rdkit.Chem.rdFMCS module

Module containing a C++ implementation of the FMCS algorithm

class rdkit.Chem.rdFMCS.AtomCompare

Bases: enum

CompareAny = rdkit.Chem.rdFMCS.AtomCompare.CompareAny

CompareAnyHeavyAtom = rdkit.Chem.rdFMCS.AtomCompare.CompareAnyHeavyAtom

CompareElements = rdkit.Chem.rdFMCS.AtomCompare.CompareElements

CompareIsotopes = rdkit.Chem.rdFMCS.AtomCompare.CompareIsotopes

names = {'CompareAny': rdkit.Chem.rdFMCS.AtomCompare.CompareAny, 'CompareAnyHeavyAtom': rdkit.Chem.rdFMCS.AtomCompare.CompareAnyHeavyAtom, 'CompareElements': rdkit.Chem.rdFMCS.AtomCompare.CompareElements, 'CompareIsotopes': rdkit.Chem.rdFMCS.AtomCompare.CompareIsotopes}

values = {0: rdkit.Chem.rdFMCS.AtomCompare.CompareAny, 1: rdkit.Chem.rdFMCS.AtomCompare.CompareElements, 2: rdkit.Chem.rdFMCS.AtomCompare.CompareIsotopes, 3: rdkit.Chem.rdFMCS.AtomCompare.CompareAnyHeavyAtom}

class rdkit.Chem.rdFMCS.BondCompare

Bases: enum

CompareAny = rdkit.Chem.rdFMCS.BondCompare.CompareAny

CompareOrder = rdkit.Chem.rdFMCS.BondCompare.CompareOrder

CompareOrderExact = rdkit.Chem.rdFMCS.BondCompare.CompareOrderExact

names = {'CompareAny': rdkit.Chem.rdFMCS.BondCompare.CompareAny, 'CompareOrder': rdkit.Chem.rdFMCS.BondCompare.CompareOrder, 'CompareOrderExact': rdkit.Chem.rdFMCS.BondCompare.CompareOrderExact}

values = {0: rdkit.Chem.rdFMCS.BondCompare.CompareAny, 1: rdkit.Chem.rdFMCS.BondCompare.CompareOrder, 2: rdkit.Chem.rdFMCS.BondCompare.CompareOrderExact}

rdkit.Chem.rdFMCS.FindMCS((AtomPairsParameters)mols[, (bool)maximizeBonds=True[, (float)threshold=1.0[, (int)timeout=3600[, (bool)verbose=False[, (bool)matchValences=False[, (bool)ringMatchesRingOnly=False[, (bool)completeRingsOnly=False[, (bool)matchChiralTag=False[, (AtomCompare)atomCompare=rdkit.Chem.rdFMCS.AtomCompare.CompareElements[, (BondCompare)bondCompare=rdkit.Chem.rdFMCS.BondCompare.CompareOrder[, (RingCompare)ringCompare=rdkit.Chem.rdFMCS.RingCompare.IgnoreRingFusion[, (str)seedSmarts='']]]]]]]]]]]]) → MCSResult :

Find the MCS for a set of molecules

C++ signature :

RDKit::MCSResult* FindMCS(boost::python::api::object [,bool=True [,double=1.0 [,unsigned int=3600 [,bool=False [,bool=False [,bool=False [,bool=False [,bool=False [,RDKit::AtomComparator=rdkit.Chem.rdFMCS.AtomCompare.CompareElements [,RDKit::BondComparator=rdkit.Chem.rdFMCS.BondCompare.CompareOrder [,RDKit::RingComparator=rdkit.Chem.rdFMCS.RingCompare.IgnoreRingFusion [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’’]]]]]]]]]]]])

FindMCS( (AtomPairsParameters)mols, (MCSParameters)parameters) -> MCSResult :

Find the MCS for a set of molecules

C++ signature :

RDKit::MCSResult* FindMCS(boost::python::api::object,RDKit::PyMCSParameters {lvalue})

class rdkit.Chem.rdFMCS.MCSAcceptance((object)arg1)

