rdkit.Chem.rdFingerprintGenerator module

class rdkit.Chem.rdFingerprintGenerator.AdditionalOutput((object)arg1) → None :

Bases: instance

C++ signature :

void __init__(_object*)

AllocateAtomCounts((AdditionalOutput)self) → None :

synonym for CollectAtomCounts()

C++ signature :

void AllocateAtomCounts(RDKit::AdditionalOutput {lvalue})

AllocateAtomToBits((AdditionalOutput)self) → None :

synonym for CollectAtomToBits()

C++ signature :

void AllocateAtomToBits(RDKit::AdditionalOutput {lvalue})

AllocateAtomsPerBit((AdditionalOutput)self) → None :

synonym for CollectAtomsPerBit()

C++ signature :

void AllocateAtomsPerBit(RDKit::AdditionalOutput {lvalue})

AllocateBitInfoMap((AdditionalOutput)self) → None :

synonym for CollectBitInfoMap()

C++ signature :

void AllocateBitInfoMap(RDKit::AdditionalOutput {lvalue})

AllocateBitPaths((AdditionalOutput)self) → None :

synonym for CollectBitPaths()

C++ signature :

void AllocateBitPaths(RDKit::AdditionalOutput {lvalue})

CollectAtomCounts((AdditionalOutput)self) → None :

toggles collection of information about the number of bits each atom is involved in

C++ signature :

void CollectAtomCounts(RDKit::AdditionalOutput {lvalue})

CollectAtomToBits((AdditionalOutput)self) → None :

toggle collection of information mapping each atom to the bits it is involved in.

C++ signature :

void CollectAtomToBits(RDKit::AdditionalOutput {lvalue})

CollectAtomsPerBit((AdditionalOutput)self) → None :

toggles collection of information about all atoms involved in setting each bit

C++ signature :

void CollectAtomsPerBit(RDKit::AdditionalOutput {lvalue})

CollectBitInfoMap((AdditionalOutput)self) → None :

toggles collection of information mapping each atom to more detail about the atom environment (not available from all fingerprints)

C++ signature :

void CollectBitInfoMap(RDKit::AdditionalOutput {lvalue})

CollectBitPaths((AdditionalOutput)self) → None :

toggles collection of information matching each atom to information about the paths it is involved in (not available from all fingerprints).

C++ signature :

void CollectBitPaths(RDKit::AdditionalOutput {lvalue})

GetAtomCounts((AdditionalOutput)self) → object :
C++ signature :

boost::python::api::object GetAtomCounts(RDKit::AdditionalOutput)

GetAtomToBits((AdditionalOutput)self) → object :
C++ signature :

boost::python::api::object GetAtomToBits(RDKit::AdditionalOutput)

GetAtomsPerBit((AdditionalOutput)self) → object :
C++ signature :

boost::python::api::object GetAtomsPerBit(RDKit::AdditionalOutput)

GetBitInfoMap((AdditionalOutput)self) → object :
C++ signature :

boost::python::api::object GetBitInfoMap(RDKit::AdditionalOutput)

GetBitPaths((AdditionalOutput)self) → object :
C++ signature :

boost::python::api::object GetBitPaths(RDKit::AdditionalOutput)

class rdkit.Chem.rdFingerprintGenerator.AtomInvariantsGenerator

Bases: instance

Raises an exception This class cannot be instantiated from Python

class rdkit.Chem.rdFingerprintGenerator.AtomPairFingerprintOptions

Bases: FingerprintOptions

Raises an exception This class cannot be instantiated from Python

property maxDistance

maximum distance to be included

property minDistance

minimum distance to be included

property use2D

use 2D distances

class rdkit.Chem.rdFingerprintGenerator.BondInvariantsGenerator

Bases: instance

Raises an exception This class cannot be instantiated from Python

class rdkit.Chem.rdFingerprintGenerator.FPType

Bases: enum

AtomPairFP = rdkit.Chem.rdFingerprintGenerator.FPType.AtomPairFP
MorganFP = rdkit.Chem.rdFingerprintGenerator.FPType.MorganFP
RDKitFP = rdkit.Chem.rdFingerprintGenerator.FPType.RDKitFP
TopologicalTorsionFP = rdkit.Chem.rdFingerprintGenerator.FPType.TopologicalTorsionFP
names = {'AtomPairFP': rdkit.Chem.rdFingerprintGenerator.FPType.AtomPairFP, 'MorganFP': rdkit.Chem.rdFingerprintGenerator.FPType.MorganFP, 'RDKitFP': rdkit.Chem.rdFingerprintGenerator.FPType.RDKitFP, 'TopologicalTorsionFP': rdkit.Chem.rdFingerprintGenerator.FPType.TopologicalTorsionFP}
values = {0: rdkit.Chem.rdFingerprintGenerator.FPType.AtomPairFP, 1: rdkit.Chem.rdFingerprintGenerator.FPType.MorganFP, 2: rdkit.Chem.rdFingerprintGenerator.FPType.RDKitFP, 3: rdkit.Chem.rdFingerprintGenerator.FPType.TopologicalTorsionFP}
class rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator32

