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RDKit::MolStandardize Namespace Reference

Namespaces

namespace  defaults
 
namespace  Operations
 
namespace  TautomerScoringFunctions
 

Classes

class  AcidBaseCatalogEntry
 
class  AcidBaseCatalogParams
 
class  AllowedAtomsValidation
 
struct  ChargeCorrection
 
struct  CleanupParameters
 
class  CompositeValidation
 The CompositeValidation class provides a simple way to apply a collection of. More...
 
class  DisallowedAtomsValidation
 
class  DisallowedRadicalValidation
 
class  FeaturesValidation
 
class  FragmentCatalogEntry
 
class  FragmentCatalogParams
 
class  FragmentRemover
 
class  FragmentValidation
 The FragmentValidation class logs if certain fragments are present. More...
 
class  Is2DValidation
 
class  IsotopeValidation
 The IsotopeValidation class logs if molecule contains isotopes. More...
 
class  LargestFragmentChooser
 
class  Layout2DValidation
 
class  MetalDisconnector
 
struct  MetalDisconnectorOptions
 
class  MolVSValidation
 
class  NeutralValidation
 The NeutralValidation class logs if not an overall neutral system. More...
 
class  NoAtomValidation
 MolVS Validations. More...
 
class  Normalizer
 The Normalizer class for applying Normalization transforms. More...
 
class  Pipeline
 
struct  PipelineLogEntry
 
struct  PipelineOptions
 
struct  PipelineResult
 
class  RDKitValidation
 
class  Reionizer
 
class  StereoValidation
 
class  Tautomer
 
class  TautomerCatalogEntry
 
class  TautomerCatalogParams
 
class  TautomerEnumerator
 
class  TautomerEnumeratorCallback
 
class  TautomerEnumeratorResult
 Contains results of tautomer enumeration. More...
 
class  TautomerTransform
 
class  TransformCatalogEntry
 
class  TransformCatalogParams
 
class  Uncharger
 The Uncharger class for neutralizing ionized acids and bases. More...
 
class  ValidationMethod
 

Typedefs

typedef RDCatalog::HierarchCatalog< AcidBaseCatalogEntry, AcidBaseCatalogParams, int > AcidBaseCatalog
 
typedef RDCatalog::HierarchCatalog< FragmentCatalogEntry, FragmentCatalogParams, int > FragmentCatalog
 
typedef RDCatalog::HierarchCatalog< TransformCatalogEntry, TransformCatalogParams, int > TransformCatalog
 
typedef std::pair< std::string, ROMOL_SPTR > SmilesMolPair
 
using PipelineLog = std::vector<PipelineLogEntry>
 
using RWMOL_SPTR_PAIR = std::pair<RWMOL_SPTR, RWMOL_SPTR>
 
typedef RDCatalog::HierarchCatalog< TautomerCatalogEntry, TautomerCatalogParams, int > TautomerCatalog
 
typedef std::map< std::string, Tautomer > SmilesTautomerMap
 
typedef std::pair< std::string, Tautomer > SmilesTautomerPair
 
using TautomerTransformDefs
 
using ValidationErrorInfo = std::string
 

Enumerations

enum class  TautomerEnumeratorStatus { Completed = 0 , MaxTautomersReached , MaxTransformsReached , Canceled }
 

Functions

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > readPairs (std::string fileName)
 
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > readPairs (std::istream &inStream, int nToRead=-1)
 
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > readPairs (const std::vector< std::tuple< std::string, std::string, std::string > > &data)
 
Reionizer * reionizerFromParams (const CleanupParameters &params)
 
FragmentRemover * fragmentRemoverFromParams (const CleanupParameters &params, bool leave_last=true, bool skip_if_all_match=false)
 
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ROMol > > readFuncGroups (std::string fileName)
 
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ROMol > > readFuncGroups (std::istream &inStream, int nToRead=-1)
 
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ROMol > > readFuncGroups (const std::vector< std::pair< std::string, std::string > > &data)
 
RDKIT_MOLSTANDARDIZE_EXPORT void updateCleanupParamsFromJSON (CleanupParameters &params, const std::string &json)
 
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * cleanup (const RWMol *mol, const CleanupParameters &params=defaultCleanupParameters)
 
RWMol * cleanup (const RWMol &mol, const CleanupParameters &params=defaultCleanupParameters)
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
 
RDKIT_MOLSTANDARDIZE_EXPORT void cleanupInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters)
 Works the same as cleanup(mol)
 
RDKIT_MOLSTANDARDIZE_EXPORT void cleanupInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters)
 Operates on multiple molecules.
 
