rdkit.Chem.rdSubstructLibrary module¶

rdkit.Chem.rdSubstructLibrary.AddPatterns((SubstructLibrary)sslib[, (int)numThreads=1]) → None :¶

Add pattern fingerprints to the given library, use numThreads=-1 to use all available cores

C++ signature :
void AddPatterns(RDKit::SubstructLibraryWrap {lvalue} [,int=1])

AddPatterns( (SubstructLibrary)sslib, (FPHolderBase)patterns [, (int)numThreads=1]) -> None :

Add pattern fingerprints to the given library, use numThreads=-1 to use all available cores

C++ signature :: void AddPatterns(RDKit::SubstructLibraryWrap {lvalue},boost::shared_ptr<RDKit::FPHolderBase> [,int=1])

class rdkit.Chem.rdSubstructLibrary.CachedMolHolder((object)self)¶

Bases: MolHolderBase

Holds molecules in their binary representation. This allows more molecules to be held in memory at a time

AddMol(mol) -> adds a molecule to the molecule holder, returns index of molecule

AddBinary(data) -> adds a picked molecule molecule to the molecule holder, returns index of molecule
The data is stored as-is, no checking is done for validity.

GetMol(idx) -> return the molecule at index idx

C++ signature :: void __init__(_object*)

AddBinary((CachedMolHolder)self, (str)pickle) → int :¶

Add a binary pickle to the molecule holder, no checking is done on the input data

C++ signature :: unsigned int AddBinary(RDKit::CachedMolHolder {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

class rdkit.Chem.rdSubstructLibrary.CachedSmilesMolHolder((object)self)¶

Bases: MolHolderBase

Holds molecules as smiles string This allows more molecules to be held in memory at a time

AddMol(mol) -> adds a molecule to the molecule holder, returns index of molecule

AddSmiles(smiles) -> adds a smiles string to the molecule holder, returns index of molecule
The smiles is stored as-is, no checking is done for validity.

GetMol(idx) -> return the molecule at index idx

C++ signature :: void __init__(_object*)

AddSmiles((CachedSmilesMolHolder)self, (str)smiles) → int :¶

Add a trusted smiles string to the molecule holder, no checking is done on the input data

C++ signature :: unsigned int AddSmiles(RDKit::CachedSmilesMolHolder {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

class rdkit.Chem.rdSubstructLibrary.CachedTrustedSmilesMolHolder((object)self)¶

Bases: MolHolderBase

Holds molecules as trusted smiles string This allows more molecules to be held in memory at a time and avoids RDKit sanitization overhead. See: http://rdkit.blogspot.com/2016/09/avoiding-unnecessary-work-and.html

AddMol(mol) -> adds a molecule to the molecule holder, returns index of molecule

AddSmiles(smiles) -> adds a smiles string to the molecule holder, returns index of molecule
The smiles is stored as-is, no checking is done for validity.

GetMol(idx,s) -> return the molecule at index idx,
note, only light sanitization is done here, for instance the molecules RingInfo is not initialized

C++ signature :: void __init__(_object*)

AddSmiles((CachedTrustedSmilesMolHolder)self, (str)smiles) → int :¶

Add a trusted smiles string to the molecule holder, no checking is done on the input data

C++ signature :: unsigned int AddSmiles(RDKit::CachedTrustedSmilesMolHolder {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

class rdkit.Chem.rdSubstructLibrary.FPHolderBase¶

Bases: instance

Raises an exception This class cannot be instantiated from Python

AddFingerprint((FPHolderBase)self, (ExplicitBitVect)v) → int :¶

Adds a raw bit vector to the fingerprint database, returns the index of the supplied pattern

C++ signature :: unsigned int AddFingerprint(RDKit::FPHolderBase {lvalue},ExplicitBitVect)

AddMol((FPHolderBase)self, (Mol)m) → int :¶

Adds a molecule to the fingerprint database, returns the index of the new pattern

C++ signature :: unsigned int AddMol(RDKit::FPHolderBase {lvalue},RDKit::ROMol)

GetFingerprint((FPHolderBase)self, (int)idx) → ExplicitBitVect :¶

Return the bit vector at the specified index

C++ signature :: ExplicitBitVect GetFingerprint(RDKit::FPHolderBase {lvalue},unsigned int)

MakeFingerprint((FPHolderBase)self, (Mol)mol) → ExplicitBitVect :¶

Compute the query bits for the holder

C++ signature :: ExplicitBitVect* MakeFingerprint(RDKit::FPHolderBase {lvalue},RDKit::ROMol)