Bases: instance

Raises an exception This class cannot be instantiated from Python

GetCountFingerprint((FingerprintGenerator32)self, (rdkit.Chem.rdchem.Mol)mol[, (object)fromAtoms=[][, (object)ignoreAtoms=[][, (int)confId=-1[, (object)customAtomInvariants=[][, (object)customBondInvariants=[][, (object)additionalOutput=None]]]]]]) → rdkit.DataStructs.cDataStructs.UIntSparseIntVect :

Generates a count fingerprint

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • fromAtoms: indices of atoms to use while generating the fingerprint

  • ignoreAtoms: indices of atoms to exclude while generating the fingerprint

  • confId: 3D confirmation to use, only used by AtomPair fingerprint

  • customAtomInvariants: custom atom invariants to be used, overrides invariants from the invariant generator

  • customBondInvariants: custom bond invariants to be used, overrides invariants from the invariant generator

  • additionalOutput: AdditionalOutput instance used to return extra information about the bits

RETURNS: a SparseIntVect containing fingerprint

C++ signature :

RDKit::SparseIntVect<unsigned int>* GetCountFingerprint(RDKit::FingerprintGenerator<unsigned int> const*,RDKit::ROMol [,boost::python::api::object=[] [,boost::python::api::object=[] [,int=-1 [,boost::python::api::object=[] [,boost::python::api::object=[] [,boost::python::api::object=None]]]]]])

GetCountFingerprintAsNumPy((FingerprintGenerator32)self, (rdkit.Chem.rdchem.Mol)mol[, (object)fromAtoms=[][, (object)ignoreAtoms=[][, (int)confId=-1[, (object)customAtomInvariants=[][, (object)customBondInvariants=[][, (object)additionalOutput=None]]]]]]) → object :

Generates a count fingerprint

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • fromAtoms: indices of atoms to use while generating the fingerprint

  • ignoreAtoms: indices of atoms to exclude while generating the fingerprint

  • confId: 3D confirmation to use, only used by AtomPair fingerprint

  • customAtomInvariants: custom atom invariants to be used, overrides invariants from the invariant generator

  • customBondInvariants: custom bond invariants to be used, overrides invariants from the invariant generator

  • additionalOutput: AdditionalOutput instance used to return extra information about the bits

RETURNS: a numpy array containing the fingerprint

C++ signature :

boost::python::api::object GetCountFingerprintAsNumPy(RDKit::FingerprintGenerator<unsigned int> const*,RDKit::ROMol [,boost::python::api::object=[] [,boost::python::api::object=[] [,int=-1 [,boost::python::api::object=[] [,boost::python::api::object=[] [,boost::python::api::object=None]]]]]])

GetCountFingerprints((FingerprintGenerator32)self, (object)mols[, (int)numThreads=1]) → tuple :

Generates count fingerprints for a sequence of molecules

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • numThreads: number of threads to use

RETURNS: a tuple of SparseIntVects

C++ signature :

boost::python::tuple GetCountFingerprints(RDKit::FingerprintGenerator<unsigned int> const*,boost::python::api::object [,int=1])

GetFingerprint((FingerprintGenerator32)self, (rdkit.Chem.rdchem.Mol)mol[, (object)fromAtoms=[][, (object)ignoreAtoms=[][, (int)confId=-1[, (object)customAtomInvariants=[][, (object)customBondInvariants=[][, (object)additionalOutput=None]]]]]]) → rdkit.DataStructs.cDataStructs.ExplicitBitVect :

Generates a fingerprint

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • fromAtoms: indices of atoms to use while generating the fingerprint

  • ignoreAtoms: indices of atoms to exclude while generating the fingerprint

  • confId: 3D confirmation to use, only used by AtomPair fingerprint

  • customAtomInvariants: custom atom invariants to be used, overrides invariants from the invariant generator

  • customBondInvariants: custom bond invariants to be used, overrides invariants from the invariant generator

  • additionalOutput: AdditionalOutput instance used to return extra information about the bits

RETURNS: a ExplicitBitVect containing fingerprint

C++ signature :

ExplicitBitVect* GetFingerprint(RDKit::FingerprintGenerator<unsigned int> const*,RDKit::ROMol [,boost::python::api::object=[] [,boost::python::api::object=[] [,int=-1 [,boost::python::api::object=[] [,boost::python::api::object=[] [,boost::python::api::object=None]]]]]])

GetFingerprintAsNumPy((FingerprintGenerator32)self, (rdkit.Chem.rdchem.Mol)mol[, (object)fromAtoms=[][, (object)ignoreAtoms=[][, (int)confId=-1[, (object)customAtomInvariants=[][, (object)customBondInvariants=[][, (object)additionalOutput=None]]]]]]) → object :