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * normalize (const RWMol *mol, const CleanupParameters &params=defaultCleanupParameters)
 Works the same as Normalizer().normalize(mol)
 
RDKIT_MOLSTANDARDIZE_EXPORT void normalizeInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters)
 Works the same as Normalizer().normalizeInPlace(mol)
 
RDKIT_MOLSTANDARDIZE_EXPORT void normalizeInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters)
 Operates on multiple molecules.
 
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * reionize (const RWMol *mol, const CleanupParameters &params=defaultCleanupParameters)
 Works the same as Reionizer().reionize(mol)
 
RDKIT_MOLSTANDARDIZE_EXPORT void reionizeInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters)
 Works the same as Reionizer().reionizeInPlace(mol)
 
RDKIT_MOLSTANDARDIZE_EXPORT void reionizeInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters)
 Operates on multiple molecules.
 
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * removeFragments (const RWMol *mol, const CleanupParameters &params=defaultCleanupParameters)
 Works the same as FragmentRemover().remove(mol)
 
RDKIT_MOLSTANDARDIZE_EXPORT void removeFragmentsInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters)
 Works the same as FragmentRemover().removeInPlace(mol)
 
RDKIT_MOLSTANDARDIZE_EXPORT void removeFragmentsInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters)
 Operates on multiple molecules.
 
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * canonicalTautomer (const RWMol *mol, const CleanupParameters &params=defaultCleanupParameters)
 Works the same as TautomerEnumerator().canonicalize(mol)
 
RDKIT_MOLSTANDARDIZE_EXPORT void canonicalTautomerInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters)
 
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * tautomerParent (const RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skipStandardize=false)
 
RDKIT_MOLSTANDARDIZE_EXPORT void tautomerParentInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skipStandardize=false)
 
RDKIT_MOLSTANDARDIZE_EXPORT void tautomerParentInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters, bool skipStandardize=false)
 
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * fragmentParent (const RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
 
RDKIT_MOLSTANDARDIZE_EXPORT void fragmentParentInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
 
RDKIT_MOLSTANDARDIZE_EXPORT void fragmentParentInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
 
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * stereoParent (const RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
 calls removeStereochemistry() on the given molecule
 
RDKIT_MOLSTANDARDIZE_EXPORT void stereoParentInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
 
RDKIT_MOLSTANDARDIZE_EXPORT void stereoParentInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
 
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * isotopeParent (const RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
 removes all isotopes specifications from the given molecule
 
RDKIT_MOLSTANDARDIZE_EXPORT void isotopeParentInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
 
RDKIT_MOLSTANDARDIZE_EXPORT void isotopeParentInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
 
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * chargeParent (const RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
 
RDKIT_MOLSTANDARDIZE_EXPORT void chargeParentInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
 
RDKIT_MOLSTANDARDIZE_EXPORT void chargeParentInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
 operates on multiple molecules
 
RDKIT_MOLSTANDARDIZE_EXPORT RWMol * superParent (const RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
 
RDKIT_MOLSTANDARDIZE_EXPORT void superParentInPlace (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
 
RDKIT_MOLSTANDARDIZE_EXPORT void superParentInPlace (std::vector< RWMol * > &mols, int numThreads=1, const CleanupParameters &params=defaultCleanupParameters, bool skip_standardize=false)
 
RDKIT_MOLSTANDARDIZE_EXPORT std::string standardizeSmiles (const std::string &smiles)
 
RDKIT_MOLSTANDARDIZE_EXPORT void disconnectOrganometallics (RWMol &mol, RDKit::MolStandardize::MetalDisconnectorOptions mdo={ true, true, false, true})
 
RDKIT_MOLSTANDARDIZE_EXPORT ROMol * disconnectOrganometallics (const ROMol &mol, RDKit::MolStandardize::MetalDisconnectorOptions mdo={ true, true, false, true})
 As above, but returns new disconnected molecule.
 
void disconnectOrganometallicsInPlace (RWMol &mol, RDKit::MolStandardize::MetalDisconnectorOptions mdo={ true, true, false, true})
 As above, included for API consistency.
 
