Namespaces
	TautomerScoringFunctions

Classes
class	AcidBaseCatalogEntry

class	AcidBaseCatalogParams

struct	ChargeCorrection

class	Reionizer
	The reionizer class to fix charges and reionize a molecule such that the. More...

class	Uncharger
	The Uncharger class for neutralizing ionized acids and bases. More...

class	FragmentRemover

class	LargestFragmentChooser

class	FragmentCatalogEntry

class	FragmentCatalogParams

class	MetalDisconnector

struct	CleanupParameters
	The CleanupParameters structure defines the default parameters for the. More...

class	Normalizer
	The Normalizer class for applying Normalization transforms. More...

class	Tautomer

class	TautomerEnumeratorResult
	Contains results of tautomer enumeration. More...

class	TautomerEnumeratorCallback

class	TautomerEnumerator

class	TautomerCatalogEntry

class	TautomerCatalogParams

class	TautomerTransform

class	TransformCatalogEntry

class	TransformCatalogParams

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

class	ValidationMethod
	The ValidationMethod class is the abstract base class upon which all the. More...

class	RDKitValidation
	The RDKitValidation class throws an error when there are no atoms in the. More...

class	MolVSValidations
	The MolVSValidations class includes most of the same validations as. More...

class	NoAtomValidation
	The NoAtomValidation class throws an error if no atoms are present in the. More...

class	FragmentValidation
	The FragmentValidation class logs if certain fragments are present. More...

class	NeutralValidation
	The NeutralValidation class logs if not an overall neutral system. More...

class	IsotopeValidation
	The IsotopeValidation class logs if molecule contains isotopes. More...

class	MolVSValidation
	The MolVSValidation class can be used to perform all MolVSValidions. More...

class	AllowedAtomsValidation

class	DisallowedAtomsValidation

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

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

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

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

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::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 RWMol *	cleanup (const RWMol &mol, const CleanupParameters &params=defaultCleanupParameters)
	The cleanup function is equivalent to the. More...

RDKIT_MOLSTANDARDIZE_EXPORT void	tautomerParent (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters)
	TODO not yet finished! More...

RDKIT_MOLSTANDARDIZE_EXPORT RWMol *	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. More...

RDKIT_MOLSTANDARDIZE_EXPORT void	stereoParent (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters)

RDKIT_MOLSTANDARDIZE_EXPORT void	isotopeParent (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters)

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

RDKIT_MOLSTANDARDIZE_EXPORT void	superParent (RWMol &mol, const CleanupParameters &params=defaultCleanupParameters)

RDKIT_MOLSTANDARDIZE_EXPORT RWMol *	normalize (const RWMol *mol, const CleanupParameters &params=defaultCleanupParameters)
	Works the same as Normalizer().normalize(mol) More...

RDKIT_MOLSTANDARDIZE_EXPORT RWMol *	reionize (const RWMol *mol, const CleanupParameters &params=defaultCleanupParameters)
	Works the same as Reionizer().reionize(mol) More...

RDKIT_MOLSTANDARDIZE_EXPORT std::string	standardizeSmiles (const std::string &smiles)
	Convenience function for quickly standardizing a single SMILES string. More...

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< std::string >	enumerateTautomerSmiles (const std::string &smiles, const CleanupParameters &params=defaultCleanupParameters)
	TODO. More...

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< 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< ValidationErrorInfo >	validateSmiles (const std::string &smiles)
	A convenience function for quickly validating a single SMILES string. More...

Variables
RDKIT_MOLSTANDARDIZE_EXPORT const CleanupParameters	defaultCleanupParameters

RDKIT_MOLSTANDARDIZE_EXPORT std::vector< ChargeCorrection >	CHARGE_CORRECTIONS

Typedef Documentation

◆ AcidBaseCatalog

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

Definition at line 35 of file Charge.h.

◆ FragmentCatalog

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

Definition at line 29 of file Fragment.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 71 of file MolStandardize/Tautomer.h.

◆ SmilesTautomerPair

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

Definition at line 72 of file MolStandardize/Tautomer.h.

◆ TautomerCatalog

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

Definition at line 32 of file MolStandardize/Tautomer.h.

◆ TransformCatalog

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

Definition at line 34 of file Normalize.h.

Enumeration Type Documentation

◆ TautomerEnumeratorStatus

enum RDKit::MolStandardize::TautomerEnumeratorStatus

strong

Enumerator
Completed
MaxTautomersReached
MaxTransformsReached
Canceled

Definition at line 46 of file MolStandardize/Tautomer.h.

Function Documentation

◆ 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

◆ cleanup()

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

The cleanup function is equivalent to the.

◆ 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.

◆ isotopeParent()

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

◆ normalize()

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

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

◆ readFuncGroups() [1/2]

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

◆ readFuncGroups() [2/2]

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

◆ readPairs() [1/2]

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

◆ readPairs() [2/2]

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

◆ readTautomers() [1/2]

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

◆ readTautomers() [2/2]

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

◆ readTransformations() [1/2]

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

◆ readTransformations() [2/2]

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)

◆ standardizeSmiles()

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

Convenience function for quickly standardizing a single SMILES string.

◆ stereoParent()

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

◆ 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 void RDKit::MolStandardize::superParent	(	RWMol &	mol,
		const CleanupParameters &	params = `defaultCleanupParameters`
	)

◆ tautomerParent()

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

TODO not yet finished!

◆ 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

◆ defaultCleanupParameters

RDKIT_MOLSTANDARDIZE_EXPORT const CleanupParameters RDKit::MolStandardize::defaultCleanupParameters