Generates a fingerprint

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • fromAtoms: indices of atoms to use while generating the fingerprint

  • ignoreAtoms: indices of atoms to exclude while generating the fingerprint

  • confId: 3D confirmation to use, only used by AtomPair fingerprint

  • customAtomInvariants: custom atom invariants to be used, overrides invariants from the invariant generator

  • customBondInvariants: custom bond invariants to be used, overrides invariants from the invariant generator

  • additionalOutput: AdditionalOutput instance used to return extra information about the bits

RETURNS: a numpy array containing the fingerprint

C++ signature :

boost::python::api::object GetFingerprintAsNumPy(RDKit::FingerprintGenerator<unsigned int> const*,RDKit::ROMol [,boost::python::api::object=[] [,boost::python::api::object=[] [,int=-1 [,boost::python::api::object=[] [,boost::python::api::object=[] [,boost::python::api::object=None]]]]]])

GetFingerprints((FingerprintGenerator32)self, (object)mols[, (int)numThreads=1]) → tuple :

Generates fingerprints for a sequence of molecules

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • numThreads: number of threads to use

RETURNS: a tuple of ExplicitBitVects

C++ signature :

boost::python::tuple GetFingerprints(RDKit::FingerprintGenerator<unsigned int> const*,boost::python::api::object [,int=1])

GetInfoString((FingerprintGenerator32)self) → str :

Returns a string containing information about the fingerprint generator

RETURNS: an information string

C++ signature :

std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetInfoString(RDKit::FingerprintGenerator<unsigned int> const*)

GetOptions((FingerprintGenerator32)self) → FingerprintOptions :

return the fingerprint options object

C++ signature :

RDKit::FingerprintArguments* GetOptions(RDKit::FingerprintGenerator<unsigned int>*)

GetSparseCountFingerprint((FingerprintGenerator32)self, (rdkit.Chem.rdchem.Mol)mol[, (object)fromAtoms=[][, (object)ignoreAtoms=[][, (int)confId=-1[, (object)customAtomInvariants=[][, (object)customBondInvariants=[][, (object)additionalOutput=None]]]]]]) → rdkit.DataStructs.cDataStructs.UIntSparseIntVect :

Generates a sparse count fingerprint

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • fromAtoms: indices of atoms to use while generating the fingerprint

  • ignoreAtoms: indices of atoms to exclude while generating the fingerprint

  • confId: 3D confirmation to use, only used by AtomPair fingerprint

  • customAtomInvariants: custom atom invariants to be used, overrides invariants from the invariant generator

  • customBondInvariants: custom bond invariants to be used, overrides invariants from the invariant generator

  • additionalOutput: AdditionalOutput instance used to return extra information about the bits

RETURNS: a SparseIntVect containing fingerprint

C++ signature :

RDKit::SparseIntVect<unsigned int>* GetSparseCountFingerprint(RDKit::FingerprintGenerator<unsigned int> const*,RDKit::ROMol [,boost::python::api::object=[] [,boost::python::api::object=[] [,int=-1 [,boost::python::api::object=[] [,boost::python::api::object=[] [,boost::python::api::object=None]]]]]])

GetSparseCountFingerprints((FingerprintGenerator32)self, (object)mols[, (int)numThreads=1]) → tuple :

Generates sparse count fingerprints for a sequence of molecules

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • numThreads: number of threads to use

RETURNS: a tuple of SparseIntVects

C++ signature :

boost::python::tuple GetSparseCountFingerprints(RDKit::FingerprintGenerator<unsigned int> const*,boost::python::api::object [,int=1])

GetSparseFingerprint((FingerprintGenerator32)self, (rdkit.Chem.rdchem.Mol)mol[, (object)fromAtoms=[][, (object)ignoreAtoms=[][, (int)confId=-1[, (object)customAtomInvariants=[][, (object)customBondInvariants=[][, (object)additionalOutput=None]]]]]]) → rdkit.DataStructs.cDataStructs.SparseBitVect :

Generates a sparse fingerprint

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • fromAtoms: indices of atoms to use while generating the fingerprint

  • ignoreAtoms: indices of atoms to exclude while generating the fingerprint

  • confId: 3D confirmation to use, only used by AtomPair fingerprint

  • customAtomInvariants: custom atom invariants to be used, overrides invariants from the invariant generator

  • customBondInvariants: custom bond invariants to be used, overrides invariants from the invariant generator

  • additionalOutput: AdditionalOutput instance used to return extra information about the bits

RETURNS: a SparseBitVect containing fingerprint

C++ signature :