PassesFilter((FPHolderBase)self, (int)idx, (ExplicitBitVect)query) → bool :¶

Returns True if the specified index passes the filter supplied by the query bit vector

C++ signature :: bool PassesFilter(RDKit::FPHolderBase {lvalue},unsigned int,ExplicitBitVect)

class rdkit.Chem.rdSubstructLibrary.KeyFromPropHolder((object)self)¶

Bases: KeyHolderBase

Holds keys to return external references to the molecules in the molholder. By default use the _Name property but can be overridden to be any property

C++ signature :
void __init__(_object*)

__init__( (object)self, (str)propname) -> None :

C++ signature :
void __init__(_object*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

GetPropName((KeyFromPropHolder)self) → str :¶

Return the key for the given molecule index

C++ signature :: std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetPropName(RDKit::KeyFromPropHolder {lvalue})

class rdkit.Chem.rdSubstructLibrary.KeyHolderBase¶

Bases: instance

Raises an exception This class cannot be instantiated from Python

AddKey((KeyHolderBase)self, (str)arg1) → int :¶

Add a key to the key holder, must be manually synced

C++ signature :: unsigned int AddKey(RDKit::KeyHolderBase {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

AddMol((KeyHolderBase)self, (Mol)m) → int :¶

Adds a molecule to the fingerprint database, returns the index of the new pattern

C++ signature :: unsigned int AddMol(RDKit::KeyHolderBase {lvalue},RDKit::ROMol)

GetKey((KeyHolderBase)self, (int)arg1) → str :¶

Return the key at the specified index

C++ signature :: std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetKey(RDKit::KeyHolderBase {lvalue},unsigned int)

GetKeys((KeyHolderBase)self, (_vectj)indices) → _vectNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE :¶

Returns the keys for the given indices as return by GetMatches

ARGUMENTS:

indices: The indices of the keys

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> > > > GetKeys(RDKit::KeyHolderBase {lvalue},std::vector<unsigned int, std::allocator<unsigned int> >)

class rdkit.Chem.rdSubstructLibrary.MolHolder((object)self)¶

Bases: MolHolderBase

Holds raw in-memory molecules AddMol(mol) -> adds a molecule to the molecule holder, returns index of molecule GetMol(idx,sanitize=True) -> return the molecule at index idx

C++ signature :: void __init__(_object*)

class rdkit.Chem.rdSubstructLibrary.MolHolderBase¶

Bases: instance

Raises an exception This class cannot be instantiated from Python

AddMol((MolHolderBase)self, (Mol)m) → int :¶

Adds molecule to the molecule holder

C++ signature :: unsigned int AddMol(RDKit::MolHolderBase {lvalue},RDKit::ROMol)

GetMol((MolHolderBase)self, (int)arg1) → Mol :¶

Returns a particular molecule in the molecule holder

ARGUMENTS:

idx: which molecule to return

sanitize: if sanitize is False, return the internal molecule state [default True]

NOTE: molecule indices start at 0

C++ signature :: boost::shared_ptr<RDKit::ROMol> GetMol(RDKit::MolHolderBase {lvalue},unsigned int)

class rdkit.Chem.rdSubstructLibrary.PatternHolder((object)self)¶

Bases: FPHolderBase

Holds fingerprints with optional, user-defined number of bits (default: 2048) used for filtering of molecules.

C++ signature :
void __init__(_object*)

__init__( (object)self, (int)numBits) -> None :

C++ signature :
void __init__(_object*,unsigned int)

class rdkit.Chem.rdSubstructLibrary.SubstructLibrary((object)self)¶

Bases: instance

SubstructLibrary: This provides a simple API for substructure searching large datasets The SubstructLibrary takes full advantage of available threads during the search operation. Basic operation is simple

>>> from __future__ import print_function
>>> import os
>>> from rdkit import Chem, RDConfig
>>> from rdkit.Chem import rdSubstructLibrary
>>> library = rdSubstructLibrary.SubstructLibrary()
>>> for mol in Chem.SDMolSupplier(os.path.join(RDConfig.RDDataDir, 
...                               'NCI', 'first_200.props.sdf')):
...   idx = library.AddMol(mol)
>>> core = Chem.MolFromSmarts('CCCCOC')
>>> indices = library.GetMatches(core)
>>> len(indices)
11

Substructure matching options can be sent into GetMatches:

>>> indices = library.GetMatches(core, useChirality=False) 
>>> len(indices)
11

Controlling the number of threads or the maximum number of matches returned: is also available (the default is to run on all cores)

>>> indices = library.GetMatches(core, numThreads=2, maxResults=10) 
>>> len(indices)
10

Working on larger datasets:

Molecules are fairly large objects and will limit the number that can be kept in memory. To assist this we supply three other molecule holders:

CachedMolHolder - stores molecules as their pickled representation

CachedSmilesMolHolder - stores molecules internally as smiles strings

CachedTrustedSmilesMolHolder = excepts (and stores) molecules as trusted smiles strings

Using Pattern fingerprints as a pre-filter: Pattern fingerprints provide an easy way to indicate whether the substructure search should be be done at all. This is particularly useful with the Binary and Smiles based molecule holders as they have an expensive molecule creation step in addition to the substructure searching step

>>> library = rdSubstructLibrary.SubstructLibrary(rdSubstructLibrary.CachedSmilesMolHolder(), 
...                                               rdSubstructLibrary.PatternHolder())
>>> for mol in Chem.SDMolSupplier(os.path.join(RDConfig.RDDataDir, 
...                               'NCI', 'first_200.props.sdf')):
...   idx = library.AddMol(mol)
>>> indices = library.GetMatches(core)
>>> len(indices)
11

This (obviously) takes longer to initialize. However, both the molecule and pattern holders can be populated with raw data, a simple example is below:

>>> import csv
>>> molholder = rdSubstructLibrary.CachedSmilesMolHolder()
>>> pattern_holder = rdSubstructLibrary.PatternHolder()
>>> with open(os.path.join(RDConfig.RDDataDir, 'NCI', 'first_200.tpsa.csv')) as inf:
...   for i, row in enumerate(csv.reader(inf)):
...     if i:
...       idx = molholder.AddSmiles(row[0])
...       idx2 = pattern_holder.AddFingerprint(
...           pattern_holder.MakeFingerprint(Chem.MolFromSmiles(row[0])))
...       assert idx==idx2
>>> library = rdSubstructLibrary.SubstructLibrary(molholder,pattern_holder)
>>> indices = library.GetMatches(core)
>>> len(indices)
11

Finally, the KeyFromPropHolder can be used to use external keys such as compound names. By default the holder uses the ‘_Name’ property but can be changed to any property.

>>> library = rdSubstructLibrary.SubstructLibrary(rdSubstructLibrary.MolHolder(), rdSubstructLibrary.KeyFromPropHolder())
>>> m = Chem.MolFromSmiles('CCC')
>>> m.SetProp('_Name', 'Z11234')
>>> idx = library.AddMol(m)
>>> indices = library.GetMatches(m)
>>> list(library.GetKeyHolder().GetKeys(indices))
['Z11234']

C++ signature :
void __init__(_object*)

__init__( (object)self, (MolHolderBase)molecules) -> None :

C++ signature :
void __init__(_object*,boost::shared_ptr<RDKit::MolHolderBase>)

__init__( (object)self, (MolHolderBase)molecules, (FPHolderBase)fingerprints) -> None :

C++ signature :
void __init__(_object*,boost::shared_ptr<RDKit::MolHolderBase>,boost::shared_ptr<RDKit::FPHolderBase>)

__init__( (object)self, (MolHolderBase)molecules, (KeyHolderBase)keys) -> None :

C++ signature :
void __init__(_object*,boost::shared_ptr<RDKit::MolHolderBase>,boost::shared_ptr<RDKit::KeyHolderBase>)

__init__( (object)self, (MolHolderBase)molecules, (FPHolderBase)fingerprints, (KeyHolderBase)keys) -> None :

C++ signature :
void __init__(_object*,boost::shared_ptr<RDKit::MolHolderBase>,boost::shared_ptr<RDKit::FPHolderBase>,boost::shared_ptr<RDKit::KeyHolderBase>)

__init__( (object)self, (str)pickle) -> None :

C++ signature :
void __init__(_object*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

AddMol((SubstructLibrary)self, (Mol)mol) → int :¶

Adds a molecule to the substruct library

C++ signature :: unsigned int AddMol(RDKit::SubstructLibraryWrap {lvalue},RDKit::ROMol)

CountMatches((SubstructLibrary)self, (Mol)query[, (bool)recursionPossible=True[, (bool)useChirality=True[, (bool)useQueryQueryMatches=False[, (int)numThreads=-1]]]]) → int :¶