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::string > enumerateTautomerSmiles (const std::string &smiles, const CleanupParameters &params=defaultCleanupParameters)
 TODO.
 
Normalizer * normalizerFromParams (const CleanupParameters &params)
 
TautomerEnumerator * tautomerEnumeratorFromParams (const CleanupParameters &params)
 
TautomerEnumerator * getV1TautomerEnumerator ()
 
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< Bond::BondType > stringToBondType (std::string bond_str)
 
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< int > stringToCharge (std::string charge_str)
 
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< TautomerTransform > readTautomers (std::string fileName)
 
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< TautomerTransform > readTautomers (std::istream &inStream, int nToRead=-1)
 
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< TautomerTransform > readTautomers (const std::vector< std::tuple< std::string, std::string, std::string, std::string > > &data)
 
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ChemicalReaction > > readTransformations (std::string fileName)
 
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ChemicalReaction > > readTransformations (std::istream &inStream, int nToRead=-1)
 
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ChemicalReaction > > readTransformations (const std::vector< std::pair< std::string, std::string > > &data)
 
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< ValidationErrorInfo > validateSmiles (const std::string &smiles)
 A convenience function for quickly validating a single SMILES string.
 

Variables

RDKIT_MOLSTANDARDIZE_EXPORT const CleanupParameters defaultCleanupParameters
 
RDKIT_MOLSTANDARDIZE_EXPORT std::vector< ChargeCorrection > CHARGE_CORRECTIONS
 
enum RDKIT_MOLSTANDARDIZE_EXPORT PipelineStage
 
enum RDKIT_MOLSTANDARDIZE_EXPORT PARSING_INPUT
 
enum RDKIT_MOLSTANDARDIZE_EXPORT PREPARE_FOR_VALIDATION
 
enum RDKIT_MOLSTANDARDIZE_EXPORT VALIDATION
 
enum RDKIT_MOLSTANDARDIZE_EXPORT PREPARE_FOR_STANDARDIZATION
 
enum RDKIT_MOLSTANDARDIZE_EXPORT STANDARDIZATION
 
enum RDKIT_MOLSTANDARDIZE_EXPORT REAPPLY_WEDGING
 
enum RDKIT_MOLSTANDARDIZE_EXPORT CLEANUP_2D
 
enum RDKIT_MOLSTANDARDIZE_EXPORT MAKE_PARENT
 
enum RDKIT_MOLSTANDARDIZE_EXPORT SERIALIZING_OUTPUT
 
enum RDKIT_MOLSTANDARDIZE_EXPORT COMPLETED
 

Typedef Documentation

◆ AcidBaseCatalog

typedef RDCatalog::HierarchCatalog<AcidBaseCatalogEntry, AcidBaseCatalogParams, int> RDKit::MolStandardize::AcidBaseCatalog

Definition at line 36 of file Charge.h.

◆ FragmentCatalog

typedef RDCatalog::HierarchCatalog<FragmentCatalogEntry, FragmentCatalogParams, int> RDKit::MolStandardize::FragmentCatalog

Definition at line 29 of file Fragment.h.

◆ PipelineLog

using RDKit::MolStandardize::PipelineLog = std::vector<PipelineLogEntry>

Definition at line 141 of file Pipeline.h.

◆ RWMOL_SPTR_PAIR

using RDKit::MolStandardize::RWMOL_SPTR_PAIR = std::pair<RWMOL_SPTR, RWMOL_SPTR>

Definition at line 154 of file Pipeline.h.

◆ SmilesMolPair

typedef std::pair<std::string, ROMOL_SPTR> RDKit::MolStandardize::SmilesMolPair

Definition at line 35 of file Normalize.h.

◆ SmilesTautomerMap

typedef std::map<std::string, Tautomer> RDKit::MolStandardize::SmilesTautomerMap

Definition at line 121 of file MolStandardize/Tautomer.h.

