Package rdkit :: Package Chem :: Module rdMolDescriptors

Module rdMolDescriptors

Module containing functions to compute molecular descriptors

Classes

[hide private]

AtomPairsParameters

Functions

[hide private]

CalcCrippenDescriptors(...)
CalcCrippenDescriptors( (Mol)mol [, (bool)includeHs=True [, (bool)force=False]]) -> tuple : returns a 2-tuple with the Wildman-Crippen logp,mr values

CalcExactMolWt(...)
CalcExactMolWt( (Mol)mol [, (bool)onlyHeavy=False]) -> float : returns the molecule's exact molecular weight

CalcLabuteASA(...)
CalcLabuteASA( (Mol)mol [, (bool)includeHs=True [, (bool)force=False]]) -> float : returns the Labute ASA value for a molecule

CalcMolFormula(...)
CalcMolFormula( (Mol)mol) -> str : returns the molecule's formula

CalcNumAmideBonds(...)
CalcNumAmideBonds( (Mol)mol) -> int : returns the number of amide bonds in a molecule

CalcNumHBA(...)
CalcNumHBA( (Mol)mol) -> int : returns the number of H-bond acceptors for a molecule

CalcNumHBD(...)
CalcNumHBD( (Mol)mol) -> int : returns the number of H-bond donors for a molecule

CalcNumHeteroatoms(...)
CalcNumHeteroatoms( (Mol)mol) -> int : returns the number of heteroatoms for a molecule

CalcNumLipinskiHBA(...)
CalcNumLipinskiHBA( (Mol)mol) -> int : returns the number of Lipinski H-bond acceptors for a molecule

CalcNumLipinskiHBD(...)
CalcNumLipinskiHBD( (Mol)mol) -> int : returns the number of Lipinski H-bond donors for a molecule

CalcNumRings(...)
CalcNumRings( (Mol)mol) -> int : returns the number of rings for a molecule

CalcNumRotatableBonds(...)
CalcNumRotatableBonds( (Mol)mol) -> int : returns the number of rotatable bonds for a molecule

CalcTPSA(...)
CalcTPSA( (Mol)mol [, (bool)force=False]) -> float : returns the TPSA value for a molecule

GetAtomPairAtomCode(...)
GetAtomPairAtomCode( (Atom)atom [, (int)branchSubtract=0]) -> int : Returns the atom code (hash) for an atom

GetAtomPairFingerprint(...)
GetAtomPairFingerprint( (Mol)mol [, (int)minLength=1 [, (int)maxLength=30 [, (AtomPairsParameters)fromAtoms=0 [, (AtomPairsParameters)ignoreAtoms=0]]]]) -> IntSparseIntVect : Returns the atom-pair fingerprint for a molecule as an IntSparseIntVect

GetConnectivityInvariants(...)
GetConnectivityInvariants( (Mol)mol [, (bool)includeRingMembership=True]) -> list : Returns connectivity invariants (ECFP-like) for a molecule.

GetFeatureInvariants(...)
GetFeatureInvariants( (Mol)mol) -> list : Returns feature invariants (FCFP-like) for a molecule.

GetHashedAtomPairFingerprint(...)
GetHashedAtomPairFingerprint( (Mol)mol [, (int)nBits=2048 [, (int)minLength=1 [, (int)maxLength=30 [, (AtomPairsParameters)fromAtoms=0 [, (AtomPairsParameters)ignoreAtoms=0]]]]]) -> IntSparseIntVect : Returns the atom-pair fingerprint for a molecule as an IntSparseIntVect

GetHashedAtomPairFingerprintAsBitVect(...)
GetHashedAtomPairFingerprintAsBitVect( (Mol)mol [, (int)nBits=2048 [, (int)minLength=1 [, (int)maxLength=30 [, (AtomPairsParameters)fromAtoms=0 [, (AtomPairsParameters)ignoreAtoms=0 [, (int)nBitsPerEntry=4]]]]]]) -> ExplicitBitVect : Returns the atom-pair fingerprint for a molecule as an ExplicitBitVect

GetHashedTopologicalTorsionFingerprint(...)
GetHashedTopologicalTorsionFingerprint( (Mol)mol [, (int)nBits=2048 [, (int)targetSize=4 [, (AtomPairsParameters)fromAtoms=0 [, (AtomPairsParameters)ignoreAtoms=0]]]]) -> LongSparseIntVect : Returns the topological-torsion fingerprint for a molecule as a LongIntSparseIntVect

GetHashedTopologicalTorsionFingerprintAsBitVect(...)
GetHashedTopologicalTorsionFingerprintAsBitVect( (Mol)mol [, (int)nBits=2048 [, (int)targetSize=4 [, (AtomPairsParameters)fromAtoms=0 [, (AtomPairsParameters)ignoreAtoms=0 [, (int)nBitsPerEntry=4]]]]]) -> ExplicitBitVect : Returns the topological-torsion fingerprint for a molecule as an ExplicitBitVect