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

C++ signature :
unsigned int CountMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::ROMol [,bool=True [,bool=True [,bool=False [,int=-1]]]])

CountMatches( (SubstructLibrary)self, (Mol)query, (int)startIdx, (int)endIdx [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1]]]]) -> int :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

C++ signature :: unsigned int CountMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::ROMol,unsigned int,unsigned int [,bool=True [,bool=True [,bool=False [,int=-1]]]])

CountMatches( (SubstructLibrary)self, (Mol)query, (SubstructMatchParameters)parameters [, (int)numThreads=-1]) -> int :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

C++ signature :: unsigned int CountMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::ROMol,RDKit::SubstructMatchParameters [,int=-1])

CountMatches( (SubstructLibrary)self, (Mol)query, (int)startIdx, (int)endIdx, (SubstructMatchParameters)parameters [, (int)numThreads=-1]) -> int :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

C++ signature :: unsigned int CountMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::ROMol,unsigned int,unsigned int,RDKit::SubstructMatchParameters [,int=-1])

CountMatches( (SubstructLibrary)self, (object)query [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1]]]]) -> int :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

C++ signature :: unsigned int CountMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::TautomerQuery [,bool=True [,bool=True [,bool=False [,int=-1]]]])

CountMatches( (SubstructLibrary)self, (object)query, (int)startIdx, (int)endIdx [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1]]]]) -> int :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

C++ signature :: unsigned int CountMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::TautomerQuery,unsigned int,unsigned int [,bool=True [,bool=True [,bool=False [,int=-1]]]])

CountMatches( (SubstructLibrary)self, (object)query, (SubstructMatchParameters)parameters [, (int)numThreads=-1]) -> int :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

C++ signature :: unsigned int CountMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::TautomerQuery,RDKit::SubstructMatchParameters [,int=-1])

CountMatches( (SubstructLibrary)self, (object)query, (int)startIdx, (int)endIdx, (SubstructMatchParameters)parameters [, (int)numThreads=-1]) -> int :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

C++ signature :: unsigned int CountMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::TautomerQuery,unsigned int,unsigned int,RDKit::SubstructMatchParameters [,int=-1])

CountMatches( (SubstructLibrary)self, (MolBundle)query [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1]]]]) -> int :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

C++ signature :: unsigned int CountMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::MolBundle [,bool=True [,bool=True [,bool=False [,int=-1]]]])

CountMatches( (SubstructLibrary)self, (MolBundle)query, (int)startIdx, (int)endIdx [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1]]]]) -> int :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

C++ signature :: unsigned int CountMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::MolBundle,unsigned int,unsigned int [,bool=True [,bool=True [,bool=False [,int=-1]]]])

CountMatches( (SubstructLibrary)self, (MolBundle)query, (SubstructMatchParameters)parameters [, (int)numThreads=-1]) -> int :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

C++ signature :: unsigned int CountMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::MolBundle,RDKit::SubstructMatchParameters [,int=-1])

CountMatches( (SubstructLibrary)self, (MolBundle)query, (int)startIdx, (int)endIdx, (SubstructMatchParameters)parameters [, (int)numThreads=-1]) -> int :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

C++ signature :: unsigned int CountMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::MolBundle,unsigned int,unsigned int,RDKit::SubstructMatchParameters [,int=-1])

CountMatches( (SubstructLibrary)self, (object)query [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1]]]]) -> int :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

C++ signature :: unsigned int CountMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::GeneralizedSubstruct::ExtendedQueryMol [,bool=True [,bool=True [,bool=False [,int=-1]]]])

CountMatches( (SubstructLibrary)self, (object)query, (int)startIdx, (int)endIdx [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1]]]]) -> int :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

C++ signature :: unsigned int CountMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::GeneralizedSubstruct::ExtendedQueryMol,unsigned int,unsigned int [,bool=True [,bool=True [,bool=False [,int=-1]]]])

CountMatches( (SubstructLibrary)self, (object)query, (SubstructMatchParameters)parameters [, (int)numThreads=-1]) -> int :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

C++ signature :: unsigned int CountMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::GeneralizedSubstruct::ExtendedQueryMol,RDKit::SubstructMatchParameters [,int=-1])

CountMatches( (SubstructLibrary)self, (object)query, (int)startIdx, (int)endIdx, (SubstructMatchParameters)parameters [, (int)numThreads=-1]) -> int :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

