rdkit.Chem.rdTautomerQuery module

Module for tautomer-aware substructure searching.

Provides the TautomerQuery class which enables substructure searching that accounts for tautomeric forms of the query molecule.

class rdkit.Chem.rdTautomerQuery.TautomerQuery(self)
class rdkit.Chem.rdTautomerQuery.TautomerQuery(self, pickle: bytes)
class rdkit.Chem.rdTautomerQuery.TautomerQuery(self, pickle: str)
class rdkit.Chem.rdTautomerQuery.TautomerQuery(self, mol: rdkit.Chem.rdchem.Mol, tautomerTransformFile: str = '')

Bases: object

The Tautomer Query Class. Creates a query that enables structure search accounting for matching of Tautomeric forms

Overloaded function.

  1. __init__(self) -> None

  2. __init__(self, pickle: bytes) -> None

Construct a TautomerQuery from a pickle bytes.

  1. __init__(self, pickle: str) -> None

Construct a TautomerQuery from a pickle string.

  1. __init__(self, mol: rdkit.Chem.rdchem.Mol, tautomerTransformFile: str = '') -> None

Construct a TautomerQuery from a molecule.

GetModifiedAtoms(self) → list[int]

Return the indices of tautomeric atoms.

GetModifiedBonds(self) → list[int]

Return the indices of tautomeric bonds.

GetSubstructMatch(self, target: rdkit.Chem.rdchem.Mol, useChirality: bool = False, useQueryQueryMatches: bool = False) → list[int]
GetSubstructMatch(self, target: rdkit.Chem.rdchem.Mol, params: rdkit.Chem.rdchem.SubstructMatchParameters) → list[int]

Overloaded function.

  1. GetSubstructMatch(self, target: rdkit.Chem.rdchem.Mol, useChirality: bool = False, useQueryQueryMatches: bool = False) -> list[int]

Return the first substructure match of this tautomer query in the target.

Parameters:

  • target (-) – the target molecule

  • useChirality (-) – (optional) use chirality in matching (default False)

  • useQueryQueryMatches (-) – (optional) use query-query matching logic (default False)

RETURNS: a tuple of atom indices on match, or empty tuple on no match

  1. GetSubstructMatch(self, target: rdkit.Chem.rdchem.Mol, params: rdkit.Chem.rdchem.SubstructMatchParameters) -> list[int]

Return the first substructure match of this tautomer query in the target.

Parameters:

  • target (-) – the target molecule

  • params (-) – SubstructMatchParameters object

RETURNS: a tuple of atom indices on match, or empty tuple on no match

GetSubstructMatches(self, target: rdkit.Chem.rdchem.Mol, uniquify: bool = True, useChirality: bool = False, useQueryQueryMatches: bool = False, maxMatches: int = 1000) → list[list[int]]
GetSubstructMatches(self, target: rdkit.Chem.rdchem.Mol, params: rdkit.Chem.rdchem.SubstructMatchParameters) → list[list[int]]

Overloaded function.

  1. GetSubstructMatches(self, target: rdkit.Chem.rdchem.Mol, uniquify: bool = True, useChirality: bool = False, useQueryQueryMatches: bool = False, maxMatches: int = 1000) -> list[list[int]]

Return all substructure matches of this tautomer query in the target.

Parameters:

  • target (-) – the target molecule

  • uniquify (-) – (optional) only return unique matches (default True)

  • useChirality (-) – (optional) use chirality in matching (default False)

  • useQueryQueryMatches (-) – (optional) use query-query matching logic (default False)

  • maxMatches (-) – (optional) maximum number of matches to return (default 1000)

RETURNS: a tuple of tuples of atom indices

  1. GetSubstructMatches(self, target: rdkit.Chem.rdchem.Mol, params: rdkit.Chem.rdchem.SubstructMatchParameters) -> list[list[int]]

Return all substructure matches of this tautomer query in the target.