SparseBitVect* GetSparseFingerprint(RDKit::FingerprintGenerator<unsigned int> const*,RDKit::ROMol [,boost::python::api::object=[] [,boost::python::api::object=[] [,int=-1 [,boost::python::api::object=[] [,boost::python::api::object=[] [,boost::python::api::object=None]]]]]])

GetSparseFingerprints((FingerprintGenerator32)self, (object)mols[, (int)numThreads=1]) → tuple :

Generates sparse fingerprints for a sequence of molecules

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • numThreads: number of threads to use

RETURNS: a tuple of SparseBitVects

C++ signature :

boost::python::tuple GetSparseFingerprints(RDKit::FingerprintGenerator<unsigned int> const*,boost::python::api::object [,int=1])

ToJSON((FingerprintGenerator32)self) → str :

Serialize a FingerprintGenerator to JSON

C++ signature :

std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > ToJSON(RDKit::FingerprintGenerator<unsigned int>)

class rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator64

Bases: instance

Raises an exception This class cannot be instantiated from Python

GetCountFingerprint((FingerprintGenerator64)self, (rdkit.Chem.rdchem.Mol)mol[, (object)fromAtoms=[][, (object)ignoreAtoms=[][, (int)confId=-1[, (object)customAtomInvariants=[][, (object)customBondInvariants=[][, (object)additionalOutput=None]]]]]]) → rdkit.DataStructs.cDataStructs.UIntSparseIntVect :

Generates a count fingerprint

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • fromAtoms: indices of atoms to use while generating the fingerprint

  • ignoreAtoms: indices of atoms to exclude while generating the fingerprint

  • confId: 3D confirmation to use, only used by AtomPair fingerprint

  • customAtomInvariants: custom atom invariants to be used, overrides invariants from the invariant generator

  • customBondInvariants: custom bond invariants to be used, overrides invariants from the invariant generator

  • additionalOutput: AdditionalOutput instance used to return extra information about the bits

RETURNS: a SparseIntVect containing fingerprint

C++ signature :

RDKit::SparseIntVect<unsigned int>* GetCountFingerprint(RDKit::FingerprintGenerator<unsigned long> const*,RDKit::ROMol [,boost::python::api::object=[] [,boost::python::api::object=[] [,int=-1 [,boost::python::api::object=[] [,boost::python::api::object=[] [,boost::python::api::object=None]]]]]])

GetCountFingerprintAsNumPy((FingerprintGenerator64)self, (rdkit.Chem.rdchem.Mol)mol[, (object)fromAtoms=[][, (object)ignoreAtoms=[][, (int)confId=-1[, (object)customAtomInvariants=[][, (object)customBondInvariants=[][, (object)additionalOutput=None]]]]]]) → object :

Generates a count fingerprint

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • fromAtoms: indices of atoms to use while generating the fingerprint

  • ignoreAtoms: indices of atoms to exclude while generating the fingerprint

  • confId: 3D confirmation to use, only used by AtomPair fingerprint

  • customAtomInvariants: custom atom invariants to be used, overrides invariants from the invariant generator

  • customBondInvariants: custom bond invariants to be used, overrides invariants from the invariant generator

  • additionalOutput: AdditionalOutput instance used to return extra information about the bits

RETURNS: a numpy array containing the fingerprint

C++ signature :

boost::python::api::object GetCountFingerprintAsNumPy(RDKit::FingerprintGenerator<unsigned long> const*,RDKit::ROMol [,boost::python::api::object=[] [,boost::python::api::object=[] [,int=-1 [,boost::python::api::object=[] [,boost::python::api::object=[] [,boost::python::api::object=None]]]]]])

GetCountFingerprints((FingerprintGenerator64)self, (object)mols[, (int)numThreads=1]) → tuple :

Generates count fingerprints for a sequence of molecules

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • numThreads: number of threads to use

RETURNS: a tuple of SparseIntVects

C++ signature :

boost::python::tuple GetCountFingerprints(RDKit::FingerprintGenerator<unsigned long> const*,boost::python::api::object [,int=1])

GetFingerprint((FingerprintGenerator64)self, (rdkit.Chem.rdchem.Mol)mol[, (object)fromAtoms=[][, (object)ignoreAtoms=[][, (int)confId=-1[, (object)customAtomInvariants=[][, (object)customBondInvariants=[][, (object)additionalOutput=None]]]]]]) → rdkit.DataStructs.cDataStructs.ExplicitBitVect :

Generates a fingerprint

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • fromAtoms: indices of atoms to use while generating the fingerprint

  • ignoreAtoms: indices of atoms to exclude while generating the fingerprint

  • confId: 3D confirmation to use, only used by AtomPair fingerprint

  • customAtomInvariants: custom atom invariants to be used, overrides invariants from the invariant generator

  • customBondInvariants: custom bond invariants to be used, overrides invariants from the invariant generator

  • additionalOutput: AdditionalOutput instance used to return extra information about the bits