C++ signature :: unsigned int CountMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::GeneralizedSubstruct::ExtendedQueryMol,unsigned int,unsigned int,RDKit::SubstructMatchParameters [,int=-1])

GetFpHolder((SubstructLibrary)self) → FPHolderBase :¶

C++ signature :: boost::shared_ptr<RDKit::FPHolderBase> GetFpHolder(RDKit::SubstructLibraryWrap {lvalue})

GetKeyHolder((SubstructLibrary)self) → KeyHolderBase :¶

C++ signature :: boost::shared_ptr<RDKit::KeyHolderBase> GetKeyHolder(RDKit::SubstructLibraryWrap {lvalue})

GetMatches((SubstructLibrary)self, (Mol)query[, (bool)recursionPossible=True[, (bool)useChirality=True[, (bool)useQueryQueryMatches=False[, (int)numThreads=-1[, (int)maxResults=1000]]]]]) → _vectj :¶

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

maxResults: maximum number of results to return

C++ signature :
std::vector<unsigned int, std::allocator<unsigned int> > GetMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::ROMol [,bool=True [,bool=True [,bool=False [,int=-1 [,int=1000]]]]])

GetMatches( (SubstructLibrary)self, (Mol)query, (int)startIdx, (int)endIdx [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1 [, (int)maxResults=1000]]]]]) -> _vectj :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

maxResults: maximum number of results to return

C++ signature :: std::vector<unsigned int, std::allocator<unsigned int> > GetMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::ROMol,unsigned int,unsigned int [,bool=True [,bool=True [,bool=False [,int=-1 [,int=1000]]]]])

GetMatches( (SubstructLibrary)self, (Mol)query, (SubstructMatchParameters)parameters [, (int)numThreads=-1 [, (int)maxResults=1000]]) -> _vectj :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

maxResults: maximum number of results to return

C++ signature :: std::vector<unsigned int, std::allocator<unsigned int> > GetMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::ROMol,RDKit::SubstructMatchParameters [,int=-1 [,int=1000]])

GetMatches( (SubstructLibrary)self, (Mol)query, (int)startIdx, (int)endIdx, (SubstructMatchParameters)parameters [, (int)numThreads=-1 [, (int)maxResults=1000]]) -> _vectj :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

maxResults: maximum number of results to return

C++ signature :: std::vector<unsigned int, std::allocator<unsigned int> > GetMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::ROMol,unsigned int,unsigned int,RDKit::SubstructMatchParameters [,int=-1 [,int=1000]])

GetMatches( (SubstructLibrary)self, (object)query [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1 [, (int)maxResults=1000]]]]]) -> _vectj :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

maxResults: maximum number of results to return

C++ signature :: std::vector<unsigned int, std::allocator<unsigned int> > GetMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::TautomerQuery [,bool=True [,bool=True [,bool=False [,int=-1 [,int=1000]]]]])

GetMatches( (SubstructLibrary)self, (object)query, (int)startIdx, (int)endIdx [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1 [, (int)maxResults=1000]]]]]) -> _vectj :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

maxResults: maximum number of results to return

C++ signature :: std::vector<unsigned int, std::allocator<unsigned int> > GetMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::TautomerQuery,unsigned int,unsigned int [,bool=True [,bool=True [,bool=False [,int=-1 [,int=1000]]]]])

GetMatches( (SubstructLibrary)self, (object)query, (SubstructMatchParameters)parameters [, (int)numThreads=-1 [, (int)maxResults=1000]]) -> _vectj :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

maxResults: maximum number of results to return

C++ signature :: std::vector<unsigned int, std::allocator<unsigned int> > GetMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::TautomerQuery,RDKit::SubstructMatchParameters [,int=-1 [,int=1000]])

GetMatches( (SubstructLibrary)self, (object)query, (int)startIdx, (int)endIdx, (SubstructMatchParameters)parameters [, (int)numThreads=-1 [, (int)maxResults=1000]]) -> _vectj :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

maxResults: maximum number of results to return

C++ signature :: std::vector<unsigned int, std::allocator<unsigned int> > GetMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::TautomerQuery,unsigned int,unsigned int,RDKit::SubstructMatchParameters [,int=-1 [,int=1000]])

GetMatches( (SubstructLibrary)self, (MolBundle)query [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1 [, (int)maxResults=1000]]]]]) -> _vectj :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

maxResults: maximum number of results to return

C++ signature :: std::vector<unsigned int, std::allocator<unsigned int> > GetMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::MolBundle [,bool=True [,bool=True [,bool=False [,int=-1 [,int=1000]]]]])