GetMorganFingerprint(...)
GetMorganFingerprint( (Mol)mol, (int)radius [, (AtomPairsParameters)invariants=[] [, (AtomPairsParameters)fromAtoms=[] [, (bool)useChirality=False [, (bool)useBondTypes=True [, (bool)useFeatures=False [, (AtomPairsParameters)bitInfo=None]]]]]]) -> UIntSparseIntVect : Returns a Morgan fingerprint for a molecule

GetMorganFingerprintAsBitVect(...)
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

GetTopologicalTorsionFingerprint(...)
GetTopologicalTorsionFingerprint( (Mol)mol [, (int)targetSize=4 [, (AtomPairsParameters)fromAtoms=0 [, (AtomPairsParameters)ignoreAtoms=0]]]) -> LongSparseIntVect : Returns the topological-torsion fingerprint for a molecule as a LongIntSparseIntVect

PEOE_VSA_(...)
PEOE_VSA_( (Mol)mol [, (AtomPairsParameters)bins=[] [, (bool)force=False]]) -> list :

SMR_VSA_(...)
SMR_VSA_( (Mol)mol [, (AtomPairsParameters)bins=[] [, (bool)force=False]]) -> list :

SlogP_VSA_(...)
SlogP_VSA_( (Mol)mol [, (AtomPairsParameters)bins=[] [, (bool)force=False]]) -> list :

_CalcCrippenContribs(...)
_CalcCrippenContribs( (Mol)mol [, (bool)force=False]) -> list : returns (as a list of 2-tuples) the contributions of each atom to the Wildman-Cripppen logp and mr value

_CalcLabuteASAContribs(...)
_CalcLabuteASAContribs( (Mol)mol [, (bool)includeHs=True [, (bool)force=False]]) -> tuple : returns a list of atomic contributions to the Labute ASA

_CalcMolWt(...)
_CalcMolWt( (Mol)mol [, (bool)onlyHeavy=False]) -> float : returns the molecule's molecular weight

_CalcTPSAContribs(...)
_CalcTPSAContribs( (Mol)mol [, (bool)force=False]) -> tuple : returns a list of atomic contributions to the TPSA

Variables

[hide private]

_CalcCrippenDescriptors_version = '1.2.0'

_CalcExactMolWt_version = '1.0.0'

_CalcLabuteASA_version = '1.0.2'

_CalcMolFormula_version = '1.0.0'

_CalcMolWt_version = '1.0.0'

_CalcNumAmideBonds_version = '1.0.0'

_CalcNumHBA_version = '2.0.1'

_CalcNumHBD_version = '2.0.1'

_CalcNumHeteroatoms_version = '1.0.1'

_CalcNumLipinskiHBA_version = '1.0.0'

_CalcNumLipinskiHBD_version = '2.0.0'

_CalcNumRings_version = '1.0.1'

_CalcNumRotatableBonds_version = '1.0.1'

_CalcTPSA_version = '1.1.0'

_ConnectivityInvariants_version = '1.0.0'

_FeatureInvariants_version = '0.1.0'

_MorganFingerprint_version = '1.0.0'

__package__ = None

Function Details

[hide private]

CalcCrippenDescriptors(...)


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]])

CalcExactMolWt(...)


CalcExactMolWt( (Mol)mol [, (bool)onlyHeavy=False]) -> float :
    returns the molecule's exact molecular weight

    C++ signature :
        double CalcExactMolWt(RDKit::ROMol [,bool=False])

CalcLabuteASA(...)


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]])

CalcMolFormula(...)


CalcMolFormula( (Mol)mol) -> str :
    returns the molecule's formula

    C++ signature :
        std::string CalcMolFormula(RDKit::ROMol)

CalcNumAmideBonds(...)


CalcNumAmideBonds( (Mol)mol) -> int :
    returns the number of amide bonds in a molecule

    C++ signature :
        unsigned int CalcNumAmideBonds(RDKit::ROMol)

CalcNumHBA(...)


CalcNumHBA( (Mol)mol) -> int :
    returns the number of H-bond acceptors for a molecule

    C++ signature :
        unsigned int CalcNumHBA(RDKit::ROMol)

CalcNumHBD(...)


CalcNumHBD( (Mol)mol) -> int :
    returns the number of H-bond donors for a molecule

    C++ signature :
        unsigned int CalcNumHBD(RDKit::ROMol)

CalcNumHeteroatoms(...)


CalcNumHeteroatoms( (Mol)mol) -> int :
    returns the number of heteroatoms for a molecule

    C++ signature :
        unsigned int CalcNumHeteroatoms(RDKit::ROMol)

CalcNumLipinskiHBA(...)


CalcNumLipinskiHBA( (Mol)mol) -> int :
    returns the number of Lipinski H-bond acceptors for a molecule

    C++ signature :
        unsigned int CalcNumLipinskiHBA(RDKit::ROMol)

CalcNumLipinskiHBD(...)


CalcNumLipinskiHBD( (Mol)mol) -> int :
    returns the number of Lipinski H-bond donors for a molecule

    C++ signature :
        unsigned int CalcNumLipinskiHBD(RDKit::ROMol)

CalcNumRings(...)


CalcNumRings( (Mol)mol) -> int :
    returns the number of rings for a molecule

    C++ signature :
        unsigned int CalcNumRings(RDKit::ROMol)

CalcNumRotatableBonds(...)