RETURNS: a ExplicitBitVect containing fingerprint

C++ signature :

ExplicitBitVect* GetFingerprint(RDKit::FingerprintGenerator<unsigned long> const*,RDKit::ROMol [,boost::python::api::object=[] [,boost::python::api::object=[] [,int=-1 [,boost::python::api::object=[] [,boost::python::api::object=[] [,boost::python::api::object=None]]]]]])

GetFingerprintAsNumPy((FingerprintGenerator64)self, (rdkit.Chem.rdchem.Mol)mol[, (object)fromAtoms=[][, (object)ignoreAtoms=[][, (int)confId=-1[, (object)customAtomInvariants=[][, (object)customBondInvariants=[][, (object)additionalOutput=None]]]]]]) → object :

Generates a fingerprint

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • fromAtoms: indices of atoms to use while generating the fingerprint

  • ignoreAtoms: indices of atoms to exclude while generating the fingerprint

  • confId: 3D confirmation to use, only used by AtomPair fingerprint

  • customAtomInvariants: custom atom invariants to be used, overrides invariants from the invariant generator

  • customBondInvariants: custom bond invariants to be used, overrides invariants from the invariant generator

  • additionalOutput: AdditionalOutput instance used to return extra information about the bits

RETURNS: a numpy array containing the fingerprint

C++ signature :

boost::python::api::object GetFingerprintAsNumPy(RDKit::FingerprintGenerator<unsigned long> const*,RDKit::ROMol [,boost::python::api::object=[] [,boost::python::api::object=[] [,int=-1 [,boost::python::api::object=[] [,boost::python::api::object=[] [,boost::python::api::object=None]]]]]])

GetFingerprints((FingerprintGenerator64)self, (object)mols[, (int)numThreads=1]) → tuple :

Generates fingerprints for a sequence of molecules

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • numThreads: number of threads to use

RETURNS: a tuple of ExplicitBitVects

C++ signature :

boost::python::tuple GetFingerprints(RDKit::FingerprintGenerator<unsigned long> const*,boost::python::api::object [,int=1])

GetInfoString((FingerprintGenerator64)self) → str :

Returns a string containing information about the fingerprint generator

RETURNS: an information string

C++ signature :

std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetInfoString(RDKit::FingerprintGenerator<unsigned long> const*)

GetOptions((FingerprintGenerator64)self) → FingerprintOptions :

return the fingerprint options object

C++ signature :

RDKit::FingerprintArguments* GetOptions(RDKit::FingerprintGenerator<unsigned long>*)

GetSparseCountFingerprint((FingerprintGenerator64)self, (rdkit.Chem.rdchem.Mol)mol[, (object)fromAtoms=[][, (object)ignoreAtoms=[][, (int)confId=-1[, (object)customAtomInvariants=[][, (object)customBondInvariants=[][, (object)additionalOutput=None]]]]]]) → rdkit.DataStructs.cDataStructs.ULongSparseIntVect :

Generates a sparse count fingerprint

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • fromAtoms: indices of atoms to use while generating the fingerprint

  • ignoreAtoms: indices of atoms to exclude while generating the fingerprint

  • confId: 3D confirmation to use, only used by AtomPair fingerprint

  • customAtomInvariants: custom atom invariants to be used, overrides invariants from the invariant generator

  • customBondInvariants: custom bond invariants to be used, overrides invariants from the invariant generator

  • additionalOutput: AdditionalOutput instance used to return extra information about the bits

RETURNS: a SparseIntVect containing fingerprint

C++ signature :

RDKit::SparseIntVect<unsigned long>* GetSparseCountFingerprint(RDKit::FingerprintGenerator<unsigned long> const*,RDKit::ROMol [,boost::python::api::object=[] [,boost::python::api::object=[] [,int=-1 [,boost::python::api::object=[] [,boost::python::api::object=[] [,boost::python::api::object=None]]]]]])

GetSparseCountFingerprints((FingerprintGenerator64)self, (object)mols[, (int)numThreads=1]) → tuple :

Generates sparse count fingerprints for a sequence of molecules

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • numThreads: number of threads to use

RETURNS: a tuple of SparseIntVects

C++ signature :

boost::python::tuple GetSparseCountFingerprints(RDKit::FingerprintGenerator<unsigned long> const*,boost::python::api::object [,int=1])

GetSparseFingerprint((FingerprintGenerator64)self, (rdkit.Chem.rdchem.Mol)mol[, (object)fromAtoms=[][, (object)ignoreAtoms=[][, (int)confId=-1[, (object)customAtomInvariants=[][, (object)customBondInvariants=[][, (object)additionalOutput=None]]]]]]) → rdkit.DataStructs.cDataStructs.SparseBitVect :

Generates a sparse fingerprint

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • fromAtoms: indices of atoms to use while generating the fingerprint