GetMatches( (SubstructLibrary)self, (MolBundle)query, (int)startIdx, (int)endIdx [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1 [, (int)maxResults=1000]]]]]) -> _vectj :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

maxResults: maximum number of results to return

C++ signature :: std::vector<unsigned int, std::allocator<unsigned int> > GetMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::MolBundle,unsigned int,unsigned int [,bool=True [,bool=True [,bool=False [,int=-1 [,int=1000]]]]])

GetMatches( (SubstructLibrary)self, (MolBundle)query, (SubstructMatchParameters)parameters [, (int)numThreads=-1 [, (int)maxResults=1000]]) -> _vectj :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

maxResults: maximum number of results to return

C++ signature :: std::vector<unsigned int, std::allocator<unsigned int> > GetMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::MolBundle,RDKit::SubstructMatchParameters [,int=-1 [,int=1000]])

GetMatches( (SubstructLibrary)self, (MolBundle)query, (int)startIdx, (int)endIdx, (SubstructMatchParameters)parameters [, (int)numThreads=-1 [, (int)maxResults=1000]]) -> _vectj :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

maxResults: maximum number of results to return

C++ signature :: std::vector<unsigned int, std::allocator<unsigned int> > GetMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::MolBundle,unsigned int,unsigned int,RDKit::SubstructMatchParameters [,int=-1 [,int=1000]])

GetMatches( (SubstructLibrary)self, (object)query [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1 [, (int)maxResults=1000]]]]]) -> _vectj :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

maxResults: maximum number of results to return

C++ signature :: std::vector<unsigned int, std::allocator<unsigned int> > GetMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::GeneralizedSubstruct::ExtendedQueryMol [,bool=True [,bool=True [,bool=False [,int=-1 [,int=1000]]]]])

GetMatches( (SubstructLibrary)self, (object)query, (int)startIdx, (int)endIdx [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1 [, (int)maxResults=1000]]]]]) -> _vectj :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

maxResults: maximum number of results to return

C++ signature :: std::vector<unsigned int, std::allocator<unsigned int> > GetMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::GeneralizedSubstruct::ExtendedQueryMol,unsigned int,unsigned int [,bool=True [,bool=True [,bool=False [,int=-1 [,int=1000]]]]])

GetMatches( (SubstructLibrary)self, (object)query, (SubstructMatchParameters)parameters [, (int)numThreads=-1 [, (int)maxResults=1000]]) -> _vectj :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

maxResults: maximum number of results to return

C++ signature :: std::vector<unsigned int, std::allocator<unsigned int> > GetMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::GeneralizedSubstruct::ExtendedQueryMol,RDKit::SubstructMatchParameters [,int=-1 [,int=1000]])

GetMatches( (SubstructLibrary)self, (object)query, (int)startIdx, (int)endIdx, (SubstructMatchParameters)parameters [, (int)numThreads=-1 [, (int)maxResults=1000]]) -> _vectj :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

maxResults: maximum number of results to return

C++ signature :: std::vector<unsigned int, std::allocator<unsigned int> > GetMatches(RDKit::SubstructLibraryWrap {lvalue},RDKit::GeneralizedSubstruct::ExtendedQueryMol,unsigned int,unsigned int,RDKit::SubstructMatchParameters [,int=-1 [,int=1000]])

GetMol((SubstructLibrary)self, (int)idx) → Mol :¶

Returns a particular molecule in the molecule holder

ARGUMENTS:

idx: which molecule to return

NOTE: molecule indices start at 0

C++ signature :: boost::shared_ptr<RDKit::ROMol> GetMol(RDKit::SubstructLibraryWrap {lvalue},unsigned int)

GetMolHolder((SubstructLibrary)self) → MolHolderBase :¶

C++ signature :: boost::shared_ptr<RDKit::MolHolderBase> GetMolHolder(RDKit::SubstructLibraryWrap {lvalue})

GetSearchOrder((SubstructLibrary)self) → tuple :¶

Returns the search order for the library

NOTE: molecule indices start at 0

C++ signature :: boost::python::tuple GetSearchOrder(RDKit::SubstructLibraryWrap)

HasMatch((SubstructLibrary)self, (Mol)query[, (bool)recursionPossible=True[, (bool)useChirality=True[, (bool)useQueryQueryMatches=False[, (int)numThreads=-1]]]]) → bool :¶

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

C++ signature :
bool HasMatch(RDKit::SubstructLibraryWrap {lvalue},RDKit::ROMol [,bool=True [,bool=True [,bool=False [,int=-1]]]])

HasMatch( (SubstructLibrary)self, (Mol)query, (int)startIdx, (int)endIdx [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1]]]]) -> bool :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

C++ signature :: bool HasMatch(RDKit::SubstructLibraryWrap {lvalue},RDKit::ROMol,unsigned int,unsigned int [,bool=True [,bool=True [,bool=False [,int=-1]]]])

HasMatch( (SubstructLibrary)self, (Mol)query, (SubstructMatchParameters)parameters [, (int)numThreads=-1]) -> bool :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

C++ signature :: bool HasMatch(RDKit::SubstructLibraryWrap {lvalue},RDKit::ROMol,RDKit::SubstructMatchParameters [,int=-1])

HasMatch( (SubstructLibrary)self, (Mol)query, (int)startIdx, (int)endIdx, (SubstructMatchParameters)parameters [, (int)numThreads=-1]) -> bool :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

C++ signature :: bool HasMatch(RDKit::SubstructLibraryWrap {lvalue},RDKit::ROMol,unsigned int,unsigned int,RDKit::SubstructMatchParameters [,int=-1])

HasMatch( (SubstructLibrary)self, (object)query [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1]]]]) -> bool :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

C++ signature :: bool HasMatch(RDKit::SubstructLibraryWrap {lvalue},RDKit::TautomerQuery [,bool=True [,bool=True [,bool=False [,int=-1]]]])

HasMatch( (SubstructLibrary)self, (object)query, (int)startIdx, (int)endIdx [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1]]]]) -> bool :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

C++ signature :: bool HasMatch(RDKit::SubstructLibraryWrap {lvalue},RDKit::TautomerQuery,unsigned int,unsigned int [,bool=True [,bool=True [,bool=False [,int=-1]]]])

HasMatch( (SubstructLibrary)self, (object)query, (SubstructMatchParameters)parameters [, (int)numThreads=-1]) -> bool :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

C++ signature :: bool HasMatch(RDKit::SubstructLibraryWrap {lvalue},RDKit::TautomerQuery,RDKit::SubstructMatchParameters [,int=-1])

HasMatch( (SubstructLibrary)self, (object)query, (int)startIdx, (int)endIdx, (SubstructMatchParameters)parameters [, (int)numThreads=-1]) -> bool :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

C++ signature :: bool HasMatch(RDKit::SubstructLibraryWrap {lvalue},RDKit::TautomerQuery,unsigned int,unsigned int,RDKit::SubstructMatchParameters [,int=-1])

HasMatch( (SubstructLibrary)self, (MolBundle)query [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1]]]]) -> bool :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

C++ signature :: bool HasMatch(RDKit::SubstructLibraryWrap {lvalue},RDKit::MolBundle [,bool=True [,bool=True [,bool=False [,int=-1]]]])

HasMatch( (SubstructLibrary)self, (MolBundle)query, (int)startIdx, (int)endIdx [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1]]]]) -> bool :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

C++ signature :: bool HasMatch(RDKit::SubstructLibraryWrap {lvalue},RDKit::MolBundle,unsigned int,unsigned int [,bool=True [,bool=True [,bool=False [,int=-1]]]])

HasMatch( (SubstructLibrary)self, (MolBundle)query, (SubstructMatchParameters)parameters [, (int)numThreads=-1]) -> bool :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

C++ signature :: bool HasMatch(RDKit::SubstructLibraryWrap {lvalue},RDKit::MolBundle,RDKit::SubstructMatchParameters [,int=-1])

HasMatch( (SubstructLibrary)self, (MolBundle)query, (int)startIdx, (int)endIdx, (SubstructMatchParameters)parameters [, (int)numThreads=-1]) -> bool :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

C++ signature :: bool HasMatch(RDKit::SubstructLibraryWrap {lvalue},RDKit::MolBundle,unsigned int,unsigned int,RDKit::SubstructMatchParameters [,int=-1])

HasMatch( (SubstructLibrary)self, (object)query [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1]]]]) -> bool :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

C++ signature :: bool HasMatch(RDKit::SubstructLibraryWrap {lvalue},RDKit::GeneralizedSubstruct::ExtendedQueryMol [,bool=True [,bool=True [,bool=False [,int=-1]]]])

HasMatch( (SubstructLibrary)self, (object)query, (int)startIdx, (int)endIdx [, (bool)recursionPossible=True [, (bool)useChirality=True [, (bool)useQueryQueryMatches=False [, (int)numThreads=-1]]]]) -> bool :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

C++ signature :: bool HasMatch(RDKit::SubstructLibraryWrap {lvalue},RDKit::GeneralizedSubstruct::ExtendedQueryMol,unsigned int,unsigned int [,bool=True [,bool=True [,bool=False [,int=-1]]]])

HasMatch( (SubstructLibrary)self, (object)query, (SubstructMatchParameters)parameters [, (int)numThreads=-1]) -> bool :

Get the matches for the query.