CalcNumRotatableBonds( (Mol)mol) -> int :
    returns the number of rotatable bonds for a molecule

    C++ signature :
        unsigned int CalcNumRotatableBonds(RDKit::ROMol)

CalcTPSA(...)


CalcTPSA( (Mol)mol [, (bool)force=False]) -> float :
    returns the TPSA value for a molecule

    C++ signature :
        double CalcTPSA(RDKit::ROMol [,bool=False])

GetAtomPairAtomCode(...)


GetAtomPairAtomCode( (Atom)atom [, (int)branchSubtract=0]) -> int :
    Returns the atom code (hash) for an atom

    C++ signature :
        unsigned int GetAtomPairAtomCode(RDKit::Atom const* [,unsigned int=0])

GetAtomPairFingerprint(...)


GetAtomPairFingerprint( (Mol)mol [, (int)minLength=1 [, (int)maxLength=30 [, (AtomPairsParameters)fromAtoms=0 [, (AtomPairsParameters)ignoreAtoms=0]]]]) -> 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]]]])

GetConnectivityInvariants(...)


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])

GetFeatureInvariants(...)


GetFeatureInvariants( (Mol)mol) -> list :
    Returns feature invariants (FCFP-like) for a molecule.

    C++ signature :
        boost::python::list GetFeatureInvariants(RDKit::ROMol)

GetHashedAtomPairFingerprint(...)


GetHashedAtomPairFingerprint( (Mol)mol [, (int)nBits=2048 [, (int)minLength=1 [, (int)maxLength=30 [, (AtomPairsParameters)fromAtoms=0 [, (AtomPairsParameters)ignoreAtoms=0]]]]]) -> IntSparseIntVect :
    Returns the 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]]]]])

GetHashedAtomPairFingerprintAsBitVect(...)


GetHashedAtomPairFingerprintAsBitVect( (Mol)mol [, (int)nBits=2048 [, (int)minLength=1 [, (int)maxLength=30 [, (AtomPairsParameters)fromAtoms=0 [, (AtomPairsParameters)ignoreAtoms=0 [, (int)nBitsPerEntry=4]]]]]]) -> 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 [,unsigned int=4]]]]]])

GetHashedTopologicalTorsionFingerprint(...)


GetHashedTopologicalTorsionFingerprint( (Mol)mol [, (int)nBits=2048 [, (int)targetSize=4 [, (AtomPairsParameters)fromAtoms=0 [, (AtomPairsParameters)ignoreAtoms=0]]]]) -> LongSparseIntVect :
    Returns the 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]]]])

GetHashedTopologicalTorsionFingerprintAsBitVect(...)


GetHashedTopologicalTorsionFingerprintAsBitVect( (Mol)mol [, (int)nBits=2048 [, (int)targetSize=4 [, (AtomPairsParameters)fromAtoms=0 [, (AtomPairsParameters)ignoreAtoms=0 [, (int)nBitsPerEntry=4]]]]]) -> 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 [,unsigned int=4]]]]])

GetMorganFingerprint(...)


GetMorganFingerprint( (Mol)mol, (int)radius [, (AtomPairsParameters)invariants=[] [, (AtomPairsParameters)fromAtoms=[] [, (bool)useChirality=False [, (bool)useBondTypes=True [, (bool)useFeatures=False [, (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 [,boost::python::api::object=None]]]]]])

GetMorganFingerprintAsBitVect(...)


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]]]]]]])

GetTopologicalTorsionFingerprint(...)


GetTopologicalTorsionFingerprint( (Mol)mol [, (int)targetSize=4 [, (AtomPairsParameters)fromAtoms=0 [, (AtomPairsParameters)ignoreAtoms=0]]]) -> 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]]])

PEOE_VSA_(...)


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]])

SMR_VSA_(...)


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]])

SlogP_VSA_(...)


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]])

_CalcCrippenContribs(...)


_CalcCrippenContribs( (Mol)mol [, (bool)force=False]) -> list :
    returns (as a list of 2-tuples) the contributions of each atom to
    the Wildman-Cripppen logp and mr value

    C++ signature :
        boost::python::list _CalcCrippenContribs(RDKit::ROMol [,bool=False])

_CalcLabuteASAContribs(...)


_CalcLabuteASAContribs( (Mol)mol [, (bool)includeHs=True [, (bool)force=False]]) -> tuple :
    returns a list of atomic contributions to the Labute ASA

    C++ signature :
        boost::python::tuple _CalcLabuteASAContribs(RDKit::ROMol [,bool=True [,bool=False]])

_CalcMolWt(...)


_CalcMolWt( (Mol)mol [, (bool)onlyHeavy=False]) -> float :
    returns the molecule's molecular weight

    C++ signature :
        double _CalcMolWt(RDKit::ROMol [,bool=False])

_CalcTPSAContribs(...)


_CalcTPSAContribs( (Mol)mol [, (bool)force=False]) -> tuple :
    returns a list of atomic contributions to the TPSA

    C++ signature :
        boost::python::tuple _CalcTPSAContribs(RDKit::ROMol [,bool=False])