RDKit
Open-source cheminformatics and machine learning.
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RDKit::MolStandardize::TautomerEnumerator Class Reference

#include <Tautomer.h>

Public Member Functions

 TautomerEnumerator (TautomerCatalog *tautCat)
 TautomerEnumerator (const CleanupParameters &params=CleanupParameters())
 TautomerEnumerator (const TautomerEnumerator &other)
TautomerEnumerator & operator= (const TautomerEnumerator &other)
void setMaxTautomers (unsigned int maxTautomers)
unsigned int getMaxTautomers ()
void setMaxTransforms (unsigned int maxTransforms)
unsigned int getMaxTransforms ()
void setRemoveSp3Stereo (bool removeSp3Stereo)
bool getRemoveSp3Stereo ()
void setRemoveBondStereo (bool removeBondStereo)
bool getRemoveBondStereo ()
void setRemoveIsotopicHs (bool removeIsotopicHs)
bool getRemoveIsotopicHs ()
void setReassignStereo (bool reassignStereo)
bool getReassignStereo ()
void setCallback (TautomerEnumeratorCallback *callback)
void setCallback (std::shared_ptr< TautomerEnumeratorCallback > callback)
TautomerEnumeratorCallback * getCallback () const
TautomerEnumeratorResult enumerate (const ROMol &mol) const
 returns a TautomerEnumeratorResult structure for the input molecule
std::vector< ROMOL_SPTR > enumerate (const ROMol &mol, boost::dynamic_bitset<> *modifiedAtoms, boost::dynamic_bitset<> *modifiedBonds=nullptr) const
ROMol * pickCanonical (const TautomerEnumeratorResult &tautRes, boost::function< int(const ROMol &mol)> scoreFunc=TautomerScoringFunctions::scoreTautomer) const
 returns the canonical tautomer from a TautomerEnumeratorResult
template<class Iterable, typename std::enable_if< !std::is_same< Iterable, TautomerEnumeratorResult >::value, int >::type = 0>
ROMol * pickCanonical (const Iterable &tautomers, boost::function< int(const ROMol &mol)> scoreFunc=TautomerScoringFunctions::scoreTautomer) const
ROMol * canonicalize (const ROMol &mol, boost::function< int(const ROMol &mol)> scoreFunc={}) const
 returns the canonical tautomer for a molecule
void canonicalizeInPlace (RWMol &mol, boost::function< int(const ROMol &mol)> scoreFunc={}) const

Detailed Description

Definition at line 335 of file MolStandardize/Tautomer.h.

Constructor & Destructor Documentation

◆ TautomerEnumerator() [1/3]

RDKit::MolStandardize::TautomerEnumerator::TautomerEnumerator ( TautomerCatalog * tautCat)
inline

Definition at line 337 of file MolStandardize/Tautomer.h.

Referenced by operator=(), and TautomerEnumerator().

◆ TautomerEnumerator() [2/3]

RDKit::MolStandardize::TautomerEnumerator::TautomerEnumerator ( const CleanupParameters & params = CleanupParameters())

◆ TautomerEnumerator() [3/3]

RDKit::MolStandardize::TautomerEnumerator::TautomerEnumerator ( const TautomerEnumerator & other)
inline

Definition at line 346 of file MolStandardize/Tautomer.h.

References TautomerEnumerator().

Member Function Documentation

◆ canonicalize()

ROMol * RDKit::MolStandardize::TautomerEnumerator::canonicalize ( const ROMol & mol,
boost::function< int(const ROMol &mol)> scoreFunc = {} ) const

returns the canonical tautomer for a molecule

Note that the canonical tautomer is very likely not the most stable tautomer for any given conditions. The default scoring rules are designed to produce "reasonable" tautomers, but the primary concern is that the results are canonical: you always get the same canonical tautomer for a molecule regardless of what the input tautomer or atom ordering were.