Arguments:

query: substructure query

numThreads: number of threads to use, -1 means all threads

C++ signature :: bool HasMatch(RDKit::SubstructLibraryWrap {lvalue},RDKit::GeneralizedSubstruct::ExtendedQueryMol,RDKit::SubstructMatchParameters [,int=-1])

HasMatch( (SubstructLibrary)self, (object)query, (int)startIdx, (int)endIdx, (SubstructMatchParameters)parameters [, (int)numThreads=-1]) -> bool :

Get the matches for the query.

Arguments:

query: substructure query

startIdx: index to search from

endIdx: index (non-inclusize) to search to

numThreads: number of threads to use, -1 means all threads

C++ signature :: bool HasMatch(RDKit::SubstructLibraryWrap {lvalue},RDKit::GeneralizedSubstruct::ExtendedQueryMol,unsigned int,unsigned int,RDKit::SubstructMatchParameters [,int=-1])

InitFromStream((SubstructLibrary)self, (AtomPairsParameters)stream) → None :¶

Deserialize a substructure library from a python bytes stream. Python doesn’t allow seeking operations inside a unicode or string stream anymore so this requires opening a file in binary mode or using an io.ByteIO type object

ARGUMENTS:

stream: a binary stream like object

SubstructLibrary.Serialize already writes a binary stream

>>> from rdkit.Chem import rdSubstructLibrary
>>> import io
>>> lib = rdSubstructLibrary.SubstructLibrary()
>>> stream = io.BytesIO( lib.Serialize() )
>>> lib.InitFromStream(stream)

remember to write to text and read from a binary stream

>>> with open('rdkit.sslib', 'w') as f: lib.ToStream(f)
>>> with open('rdkit.sslib', 'rb') as f: lib.InitFromStream(f)

C++ signature :: void InitFromStream(RDKit::SubstructLibraryWrap {lvalue},boost::python::api::object {lvalue})

Serialize((SubstructLibrary)self) → object :¶

C++ signature :: boost::python::api::object Serialize(RDKit::SubstructLibraryWrap)

SetSearchOrder((SubstructLibrary)self, (AtomPairsParameters)seq) → None :¶

Sets the search order for the library

ARGUMENTS:

order: sequence of molecule indices

NOTE: molecule indices start at 0

C++ signature :: void SetSearchOrder(RDKit::SubstructLibraryWrap {lvalue},boost::python::api::object)

ToStream((SubstructLibrary)self, (AtomPairsParameters)stream) → None :¶

Serialize a substructure library to a python text stream. The stream can be a file in text mode or an io.StringIO type object

ARGUMENTS:

stream: a text or text stream like object

>>> from rdkit.Chem import rdSubstructLibrary
>>> import io
>>> lib = rdSubstructLibrary.SubstructLibrary()
>>> stream = io.StringIO()
>>> lib.ToStream(stream)

or

>>> with open('rdkit.sslib', 'w') as stream:
...  lib.ToStream(stream)

C++ signature :: void ToStream(RDKit::SubstructLibraryWrap,boost::python::api::object {lvalue})

rdkit.Chem.rdSubstructLibrary.SubstructLibraryCanSerialize() → bool :¶

Returns True if the SubstructLibrary is serializable (requires boost serialization

C++ signature :: bool SubstructLibraryCanSerialize()

class rdkit.Chem.rdSubstructLibrary.TautomerPatternHolder((object)self)¶

Bases: FPHolderBase

Holds tautomeric fingerprints with optional, user-defined number of bits (default: 2048) used for filtering of molecules. These fingerprints are designed to be used with TautomerQueries.

C++ signature :
void __init__(_object*)

__init__( (object)self, (int)numBits) -> None :

C++ signature :
void __init__(_object*,unsigned int)

rdkit.Chem.rdSubstructLibrary module¶

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