Bases: instance

Base class. Subclass and override MCSAcceptance.__call__() to define a custom boolean callback function. Returning True will cause the MCS candidate to be accepted, False to be rejected

C++ signature :

void __init__(_object*)

class rdkit.Chem.rdFMCS.MCSAtomCompare((object)arg1)

Bases: instance

Base class. Subclass and override MCSAtomCompare.__call__() to define custom atom compare functions, then set MCSParameters.AtomTyper to an instance of the subclass

C++ signature :

void __init__(_object*)

CheckAtomCharge((MCSAtomCompare)self, (MCSAtomCompareParameters)parameters, (Mol)mol1, (int)atom1, (Mol)mol2, (int)atom2) → bool :

Return True if both atoms have the same formal charge

C++ signature :

bool CheckAtomCharge(RDKit::PyMCSAtomCompare {lvalue},RDKit::MCSAtomCompareParameters,RDKit::ROMol,unsigned int,RDKit::ROMol,unsigned int)

CheckAtomChirality((MCSAtomCompare)self, (MCSAtomCompareParameters)parameters, (Mol)mol1, (int)atom1, (Mol)mol2, (int)atom2) → bool :

Return True if both atoms have, or have not, a chiral tag

C++ signature :

bool CheckAtomChirality(RDKit::PyMCSAtomCompare {lvalue},RDKit::MCSAtomCompareParameters,RDKit::ROMol,unsigned int,RDKit::ROMol,unsigned int)

CheckAtomRingMatch((MCSAtomCompare)self, (MCSAtomCompareParameters)parameters, (Mol)mol1, (int)atom1, (Mol)mol2, (int)atom2) → bool :

Return True if both atoms are, or are not, in a ring

C++ signature :

bool CheckAtomRingMatch(RDKit::PyMCSAtomCompare {lvalue},RDKit::MCSAtomCompareParameters,RDKit::ROMol,unsigned int,RDKit::ROMol,unsigned int)

class rdkit.Chem.rdFMCS.MCSAtomCompareParameters((object)arg1)

Bases: instance

Parameters controlling how atom-atom matching is done

C++ signature :

void __init__(_object*)

property CompleteRingsOnly

results cannot include lone ring atoms

property MatchChiralTag

include atom chirality in the match

property MatchFormalCharge

include formal charge in the match

property MatchIsotope

use isotope atom queries in MCSResults

property MatchValences

include atom valences in the match

property MaxDistance

Require atoms to be within this many angstroms in 3D

property RingMatchesRingOnly

ring atoms are only allowed to match other ring atoms

class rdkit.Chem.rdFMCS.MCSBondCompare((object)arg1)

Bases: instance

Base class. Subclass and override MCSBondCompare.__call__() to define custom bond compare functions, then set MCSParameters.BondTyper to an instance of the subclass

C++ signature :

void __init__(_object*)

CheckBondRingMatch((MCSBondCompare)self, (MCSBondCompareParameters)parameters, (Mol)mol1, (int)bond1, (Mol)mol2, (int)bond2) → bool :

Return True if both bonds are, or are not, part of a ring

C++ signature :

bool CheckBondRingMatch(RDKit::PyMCSBondCompare {lvalue},RDKit::MCSBondCompareParameters,RDKit::ROMol,unsigned int,RDKit::ROMol,unsigned int)

CheckBondStereo((MCSBondCompare)self, (MCSBondCompareParameters)parameters, (Mol)mol1, (int)bond1, (Mol)mol2, (int)bond2) → bool :

Return True if both bonds have, or have not, a stereo descriptor

C++ signature :

bool CheckBondStereo(RDKit::PyMCSBondCompare {lvalue},RDKit::MCSBondCompareParameters,RDKit::ROMol,unsigned int,RDKit::ROMol,unsigned int)

class rdkit.Chem.rdFMCS.MCSBondCompareParameters((object)arg1)