The default scoring scheme is inspired by the publication: M. Sitzmann et al., “Tautomerism in Large Databases.”, JCAMD 24:521 (2010) https://doi.org/10.1007/s10822-010-9346-4 When scoreFunc is empty (default), an optimized scorer is created that pre-filters substructure patterns once for the input molecule. caller owns the pointer

◆ canonicalizeInPlace()

void RDKit::MolStandardize::TautomerEnumerator::canonicalizeInPlace ( RWMol & mol,
boost::function< int(const ROMol &mol)> scoreFunc = {} ) const

◆ enumerate() [1/2]

TautomerEnumeratorResult RDKit::MolStandardize::TautomerEnumerator::enumerate ( const ROMol & mol) const

returns a TautomerEnumeratorResult structure for the input molecule

The enumeration rules are inspired by the publication: M. Sitzmann et al., “Tautomerism in Large Databases.”, JCAMD 24:521 (2010) https://doi.org/10.1007/s10822-010-9346-4

Parameters
molthe molecule to be enumerated

Notes:

  • the definitions used here are that the atoms modified during tautomerization are the atoms at the beginning and end of each tautomer transform (the H "donor" and H "acceptor" in the transform) and the bonds modified during transformation are any bonds whose order is changed during the tautomer transform (these are the bonds between the "donor" and the "acceptor")
  • if any atoms in the molecule have the common_properties::_protected property set, they will not be considered for tautomerization. Any transformations involving these atoms will be skipped.

◆ enumerate() [2/2]

std::vector< ROMOL_SPTR > RDKit::MolStandardize::TautomerEnumerator::enumerate ( const ROMol & mol,
boost::dynamic_bitset<> * modifiedAtoms,
boost::dynamic_bitset<> * modifiedBonds = nullptr ) const

Deprecated, please use the form returning a TautomerEnumeratorResult instead

◆ getCallback()

TautomerEnumeratorCallback * RDKit::MolStandardize::TautomerEnumerator::getCallback ( ) const
inline
Returns
pointer to an instance of a class derived from TautomerEnumeratorCallback. DO NOT delete the instance as ownership of the pointer is transferred to the TautomerEnumerator

Definition at line 451 of file MolStandardize/Tautomer.h.

◆ getMaxTautomers()

unsigned int RDKit::MolStandardize::TautomerEnumerator::getMaxTautomers ( )
inline
Returns
maximum number of tautomers to be generated

Definition at line 374 of file MolStandardize/Tautomer.h.

◆ getMaxTransforms()

unsigned int RDKit::MolStandardize::TautomerEnumerator::getMaxTransforms ( )
inline
Returns
maximum number of transformations to be applied

Definition at line 384 of file MolStandardize/Tautomer.h.

◆ getReassignStereo()

bool RDKit::MolStandardize::TautomerEnumerator::getReassignStereo ( )
inline
Returns
whether assignStereochemistry will be called on each tautomer generated by the enumerate() method

Definition at line 433 of file MolStandardize/Tautomer.h.

◆ getRemoveBondStereo()

bool RDKit::MolStandardize::TautomerEnumerator::getRemoveBondStereo ( )
inline
Returns
whether stereochemistry information will be removed from double bonds involved in tautomerism

Definition at line 412 of file MolStandardize/Tautomer.h.

◆ getRemoveIsotopicHs()

bool RDKit::MolStandardize::TautomerEnumerator::getRemoveIsotopicHs ( )
inline
Returns
whether isotpoic Hs will be removed from centers involved in tautomerism

Definition at line 422 of file MolStandardize/Tautomer.h.

◆ getRemoveSp3Stereo()

bool RDKit::MolStandardize::TautomerEnumerator::getRemoveSp3Stereo ( )
inline
Returns
whether stereochemistry information will be removed from sp3 atoms involved in tautomerism

Definition at line 398 of file MolStandardize/Tautomer.h.

◆ operator=()

TautomerEnumerator & RDKit::MolStandardize::TautomerEnumerator::operator= ( const TautomerEnumerator & other)
inline

Definition at line 355 of file MolStandardize/Tautomer.h.

References TautomerEnumerator().

◆ pickCanonical() [1/2]

template<class Iterable, typename std::enable_if< !std::is_same< Iterable, TautomerEnumeratorResult >::value, int >::type = 0>
ROMol * RDKit::MolStandardize::TautomerEnumerator::pickCanonical ( const Iterable & tautomers,
boost::function< int(const ROMol &mol)> scoreFunc = TautomerScoringFunctions::scoreTautomer ) const
inline

returns the canonical tautomer from an iterable of possible tautomers When Iterable is TautomerEnumeratorResult we use the other non-templated overload for efficiency (TautomerEnumeratorResult already has SMILES so no need to recompute them) caller owns the pointer

Definition at line 497 of file MolStandardize/Tautomer.h.