◆ SmilesTautomerPair

typedef std::pair<std::string, Tautomer> RDKit::MolStandardize::SmilesTautomerPair

Definition at line 122 of file MolStandardize/Tautomer.h.

◆ TautomerCatalog

typedef RDCatalog::HierarchCatalog<TautomerCatalogEntry, TautomerCatalogParams, int> RDKit::MolStandardize::TautomerCatalog

Definition at line 33 of file MolStandardize/Tautomer.h.

◆ TautomerTransformDefs

using RDKit::MolStandardize::TautomerTransformDefs
Initial value:
std::vector<std::tuple<std::string, std::string, std::string, std::string>>

Definition at line 24 of file TautomerCatalogParams.h.

◆ TransformCatalog

typedef RDCatalog::HierarchCatalog<TransformCatalogEntry, TransformCatalogParams, int> RDKit::MolStandardize::TransformCatalog

Definition at line 34 of file Normalize.h.

◆ ValidationErrorInfo

using RDKit::MolStandardize::ValidationErrorInfo = std::string

The ValidationErrorInfo class is used to store the information returned by a ValidationMethod validate.

Definition at line 38 of file Validate.h.

Enumeration Type Documentation

◆ TautomerEnumeratorStatus

enum class RDKit::MolStandardize::TautomerEnumeratorStatus
strong
Enumerator
Completed 
MaxTautomersReached 
MaxTransformsReached 
Canceled 

Definition at line 94 of file MolStandardize/Tautomer.h.

Function Documentation

◆ canonicalTautomer()

RDKIT_MOLSTANDARDIZE_EXPORT RWMol * RDKit::MolStandardize::canonicalTautomer ( const RWMol * mol,
const CleanupParameters & params = defaultCleanupParameters )

Works the same as TautomerEnumerator().canonicalize(mol)

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ canonicalTautomerInPlace()

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::canonicalTautomerInPlace ( RWMol & mol,
const CleanupParameters & params = defaultCleanupParameters )

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ chargeParent()

RDKIT_MOLSTANDARDIZE_EXPORT RWMol * RDKit::MolStandardize::chargeParent ( const RWMol & mol,
const CleanupParameters & params = defaultCleanupParameters,
bool skip_standardize = false )

Returns the charge parent of a given molecule. The charge parent is the uncharged version of the fragment parent.

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ chargeParentInPlace() [1/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::chargeParentInPlace ( RWMol & mol,
const CleanupParameters & params = defaultCleanupParameters,
bool skip_standardize = false )

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ chargeParentInPlace() [2/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::chargeParentInPlace ( std::vector< RWMol * > & mols,
int numThreads = 1,
const CleanupParameters & params = defaultCleanupParameters,
bool skip_standardize = false )

operates on multiple molecules

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ cleanup() [1/2]

RWMol * RDKit::MolStandardize::cleanup ( const RWMol & mol,
const CleanupParameters & params = defaultCleanupParameters )
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 102 of file MolStandardize.h.

References cleanup(), and defaultCleanupParameters.

◆ cleanup() [2/2]

RDKIT_MOLSTANDARDIZE_EXPORT RWMol * RDKit::MolStandardize::cleanup ( const RWMol * mol,
const CleanupParameters & params = defaultCleanupParameters )

The cleanup function is equivalent to the molvs.Standardizer().standardize(mol) function. It calls the same steps, namely: RemoveHs, RDKit SanitizeMol, MetalDisconnector, Normalizer, Reionizer, RDKit AssignStereochemistry.

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

Referenced by cleanup().

◆ cleanupInPlace() [1/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::cleanupInPlace ( RWMol & mol,
const CleanupParameters & params = defaultCleanupParameters )

Works the same as cleanup(mol)

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ cleanupInPlace() [2/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::cleanupInPlace ( std::vector< RWMol * > & mols,
int numThreads = 1,
const CleanupParameters & params = defaultCleanupParameters )

Operates on multiple molecules.

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ disconnectOrganometallics() [1/2]

RDKIT_MOLSTANDARDIZE_EXPORT ROMol * RDKit::MolStandardize::disconnectOrganometallics ( const ROMol & mol,
RDKit::MolStandardize::MetalDisconnectorOptions mdo = { true, true, false, true} )

As above, but returns new disconnected molecule.