Bases: instance

Parameters controlling how bond-bond matching is done

C++ signature :

void __init__(_object*)

property CompleteRingsOnly

results cannot include partial rings

property MatchFusedRings

enforce check on ring fusion, i.e. alpha-methylnaphthalene won’t match beta-methylnaphtalene, but decalin will match cyclodecane unless MatchFusedRingsStrict is True

property MatchFusedRingsStrict

only enforced if MatchFusedRings is True; the ring fusion must be the same in both query and target, i.e. decalin won’t match cyclodecane

property MatchStereo

include bond stereo in the comparison

property RingMatchesRingOnly

ring bonds are only allowed to match other ring bonds

class rdkit.Chem.rdFMCS.MCSFinalMatchCheck((object)arg1)

Bases: instance

Base class. Subclass and override MCSFinalMatchCheck.__call__() to define a custom boolean callback function. Returning True will cause the growing seed to be accepted, False to be rejected

C++ signature :

void __init__(_object*)

class rdkit.Chem.rdFMCS.MCSParameters((object)arg1)

Bases: instance

Parameters controlling how the MCS is constructed

C++ signature :

void __init__(_object*)

property AtomCompareParameters

parameters for comparing atoms

property AtomTyper

atom typer to be used. Must be one of the members of the rdFMCS.AtomCompare class or an instance of a user-defined subclass of rdFMCS.MCSAtomCompare

property BondCompareParameters

parameters for comparing bonds

property BondTyper

bond typer to be used. Must be one of the members of the rdFMCS.BondCompare class or an instance of a user-defined subclass of rdFMCS.MCSBondCompare

property FinalMatchChecker

seed final match checker callback class. Must be a user-defined subclass of rdFMCS.MCSFinalMatchCheck

property InitialSeed

SMILES string to be used as the seed of the MCS

property MaximizeBonds

toggles maximizing the number of bonds (instead of the number of atoms)

property ProgressCallback

progress callback class. Must be a user-defined subclass of rdFMCS.Progress

property ShouldAcceptMCS

MCS acceptance callback class. Must be a user-defined subclass of rdFMCS.MCSAcceptance

property StoreAll

toggles storage of degenerate MCSs

property Threshold

fraction of the dataset that must contain the MCS

property Timeout

timeout (in seconds) for the calculation

property Verbose

toggles verbose mode

class rdkit.Chem.rdFMCS.MCSProgress((object)arg1)

Bases: instance

Base class. Subclass and override MCSProgress.__call__() to define a custom callback function

C++ signature :

void __init__(_object*)

class rdkit.Chem.rdFMCS.MCSProgressData((object)arg1)

Bases: instance

Information about the MCS progress

C++ signature :

void __init__(_object*)

property numAtoms

number of atoms in MCS

property numBonds

number of bonds in MCS

property seedProcessed

number of processed seeds

class rdkit.Chem.rdFMCS.MCSResult

Bases: instance

used to return MCS results

Raises an exception This class cannot be instantiated from Python

property canceled

if True, the MCS calculation did not finish

property degenerateSmartsQueryMolDict

Dictionary collecting all degenerate (SMARTS, queryMol) pairs (empty if MCSParameters.StoreAll is False)

property numAtoms

number of atoms in MCS

property numBonds

number of bonds in MCS

property queryMol

query molecule for the MCS

property smartsString

SMARTS string for the MCS

class rdkit.Chem.rdFMCS.RingCompare

Bases: enum

IgnoreRingFusion = rdkit.Chem.rdFMCS.RingCompare.IgnoreRingFusion

PermissiveRingFusion = rdkit.Chem.rdFMCS.RingCompare.PermissiveRingFusion

StrictRingFusion = rdkit.Chem.rdFMCS.RingCompare.StrictRingFusion

names = {'IgnoreRingFusion': rdkit.Chem.rdFMCS.RingCompare.IgnoreRingFusion, 'PermissiveRingFusion': rdkit.Chem.rdFMCS.RingCompare.PermissiveRingFusion, 'StrictRingFusion': rdkit.Chem.rdFMCS.RingCompare.StrictRingFusion}

values = {0: rdkit.Chem.rdFMCS.RingCompare.IgnoreRingFusion, 1: rdkit.Chem.rdFMCS.RingCompare.PermissiveRingFusion, 2: rdkit.Chem.rdFMCS.RingCompare.StrictRingFusion}