  • ignoreAtoms: indices of atoms to exclude while generating the fingerprint

  • confId: 3D confirmation to use, only used by AtomPair fingerprint

  • customAtomInvariants: custom atom invariants to be used, overrides invariants from the invariant generator

  • customBondInvariants: custom bond invariants to be used, overrides invariants from the invariant generator

  • additionalOutput: AdditionalOutput instance used to return extra information about the bits

RETURNS: a SparseBitVect containing fingerprint

C++ signature :

SparseBitVect* GetSparseFingerprint(RDKit::FingerprintGenerator<unsigned long> const*,RDKit::ROMol [,boost::python::api::object=[] [,boost::python::api::object=[] [,int=-1 [,boost::python::api::object=[] [,boost::python::api::object=[] [,boost::python::api::object=None]]]]]])

GetSparseFingerprints((FingerprintGenerator64)self, (object)mols[, (int)numThreads=1]) → tuple :

Generates sparse fingerprints for a sequence of molecules

ARGUMENTS:

  • mol: molecule to be fingerprinted

  • numThreads: number of threads to use

RETURNS: a tuple of SparseBitVects

C++ signature :

boost::python::tuple GetSparseFingerprints(RDKit::FingerprintGenerator<unsigned long> const*,boost::python::api::object [,int=1])

ToJSON((FingerprintGenerator64)self) → str :

Serialize a FingerprintGenerator to JSON

C++ signature :

std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > ToJSON(RDKit::FingerprintGenerator<unsigned long>)

rdkit.Chem.rdFingerprintGenerator.FingerprintGeneratorFromJSON((str)jsonString) → FingerprintGenerator64 :

Deserialize a FingerprintGenerator from a JSON string

C++ signature :

RDKit::FingerprintGenerator<unsigned long>* FingerprintGeneratorFromJSON(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

class rdkit.Chem.rdFingerprintGenerator.FingerprintOptions

Bases: instance

Raises an exception This class cannot be instantiated from Python

SetCountBounds((FingerprintOptions)self, (object)bounds) → None :

set the bins for the count bounds

C++ signature :

void SetCountBounds(RDKit::FingerprintArguments {lvalue},boost::python::api::object)

property countSimulation

use count simulation

property fpSize

size of the fingerprints created

property includeChirality

include chirality in atom invariants (not for all fingerprints)

property numBitsPerFeature

number of bits to set for each feature

rdkit.Chem.rdFingerprintGenerator.GetAtomPairAtomInvGen([(bool)includeChirality=False]) → AtomInvariantsGenerator :

Get an atom pair atom-invariant generator

ARGUMENTS:

  • includeChirality: if set, chirality will be taken into account for invariants

RETURNS: AtomInvariantsGenerator

C++ signature :

RDKit::AtomInvariantsGenerator* GetAtomPairAtomInvGen([ bool=False])

rdkit.Chem.rdFingerprintGenerator.GetAtomPairGenerator([(int)minDistance=1[, (int)maxDistance=30[, (bool)includeChirality=False[, (bool)use2D=True[, (bool)countSimulation=True[, (object)countBounds=None[, (int)fpSize=2048[, (object)atomInvariantsGenerator=None]]]]]]]]) → FingerprintGenerator64 :

Get an atom pair fingerprint generator

ARGUMENTS:

  • minDistance: minimum distance between atoms to be considered in a pair, default is 1 bond

  • maxDistance: maximum distance between atoms to be considered in a pair, default is maxPathLen-1 bonds

  • includeChirality: if set, chirality will be used in the atom invariants, this is ignored if atomInvariantsGenerator is provided

  • use2D: if set, the 2D (topological) distance matrix will be used

  • countSimulation: if set, use count simulation while generating the fingerprint

  • countBounds: boundaries for count simulation, corresponding bit will be set if the count is higher than the number provided for that spot

  • fpSize: size of the generated fingerprint, does not affect the sparse versions

  • atomInvariantsGenerator: atom invariants to be used during fingerprint generation

This generator supports the following AdditionalOutput types:

  • atomToBits: which bits each atom is involved in

  • atomCounts: how many bits each atom sets

  • bitInfoMap: map from bitId to (atomId, radius) pairs

RETURNS: FingerprintGenerator

C++ signature :

