors.
GetUSRDistributionsFromPoints
((AtomPairsParameters)coords, (AtomPairsParameters)points) → list :
Returns the USR distance distributions for a set of coordinates and points
C++ signature :
boost::python::list GetUSRDistributionsFromPoints(boost::python::api::object,boost::python::api::object)
rdkit.Chem.rdMolDescriptors.
GetUSRFromDistributions
((AtomPairsParameters)distances) → list :
Returns the USR descriptor from a set of distance distributions
C++ signature :
boost::python::list GetUSRFromDistributions(boost::python::api::object)
rdkit.Chem.rdMolDescriptors.
GetUSRScore
((AtomPairsParameters)descriptor1, (AtomPairsParameters)descriptor2[, (AtomPairsParameters)weights=[]]) → float :
Returns the USR score for two USR or USRCAT descriptors
C++ signature :
double GetUSRScore(boost::python::api::object,boost::python::api::object [,boost::python::api::object=[]])
rdkit.Chem.rdMolDescriptors.
MQNs_
((Mol)mol[, (bool)force=False]) → list :
C++ signature :
boost::python::list MQNs_(RDKit::ROMol [,bool=False])
rdkit.Chem.rdMolDescriptors.
MakePropertyRangeQuery
((str)name, (float)min, (float)max) → PropertyRangeQuery :
Generates a Range property for the specified property, between min and max query = MakePropertyRangeQuery(‘exactmw’, 0, 500) query.Match( mol )
C++ signature :
Queries::RangeQuery<double, RDKit::ROMol const&, true>* MakePropertyRangeQuery(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,double,double)
class rdkit.Chem.rdMolDescriptors.
NumRotatableBondsOptions
Bases: Boost.Python.enum
Options for generating rotatble bonds NonStrict - standard loose definitions Strict - stricter definition excluding amides, esters, etc StrictLinkages - adds rotors between rotatable bonds Default - Current RDKit default
Default
= rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions.Default
NonStrict
= rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions.NonStrict
Strict
= rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions.Strict
StrictLinkages
= rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions.StrictLinkages
names
= {'Default': rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions.Default, 'NonStrict': rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions.NonStrict, 'Strict': rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions.Strict, 'StrictLinkages': rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions.StrictLinkages}
values
= {-1: rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions.Default, 0: rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions.NonStrict, 1: rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions.Strict, 2: rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions.StrictLinkages}
rdkit.Chem.rdMolDescriptors.
PEOE_VSA_
((Mol)mol[, (AtomPairsParameters)bins=[][, (bool)force=False]]) → list :
C++ signature :
boost::python::list PEOE_VSA_(RDKit::ROMol [,boost::python::api::object=[] [,bool=False]])
class rdkit.Chem.rdMolDescriptors.
Properties
((object)arg1) → None :
Bases: Boost.Python.instance
Property computation and registry system. To compute all registered properties: mol = Chem.MolFromSmiles(‘c1ccccc1’) properties = rdMolDescriptors.Properties() for name, value in zip(properties.GetPropertyNames(), properties.ComputeProperties(mol)):
print(name, value)
To compute a subset properties = rdMolDescriptors.Properties([‘exactmw’, ‘lipinskiHBA’]) for name, value in zip(properties.GetPropertyNames(), properties.ComputeProperties(mol)):
print(name, value)
C++ signature :
void __init__(_object*)
__init__( (object)arg1, (_vectNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE)arg2) -> None :
C++ signature :
void __init__(_object*,std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >)
AnnotateProperties
((Properties)arg1, (Mol)mol) → None :
Annotate the molecule with the computed properties. These properties will be available as SDData or from mol.GetProp(prop)
C++ signature :
void AnnotateProperties(RDKit::Descriptors::Properties {lvalue},RDKit::ROMol {lvalue})
ComputeProperties
((Properties)arg1, (Mol)mol[, (bool)annotateMol=False]) → _vectd :
Return a list of computed properties, if annotateMol==True, annotate the molecule with the computed properties.
C++ signature :
std::vector<double, std::allocator<double> > ComputeProperties(RDKit::Descriptors::Properties {lvalue},RDKit::ROMol [,bool=False])
static GetAvailableProperties
() → _vectNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE :
Return all available property names that can be computed
C++ signature :
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > GetAvailableProperties()
static GetProperty
((str)propName) → PropertyFunctor :
Return the named property if it exists
C++ signature :
boost::shared_ptr<RDKit::Descriptors::PropertyFunctor> GetProperty(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)
GetPropertyNames
((Properties)arg1) → _vectNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE :
Return the property names computed by this instance
C++ signature :
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > GetPropertyNames(RDKit::Descriptors::Properties {lvalue})
static RegisterProperty
((PropertyFunctor)propertyFunctor) → int :
Register a new property object (not thread safe)
C++ signature :
int RegisterProperty(RDKit::Descriptors::PropertyFunctor*)
class rdkit.Chem.rdMolDescriptors.
PropertyFunctor
Bases: Boost.Python.instance
Property computation class stored in the property registry. See rdkit.Chem.rdMolDescriptor.Properties.GetProperty and rdkit.Chem.Descriptor.Properties.PropertyFunctor for creating new ones
Raises an exception This class cannot be instantiated from Python
GetName
((PropertyFunctor)arg1) → str :
Return the name of the property to calculate
C++ signature :
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetName(RDKit::Descriptors::PropertyFunctor {lvalue})
GetVersion
((PropertyFunctor)arg1) → str :
Return the version of the calculated property
C++ signature :
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetVersion(RDKit::Descriptors::PropertyFunctor {lvalue})
class rdkit.Chem.rdMolDescriptors.
PropertyRangeQuery
Bases: Boost.Python.instance
Property Range Query for a molecule. Match(mol) -> true if in range
Raises an exception This class cannot be instantiated from Python
Match
((PropertyRangeQuery)arg1, (Mol)arg2) → bool :
C++ signature :
bool Match(Queries::RangeQuery<double, RDKit::ROMol const&, true> {lvalue},RDKit::ROMol)
class rdkit.Chem.rdMolDescriptors.
PythonPropertyFunctor
((object)arg1, (object)arg2, (str)arg3, (str)arg4) → None :
Bases: rdkit.Chem.rdMolDescriptors.PropertyFunctor
C++ signature :
void __init__(_object*,_object*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)
rdkit.Chem.rdMolDescriptors.
SMR_VSA_
((Mol)mol[, (AtomPairsParameters)bins=[][, (bool)force=False]]) → list :
C++ signature :
boost::python::list SMR_VSA_(RDKit::ROMol [,boost::python::api::object=[] [,bool=False]])
rdkit.Chem.rdMolDescriptors.
SlogP_VSA_
((Mol)mol[, (AtomPairsParameters)bins=[][, (bool)force=False]]) → list :
C++ signature :
boost::python::list SlogP_VSA_(RDKit::ROMol [,boost::python::api::object=[] [,bool=False]])