Parameters:

  • target (-) – the target molecule

  • params (-) – SubstructMatchParameters object

RETURNS: a tuple of tuples of atom indices

GetSubstructMatchesWithTautomers(self, target: rdkit.Chem.rdchem.Mol, uniquify: bool = True, useChirality: bool = False, useQueryQueryMatches: bool = False, maxMatches: int = 1000) → list[tuple[list[int], rdkit.Chem.rdchem.Mol]]
GetSubstructMatchesWithTautomers(self, target: rdkit.Chem.rdchem.Mol, params: rdkit.Chem.rdchem.SubstructMatchParameters) → list[tuple[list[int], rdkit.Chem.rdchem.Mol]]

Overloaded function.

  1. GetSubstructMatchesWithTautomers(self, target: rdkit.Chem.rdchem.Mol, uniquify: bool = True, useChirality: bool = False, useQueryQueryMatches: bool = False, maxMatches: int = 1000) -> list[tuple[list[int], rdkit.Chem.rdchem.Mol]]

Return all substructure matches with their matching tautomers.

Parameters:

  • target (-) – the target molecule

  • uniquify (-) – (optional) only return unique matches (default True)

  • useChirality (-) – (optional) use chirality in matching (default False)

  • useQueryQueryMatches (-) – (optional) use query-query matching logic (default False)

  • maxMatches (-) – (optional) maximum number of matches to return (default 1000)

RETURNS: a list of (match, tautomer) pairs

  1. GetSubstructMatchesWithTautomers(self, target: rdkit.Chem.rdchem.Mol, params: rdkit.Chem.rdchem.SubstructMatchParameters) -> list[tuple[list[int], rdkit.Chem.rdchem.Mol]]

Return all substructure matches with their matching tautomers.

Parameters:

  • target (-) – the target molecule

  • params (-) – SubstructMatchParameters object

RETURNS: a list of (match, tautomer) pairs

GetTautomers(self) → list[rdkit.Chem.rdchem.Mol]

Return the list of tautomers of the query molecule.

GetTemplateMolecule(self) → rdkit.Chem.rdchem.Mol

Return the template molecule used for substructure searching.

InitFromStream(self, fileobj: object) → None

Initialize this TautomerQuery from a file-like object.

IsSubstructOf(self, target: rdkit.Chem.rdchem.Mol, recursionPossible: bool = True, useChirality: bool = False, useQueryQueryMatches: bool = False) → bool
IsSubstructOf(self, target: rdkit.Chem.rdchem.Mol, params: rdkit.Chem.rdchem.SubstructMatchParameters) → bool

Overloaded function.

  1. IsSubstructOf(self, target: rdkit.Chem.rdchem.Mol, recursionPossible: bool = True, useChirality: bool = False, useQueryQueryMatches: bool = False) -> bool

Check if this tautomer query is a substructure of the target molecule.

Parameters:

  • target (-) – the target molecule

  • recursionPossible (-) – (optional) allow recursive queries (default True)

  • useChirality (-) – (optional) use chirality in matching (default False)

  • useQueryQueryMatches (-) – (optional) use query-query matching logic (default False)

RETURNS: True or False

  1. IsSubstructOf(self, target: rdkit.Chem.rdchem.Mol, params: rdkit.Chem.rdchem.SubstructMatchParameters) -> bool

Check if this tautomer query is a substructure of the target molecule.

Parameters:

  • target (-) – the target molecule

  • params (-) – SubstructMatchParameters object

RETURNS: True or False

PatternFingerprintTemplate(self, fingerprintSize: int = 2048) → rdkit.DataStructs.cDataStructs.ExplicitBitVect

Return the pattern fingerprint of the template molecule.

Parameters:

fingerprintSize (-) – (optional) size of the fingerprint (default 2048)

RETURNS: an ExplicitBitVect fingerprint

ToBinary(self) → bytes

Return a binary string (pickle) representation of this TautomerQuery.

ToStream(self, fileobj: object) → None

Serialize this TautomerQuery to a file-like object.