RDKit::FingerprintGenerator<unsigned long>* GetAtomPairGenerator([ unsigned int=1 [,unsigned int=30 [,bool=False [,bool=True [,bool=True [,boost::python::api::object {lvalue}=None [,unsigned int=2048 [,boost::python::api::object {lvalue}=None]]]]]]]])

rdkit.Chem.rdFingerprintGenerator.GetCountFPs([(list)molecules=[][, (FPType)fpType=rdkit.Chem.rdFingerprintGenerator.FPType.MorganFP]]) → list :
C++ signature :

boost::python::list GetCountFPs([ boost::python::list {lvalue}=[] [,RDKit::FPType=rdkit.Chem.rdFingerprintGenerator.FPType.MorganFP]])

rdkit.Chem.rdFingerprintGenerator.GetFPs([(list)molecules=[][, (FPType)fpType=rdkit.Chem.rdFingerprintGenerator.FPType.MorganFP]]) → list :
C++ signature :

boost::python::list GetFPs([ boost::python::list {lvalue}=[] [,RDKit::FPType=rdkit.Chem.rdFingerprintGenerator.FPType.MorganFP]])

rdkit.Chem.rdFingerprintGenerator.GetMorganAtomInvGen((bool)includeRingMembership) → AtomInvariantsGenerator :

Get a morgan atom invariants generator

ARGUMENTS:

  • includeRingMembership: if set, whether or not the atom is in a ring will be used in the invariant list

RETURNS: AtomInvariantsGenerator

C++ signature :

RDKit::AtomInvariantsGenerator* GetMorganAtomInvGen(bool)

rdkit.Chem.rdFingerprintGenerator.GetMorganBondInvGen([(bool)useBondTypes=True[, (bool)useChirality=False]]) → BondInvariantsGenerator :

Get a morgan bond invariants generator

ARGUMENTS:

  • useBondTypes: if set, bond types will be included as a part of the bond invariants

  • useChirality: if set, chirality information will be included as a part of the bond invariants

RETURNS: BondInvariantsGenerator

C++ signature :

RDKit::BondInvariantsGenerator* GetMorganBondInvGen([ bool=True [,bool=False]])

rdkit.Chem.rdFingerprintGenerator.GetMorganFeatureAtomInvGen([(object)patterns=None]) → AtomInvariantsGenerator :

Get a morgan feature atom invariants generator

ARGUMENTS:

  • patterns: if provided should contain the queries used to assign atom-types. if not provided, feature definitions adapted from reference: Gobbi and Poppinger, Biotech. Bioeng. _61_ 47-54 (1998) will be used for Donor, Acceptor, Aromatic, Halogen, Basic, Acidic.

RETURNS: AtomInvariantsGenerator

C++ signature :

RDKit::AtomInvariantsGenerator* GetMorganFeatureAtomInvGen([ boost::python::api::object {lvalue}=None])

rdkit.Chem.rdFingerprintGenerator.GetMorganGenerator([(int)radius=3[, (bool)countSimulation=False[, (bool)includeChirality=False[, (bool)useBondTypes=True[, (bool)onlyNonzeroInvariants=False[, (bool)includeRingMembership=True[, (object)countBounds=None[, (int)fpSize=2048[, (object)atomInvariantsGenerator=None[, (object)bondInvariantsGenerator=None[, (bool)includeRedundantEnvironments=False]]]]]]]]]]]) → FingerprintGenerator64 :

Get a morgan fingerprint generator

ARGUMENTS:

  • radius: the number of iterations to grow the fingerprint

  • countSimulation: if set, use count simulation while generating the fingerprint

  • includeChirality: if set, chirality information will be added to the generated fingerprint

  • useBondTypes: if set, bond types will be included as a part of the default bond invariants

  • countBounds: boundaries for count simulation, corresponding bit will be set if the count is higher than the number provided for that spot

  • fpSize: size of the generated fingerprint, does not affect the sparse versions

  • atomInvariantsGenerator: atom invariants to be used during fingerprint generation

This generator supports the following AdditionalOutput types:

  • atomToBits: which bits each atom is the center of

  • atomCounts: how many bits each atom sets

  • bitInfoMap: map from bitId to (atomId1, radius) pairs

RETURNS: FingerprintGenerator

C++ signature :

RDKit::FingerprintGenerator<unsigned long>* GetMorganGenerator([ unsigned int=3 [,bool=False [,bool=False [,bool=True [,bool=False [,bool=True [,boost::python::api::object {lvalue}=None [,unsigned int=2048 [,boost::python::api::object {lvalue}=None [,boost::python::api::object {lvalue}=None [,bool=False]]]]]]]]]]])

rdkit.Chem.rdFingerprintGenerator.GetRDKitAtomInvGen() → AtomInvariantsGenerator :

Get an RDKit atom invariants generator

RETURNS: AtomInvariantsGenerator

C++ signature :

RDKit::AtomInvariantsGenerator* GetRDKitAtomInvGen()

rdkit.Chem.rdFingerprintGenerator.GetRDKitFPGenerator([(int)minPath=1[, (int)maxPath=7[, (bool)useHs=True[, (bool)branchedPaths=True[, (bool)useBondOrder=True[, (bool)countSimulation=False[, (object)countBounds=None[, (int)fpSize=2048[, (int)numBitsPerFeature=2[, (object)atomInvariantsGenerator=None]]]]]]]]]]) → FingerprintGenerator64 :

Get an RDKit fingerprint generator

ARGUMENTS:

  • minPath: the minimum path length (in bonds) to be included

  • maxPath: the maximum path length (in bonds) to be included

  • useHs: toggles inclusion of Hs in paths (if the molecule has explicit Hs)

  • branchedPaths: toggles generation of branched subgraphs, not just linear paths

  • useBondOrder: toggles inclusion of bond orders in the path hashes

  • countSimulation: if set, use count simulation while generating the fingerprint

  • countBounds: boundaries for count simulation, corresponding bit will be set if the count is higher than the number provided for that spot

  • fpSize: size of the generated fingerprint, does not affect the sparse versions

  • numBitsPerFeature: the number of bits set per path/subgraph found

  • atomInvariantsGenerator: atom invariants to be used during fingerprint generation

This generator supports the following AdditionalOutput types:

  • atomToBits: which bits each atom is involved in

  • atomCounts: how many bits each atom sets

  • bitPaths: map from bitId to vectors of bond indices for the individual subgraphs

RETURNS: FingerprintGenerator

C++ signature :

RDKit::FingerprintGenerator<unsigned long>* GetRDKitFPGenerator([ unsigned int=1 [,unsigned int=7 [,bool=True [,bool=True [,bool=True [,bool=False [,boost::python::api::object {lvalue}=None [,unsigned int=2048 [,unsigned int=2 [,boost::python::api::object {lvalue}=None]]]]]]]]]])

rdkit.Chem.rdFingerprintGenerator.GetSparseCountFPs([(list)molecules=[][, (FPType)fpType=rdkit.Chem.rdFingerprintGenerator.FPType.MorganFP]]) → list :
C++ signature :

boost::python::list GetSparseCountFPs([ boost::python::list {lvalue}=[] [,RDKit::FPType=rdkit.Chem.rdFingerprintGenerator.FPType.MorganFP]])

rdkit.Chem.rdFingerprintGenerator.GetSparseFPs([(list)molecules=[][, (FPType)fpType=rdkit.Chem.rdFingerprintGenerator.FPType.MorganFP]]) → list :
C++ signature :

boost::python::list GetSparseFPs([ boost::python::list {lvalue}=[] [,RDKit::FPType=rdkit.Chem.rdFingerprintGenerator.FPType.MorganFP]])

rdkit.Chem.rdFingerprintGenerator.GetTopologicalTorsionGenerator([(bool)includeChirality=False[, (int)torsionAtomCount=4[, (bool)countSimulation=True[, (object)countBounds=None[, (int)fpSize=2048[, (object)atomInvariantsGenerator=None]]]]]]) → FingerprintGenerator64 :

Get an atom pair fingerprint generator

ARGUMENTS:

  • includeChirality: includeChirality argument for both the default atom invariants generator and the fingerprint arguments

  • torsionAtomCount: the number of atoms to include in the “torsions”

  • countSimulation: if set, use count simulation while generating the fingerprint

  • countBounds: boundaries for count simulation, corresponding bit will be set if the count is higher than the number provided for that spot

  • fpSize: size of the generated fingerprint, does not affect the sparse versions

  • atomInvariantsGenerator: atom invariants to be used during fingerprint generation

This generator supports the following AdditionalOutput types:

  • atomToBits: which bits each atom is involved in

  • atomCounts: how many bits each atom sets

  • bitPaths: map from bitId to vectors of atom indices

RETURNS: FingerprintGenerator

C++ signature :

RDKit::FingerprintGenerator<unsigned long>* GetTopologicalTorsionGenerator([ bool=False [,unsigned int=4 [,bool=True [,boost::python::api::object {lvalue}=None [,unsigned int=2048 [,boost::python::api::object {lvalue}=None]]]]]])

class rdkit.Chem.rdFingerprintGenerator.MorganFingerprintOptions

Bases: FingerprintOptions

Raises an exception This class cannot be instantiated from Python

property includeRedundantEnvironments

include redundant environments in the fingerprint

property onlyNonzeroInvariants

use include atoms which have nonzero invariants

property radius

the radius of the fingerprints to generate

class rdkit.Chem.rdFingerprintGenerator.RDKitFingerprintOptions

Bases: FingerprintOptions

Raises an exception This class cannot be instantiated from Python

property branchedPaths

generate branched subgraphs, not just linear ones

property maxPath

maximum path length (in bonds) to be included

property minPath

minimum path length (in bonds) to be included

property useBondOrder

include bond orders in the path hashes

property useHs

use explicit Hs in the paths (if molecule has explicit Hs)

class rdkit.Chem.rdFingerprintGenerator.TopologicalTorsionFingerprintOptions

Bases: FingerprintOptions

Raises an exception This class cannot be instantiated from Python

property onlyShortestPaths

whether or not to only include paths which are the shortest path between the start and end atoms

property torsionAtomCount

number of atoms to be included in the paths