References RDKIT_MOLSTANDARDIZE_EXPORT.

◆ disconnectOrganometallics() [2/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::disconnectOrganometallics ( RWMol & mol,
RDKit::MolStandardize::MetalDisconnectorOptions mdo = { true, true, false, true} )

Do a disconnection of an organometallic complex according to rules preferred by Syngenta. All bonds to metals are broken, including covalent bonds to Group I/II metals (so including Grignards, lithium complexes etc.). The ligands are left in the charge states they came in with. If there are haptic bonds defined by a dummy atom bonded to a metal by a bond that has a _MolFileBondEndPts (which will contain the indices of the atoms involved in the haptic bond) then the dummy atom is removed also. Do the disconnection in place. The options are splitGrignards, splitAromaticC, adjustCharges and removeHapticDummies. Roll on C++20 and designated initializers!

References RDKIT_MOLSTANDARDIZE_EXPORT.

◆ disconnectOrganometallicsInPlace()

void RDKit::MolStandardize::disconnectOrganometallicsInPlace ( RWMol & mol,
RDKit::MolStandardize::MetalDisconnectorOptions mdo = { true, true, false, true} )
inline

As above, included for API consistency.

Definition at line 265 of file MolStandardize.h.

◆ enumerateTautomerSmiles()

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::string > RDKit::MolStandardize::enumerateTautomerSmiles ( const std::string & smiles,
const CleanupParameters & params = defaultCleanupParameters )

TODO.

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ fragmentParent()

RDKIT_MOLSTANDARDIZE_EXPORT RWMol * RDKit::MolStandardize::fragmentParent ( const RWMol & mol,
const CleanupParameters & params = defaultCleanupParameters,
bool skip_standardize = false )

Returns the fragment parent of a given molecule. The fragment parent is the largest organic covalent unit in the molecule.

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ fragmentParentInPlace() [1/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::fragmentParentInPlace ( RWMol & mol,
const CleanupParameters & params = defaultCleanupParameters,
bool skip_standardize = false )

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ fragmentParentInPlace() [2/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::fragmentParentInPlace ( std::vector< RWMol * > & mols,
int numThreads = 1,
const CleanupParameters & params = defaultCleanupParameters,
bool skip_standardize = false )

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ fragmentRemoverFromParams()

FragmentRemover * RDKit::MolStandardize::fragmentRemoverFromParams ( const CleanupParameters & params,
bool leave_last = true,
bool skip_if_all_match = false )
inline

Definition at line 62 of file Fragment.h.

References RDKit::MolStandardize::CleanupParameters::fragmentData, and RDKit::MolStandardize::CleanupParameters::fragmentFile.

◆ getV1TautomerEnumerator()

TautomerEnumerator * RDKit::MolStandardize::getV1TautomerEnumerator ( )
inline

Definition at line 469 of file MolStandardize/Tautomer.h.

References RDKit::MolStandardize::defaults::defaultTautomerTransformsv1.

◆ isotopeParent()

RDKIT_MOLSTANDARDIZE_EXPORT RWMol * RDKit::MolStandardize::isotopeParent ( const RWMol & mol,
const CleanupParameters & params = defaultCleanupParameters,
bool skip_standardize = false )

removes all isotopes specifications from the given molecule

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ isotopeParentInPlace() [1/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::isotopeParentInPlace ( RWMol & mol,
const CleanupParameters & params = defaultCleanupParameters,
bool skip_standardize = false )

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ isotopeParentInPlace() [2/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::isotopeParentInPlace ( std::vector< RWMol * > & mols,
int numThreads = 1,
const CleanupParameters & params = defaultCleanupParameters,
bool skip_standardize = false )

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ normalize()

RDKIT_MOLSTANDARDIZE_EXPORT RWMol * RDKit::MolStandardize::normalize ( const RWMol * mol,
const CleanupParameters & params = defaultCleanupParameters )

Works the same as Normalizer().normalize(mol)

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ normalizeInPlace() [1/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::normalizeInPlace ( RWMol & mol,
const CleanupParameters & params = defaultCleanupParameters )

Works the same as Normalizer().normalizeInPlace(mol)

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ normalizeInPlace() [2/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::normalizeInPlace ( std::vector< RWMol * > & mols,
int numThreads = 1,
const CleanupParameters & params = defaultCleanupParameters )

Operates on multiple molecules.

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ normalizerFromParams()

Normalizer * RDKit::MolStandardize::normalizerFromParams ( const CleanupParameters & params)
inline

Definition at line 95 of file Normalize.h.

References RDKit::MolStandardize::CleanupParameters::maxRestarts, RDKit::MolStandardize::CleanupParameters::normalizationData, and RDKit::MolStandardize::CleanupParameters::normalizations.

◆ readFuncGroups() [1/3]

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ROMol > > RDKit::MolStandardize::readFuncGroups ( const std::vector< std::pair< std::string, std::string > > & data)

References RDKIT_MOLSTANDARDIZE_EXPORT.

◆ readFuncGroups() [2/3]

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ROMol > > RDKit::MolStandardize::readFuncGroups ( std::istream & inStream,
int nToRead = -1 )

References RDKIT_MOLSTANDARDIZE_EXPORT.

◆ readFuncGroups() [3/3]

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ROMol > > RDKit::MolStandardize::readFuncGroups ( std::string fileName)

References RDKIT_MOLSTANDARDIZE_EXPORT.

◆ readPairs() [1/3]

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > RDKit::MolStandardize::readPairs ( const std::vector< std::tuple< std::string, std::string, std::string > > & data)

◆ readPairs() [2/3]

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > RDKit::MolStandardize::readPairs ( std::istream & inStream,
int nToRead = -1 )

References RDKIT_MOLSTANDARDIZE_EXPORT.

◆ readPairs() [3/3]

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > RDKit::MolStandardize::readPairs ( std::string fileName)

References RDKIT_MOLSTANDARDIZE_EXPORT.

◆ readTautomers() [1/3]

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< TautomerTransform > RDKit::MolStandardize::readTautomers ( const std::vector< std::tuple< std::string, std::string, std::string, std::string > > & data)

References RDKIT_MOLSTANDARDIZE_EXPORT.

◆ readTautomers() [2/3]

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< TautomerTransform > RDKit::MolStandardize::readTautomers ( std::istream & inStream,
int nToRead = -1 )

References RDKIT_MOLSTANDARDIZE_EXPORT.

◆ readTautomers() [3/3]

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< TautomerTransform > RDKit::MolStandardize::readTautomers ( std::string fileName)

References RDKIT_MOLSTANDARDIZE_EXPORT.

◆ readTransformations() [1/3]

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ChemicalReaction > > RDKit::MolStandardize::readTransformations ( const std::vector< std::pair< std::string, std::string > > & data)

◆ readTransformations() [2/3]

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ChemicalReaction > > RDKit::MolStandardize::readTransformations ( std::istream & inStream,
int nToRead = -1 )

References RDKIT_MOLSTANDARDIZE_EXPORT.

◆ readTransformations() [3/3]

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ChemicalReaction > > RDKit::MolStandardize::readTransformations ( std::string fileName)

References RDKIT_MOLSTANDARDIZE_EXPORT.

◆ reionize()

RDKIT_MOLSTANDARDIZE_EXPORT RWMol * RDKit::MolStandardize::reionize ( const RWMol * mol,
const CleanupParameters & params = defaultCleanupParameters )

Works the same as Reionizer().reionize(mol)

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ reionizeInPlace() [1/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::reionizeInPlace ( RWMol & mol,
const CleanupParameters & params = defaultCleanupParameters )

Works the same as Reionizer().reionizeInPlace(mol)

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ reionizeInPlace() [2/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::reionizeInPlace ( std::vector< RWMol * > & mols,
int numThreads = 1,
const CleanupParameters & params = defaultCleanupParameters )

Operates on multiple molecules.

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ reionizerFromParams()

Reionizer * RDKit::MolStandardize::reionizerFromParams ( const CleanupParameters & params)
inline

Definition at line 106 of file Charge.h.

References RDKit::MolStandardize::CleanupParameters::acidbaseData, and RDKit::MolStandardize::CleanupParameters::acidbaseFile.

◆ removeFragments()

RDKIT_MOLSTANDARDIZE_EXPORT RWMol * RDKit::MolStandardize::removeFragments ( const RWMol * mol,
const CleanupParameters & params = defaultCleanupParameters )

Works the same as FragmentRemover().remove(mol)

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ removeFragmentsInPlace() [1/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::removeFragmentsInPlace ( RWMol & mol,
const CleanupParameters & params = defaultCleanupParameters )

Works the same as FragmentRemover().removeInPlace(mol)

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ removeFragmentsInPlace() [2/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::removeFragmentsInPlace ( std::vector< RWMol * > & mols,
int numThreads = 1,
const CleanupParameters & params = defaultCleanupParameters )

Operates on multiple molecules.

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ standardizeSmiles()

RDKIT_MOLSTANDARDIZE_EXPORT std::string RDKit::MolStandardize::standardizeSmiles ( const std::string & smiles)

Convenience function for quickly standardizing a single SMILES string. Returns a standardized canonical SMILES string given a SMILES string. This is the equivalent of calling cleanup() on each of the molecules

References RDKIT_MOLSTANDARDIZE_EXPORT.

◆ stereoParent()

RDKIT_MOLSTANDARDIZE_EXPORT RWMol * RDKit::MolStandardize::stereoParent ( const RWMol & mol,
const CleanupParameters & params = defaultCleanupParameters,
bool skip_standardize = false )

calls removeStereochemistry() on the given molecule

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ stereoParentInPlace() [1/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::stereoParentInPlace ( RWMol & mol,
const CleanupParameters & params = defaultCleanupParameters,
bool skip_standardize = false )

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ stereoParentInPlace() [2/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::stereoParentInPlace ( std::vector< RWMol * > & mols,
int numThreads = 1,
const CleanupParameters & params = defaultCleanupParameters,
bool skip_standardize = false )

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ stringToBondType()

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< Bond::BondType > RDKit::MolStandardize::stringToBondType ( std::string bond_str)

References RDKIT_MOLSTANDARDIZE_EXPORT.

◆ stringToCharge()

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< int > RDKit::MolStandardize::stringToCharge ( std::string charge_str)

References RDKIT_MOLSTANDARDIZE_EXPORT.

◆ superParent()

RDKIT_MOLSTANDARDIZE_EXPORT RWMol * RDKit::MolStandardize::superParent ( const RWMol & mol,
const CleanupParameters & params = defaultCleanupParameters,
bool skip_standardize = false )

Returns the super parent. The super parent is the fragment, charge, isotope, stereo, and tautomer parent of the molecule.

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ superParentInPlace() [1/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::superParentInPlace ( RWMol & mol,
const CleanupParameters & params = defaultCleanupParameters,
bool skip_standardize = false )

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ superParentInPlace() [2/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::superParentInPlace ( std::vector< RWMol * > & mols,
int numThreads = 1,
const CleanupParameters & params = defaultCleanupParameters,
bool skip_standardize = false )

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ tautomerEnumeratorFromParams()

TautomerEnumerator * RDKit::MolStandardize::tautomerEnumeratorFromParams ( const CleanupParameters & params)
inline

Definition at line 464 of file MolStandardize/Tautomer.h.

◆ tautomerParent()

RDKIT_MOLSTANDARDIZE_EXPORT RWMol * RDKit::MolStandardize::tautomerParent ( const RWMol & mol,
const CleanupParameters & params = defaultCleanupParameters,
bool skipStandardize = false )

Returns the tautomer parent of a given molecule. The fragment parent is the standardized canonical tautomer of the molecule

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ tautomerParentInPlace() [1/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::tautomerParentInPlace ( RWMol & mol,
const CleanupParameters & params = defaultCleanupParameters,
bool skipStandardize = false )

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ tautomerParentInPlace() [2/2]

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::tautomerParentInPlace ( std::vector< RWMol * > & mols,
int numThreads = 1,
const CleanupParameters & params = defaultCleanupParameters,
bool skipStandardize = false )

References defaultCleanupParameters, and RDKIT_MOLSTANDARDIZE_EXPORT.