References RDKit::MolOps::assignStereochemistry(), RDKit::MolStandardize::detail::countSpecifiedStereo(), RDKit::MolToSmiles(), and RDKit::MolStandardize::TautomerScoringFunctions::scoreTautomer().

◆ pickCanonical() [2/2]

ROMol * RDKit::MolStandardize::TautomerEnumerator::pickCanonical ( const TautomerEnumeratorResult & tautRes,
boost::function< int(const ROMol &mol)> scoreFunc = TautomerScoringFunctions::scoreTautomer ) const

returns the canonical tautomer from a TautomerEnumeratorResult

References RDKit::MolStandardize::TautomerScoringFunctions::scoreTautomer().

◆ setCallback() [1/2]

void RDKit::MolStandardize::TautomerEnumerator::setCallback ( std::shared_ptr< TautomerEnumeratorCallback > callback)
inline

Definition at line 442 of file MolStandardize/Tautomer.h.

◆ setCallback() [2/2]

void RDKit::MolStandardize::TautomerEnumerator::setCallback ( TautomerEnumeratorCallback * callback)
inline

set this to an instance of a class derived from TautomerEnumeratorCallback where operator() is overridden. DO NOT delete the instance as ownership of the pointer is transferred to the TautomerEnumerator

Definition at line 439 of file MolStandardize/Tautomer.h.

◆ setMaxTautomers()

void RDKit::MolStandardize::TautomerEnumerator::setMaxTautomers ( unsigned int maxTautomers)
inline
Parameters
maxTautomersmaximum number of tautomers to be generated

Definition at line 370 of file MolStandardize/Tautomer.h.

◆ setMaxTransforms()

void RDKit::MolStandardize::TautomerEnumerator::setMaxTransforms ( unsigned int maxTransforms)
inline
Parameters
maxTransformsmaximum number of transformations to be applied this limit is usually hit earlier than the maxTautomers limit and leads to a more linear scaling of CPU time with increasing number of tautomeric centers (see Sitzmann et al.)

Definition at line 380 of file MolStandardize/Tautomer.h.

◆ setReassignStereo()

void RDKit::MolStandardize::TautomerEnumerator::setReassignStereo ( bool reassignStereo)
inline
Parameters
reassignStereo;if set to true, assignStereochemistry will be called on each tautomer generated by the enumerate() method. This defaults to true.

Definition at line 427 of file MolStandardize/Tautomer.h.

◆ setRemoveBondStereo()

void RDKit::MolStandardize::TautomerEnumerator::setRemoveBondStereo ( bool removeBondStereo)
inline
Parameters
removeBondStereo;if set to true, stereochemistry information will be removed from double bonds involved in tautomerism. This means that enols will lose their E/Z stereochemistry after going through tautomer enumeration because of the keto-enolic tautomerism. This defaults to true in RDKit and also in the workflow described by Sitzmann et al.

Definition at line 406 of file MolStandardize/Tautomer.h.

◆ setRemoveIsotopicHs()

void RDKit::MolStandardize::TautomerEnumerator::setRemoveIsotopicHs ( bool removeIsotopicHs)
inline
Parameters
removeIsotopicHs;if set to true, isotopic Hs will be removed from centers involved in tautomerism.

Definition at line 416 of file MolStandardize/Tautomer.h.

◆ setRemoveSp3Stereo()

void RDKit::MolStandardize::TautomerEnumerator::setRemoveSp3Stereo ( bool removeSp3Stereo)
inline
Parameters
removeSp3Stereo;if set to true, stereochemistry information will be removed from sp3 atoms involved in tautomerism. This means that S-aminoacids will lose their stereochemistry after going through tautomer enumeration because of the amido-imidol tautomerism. This defaults to true in RDKit, false in the workflow described by Sitzmann et al.

Definition at line 392 of file MolStandardize/Tautomer.h.

The documentation for this class was generated from the following file: