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 = std::vector< std::tuple< std::string, std::string, std::string, std::string > >
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 = typedef std::vector<PipelineLogEntry>

Definition at line 141 of file Pipeline.h.

RWMOL_SPTR_PAIR

using RDKit::MolStandardize::RWMOL_SPTR_PAIR = typedef 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 = typedef std::vector<std::tuple<std::string, std::string, std::string, std::string> >

Definition at line 27 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 = typedef std::string

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

Definition at line 39 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)

canonicalTautomerInPlace()

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

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.

chargeParentInPlace() [1/2]

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

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

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().

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.

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)

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.

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.

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!

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.

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.

fragmentParentInPlace() [1/2]

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

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
	)

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, RDKit::MolStandardize::CleanupParameters::fragmentFile, and RDKit::rdvalue_is().

getV1TautomerEnumerator()

TautomerEnumerator * RDKit::MolStandardize::getV1TautomerEnumerator ( )

inline

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

References RDKit::MolStandardize::defaults::defaultTautomerTransformsv1, and RDKit::rdvalue_is().

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

isotopeParentInPlace() [1/2]

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

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
	)

normalize()

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

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

normalizeInPlace() [1/2]

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

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

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.

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

)

readFuncGroups() [2/3]

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

readFuncGroups() [3/3]

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ROMol > > RDKit::MolStandardize::readFuncGroups

(

std::string

fileName

)

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
	)

readPairs() [3/3]

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > RDKit::MolStandardize::readPairs

(

std::string

fileName

)

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

)

readTautomers() [2/3]

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

readTautomers() [3/3]

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< TautomerTransform > RDKit::MolStandardize::readTautomers

(

std::string

fileName

)

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
	)

readTransformations() [3/3]

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::shared_ptr< ChemicalReaction > > RDKit::MolStandardize::readTransformations

(

std::string

fileName

)

reionize()

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

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

reionizeInPlace() [1/2]

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

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

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.

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)

removeFragmentsInPlace() [1/2]

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

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

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.

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

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

stereoParentInPlace() [1/2]

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

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
	)

stringToBondType()

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< Bond::BondType > RDKit::MolStandardize::stringToBondType

(

std::string

bond_str

)

stringToCharge()

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< int > RDKit::MolStandardize::stringToCharge

(

std::string

charge_str

)

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.

superParentInPlace() [1/2]

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

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
	)

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

tautomerParentInPlace() [1/2]

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

tautomerParentInPlace() [2/2]

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

updateCleanupParamsFromJSON()

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

validateSmiles()

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< ValidationErrorInfo > RDKit::MolStandardize::validateSmiles

(

const std::string &

smiles

)

A convenience function for quickly validating a single SMILES string.

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.

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.