◆ updateCleanupParamsFromJSON()

RDKIT_MOLSTANDARDIZE_EXPORT void RDKit::MolStandardize::updateCleanupParamsFromJSON ( CleanupParameters & params,
const std::string & json )

References RDKIT_MOLSTANDARDIZE_EXPORT.

◆ validateSmiles()

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< ValidationErrorInfo > RDKit::MolStandardize::validateSmiles ( const std::string & smiles)

A convenience function for quickly validating a single SMILES string.

References RDKIT_MOLSTANDARDIZE_EXPORT.

Variable Documentation

◆ CHARGE_CORRECTIONS

RDKIT_MOLSTANDARDIZE_EXPORT std::vector<ChargeCorrection> RDKit::MolStandardize::CHARGE_CORRECTIONS
extern

◆ CLEANUP_2D

enum RDKIT_MOLSTANDARDIZE_EXPORT RDKit::MolStandardize::CLEANUP_2D

Definition at line 130 of file Pipeline.h.

◆ COMPLETED

enum RDKIT_MOLSTANDARDIZE_EXPORT RDKit::MolStandardize::COMPLETED

Definition at line 133 of file Pipeline.h.

◆ defaultCleanupParameters

RDKIT_MOLSTANDARDIZE_EXPORT const CleanupParameters RDKit::MolStandardize::defaultCleanupParameters
extern

Definition at line 25 of file Fragment.h.

Referenced by canonicalTautomer(), canonicalTautomerInPlace(), chargeParent(), chargeParentInPlace(), chargeParentInPlace(), cleanup(), cleanup(), cleanupInPlace(), cleanupInPlace(), enumerateTautomerSmiles(), fragmentParent(), fragmentParentInPlace(), fragmentParentInPlace(), isotopeParent(), isotopeParentInPlace(), isotopeParentInPlace(), normalize(), normalizeInPlace(), normalizeInPlace(), reionize(), reionizeInPlace(), reionizeInPlace(), removeFragments(), removeFragmentsInPlace(), removeFragmentsInPlace(), stereoParent(), stereoParentInPlace(), stereoParentInPlace(), superParent(), superParentInPlace(), superParentInPlace(), tautomerParent(), tautomerParentInPlace(), and tautomerParentInPlace().

◆ MAKE_PARENT

enum RDKIT_MOLSTANDARDIZE_EXPORT RDKit::MolStandardize::MAKE_PARENT

Definition at line 131 of file Pipeline.h.

◆ PARSING_INPUT

enum RDKIT_MOLSTANDARDIZE_EXPORT RDKit::MolStandardize::PARSING_INPUT

Definition at line 124 of file Pipeline.h.

◆ PipelineStage

enum RDKIT_MOLSTANDARDIZE_EXPORT RDKit::MolStandardize::PipelineStage
strong

Definition at line 122 of file Pipeline.h.

◆ PREPARE_FOR_STANDARDIZATION

enum RDKIT_MOLSTANDARDIZE_EXPORT RDKit::MolStandardize::PREPARE_FOR_STANDARDIZATION

Definition at line 127 of file Pipeline.h.

◆ PREPARE_FOR_VALIDATION

enum RDKIT_MOLSTANDARDIZE_EXPORT RDKit::MolStandardize::PREPARE_FOR_VALIDATION

Definition at line 125 of file Pipeline.h.

◆ REAPPLY_WEDGING

enum RDKIT_MOLSTANDARDIZE_EXPORT RDKit::MolStandardize::REAPPLY_WEDGING

Definition at line 129 of file Pipeline.h.

◆ SERIALIZING_OUTPUT

enum RDKIT_MOLSTANDARDIZE_EXPORT RDKit::MolStandardize::SERIALIZING_OUTPUT

Definition at line 132 of file Pipeline.h.

◆ STANDARDIZATION

enum RDKIT_MOLSTANDARDIZE_EXPORT RDKit::MolStandardize::STANDARDIZATION

Definition at line 128 of file Pipeline.h.

◆ VALIDATION

enum RDKIT_MOLSTANDARDIZE_EXPORT RDKit::MolStandardize::VALIDATION

Definition at line 126 of file Pipeline.h.