RDKit::MolFragmenter Namespace Reference

Classes
struct	FragmenterBondType

Functions
RDKIT_CHEMTRANSFORMS_EXPORT ROMol *	fragmentOnBonds (const ROMol &mol, const std::vector< unsigned int > &bondIndices, bool addDummies=true, const std::vector< std::pair< unsigned int, unsigned int > > *dummyLabels=nullptr, const std::vector< Bond::BondType > *bondTypes=nullptr, std::vector< unsigned int > *nCutsPerAtom=nullptr)
	Fragments a molecule by breaking a set of bonds.
RDKIT_CHEMTRANSFORMS_EXPORT ROMol *	fragmentOnBonds (const ROMol &mol, const std::vector< FragmenterBondType > &bondPatterns, const std::map< unsigned int, ROMOL_SPTR > *atomEnvirons=nullptr, std::vector< unsigned int > *nCutsPerAtom=nullptr)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_CHEMTRANSFORMS_EXPORT void	fragmentOnSomeBonds (const ROMol &mol, const std::vector< unsigned int > &bondIndices, std::vector< ROMOL_SPTR > &resMols, unsigned int maxToCut=1, bool addDummies=true, const std::vector< std::pair< unsigned int, unsigned int > > *dummyLabels=nullptr, const std::vector< Bond::BondType > *bondTypes=nullptr, std::vector< std::vector< unsigned int > > *nCutsPerAtom=nullptr)
RDKIT_CHEMTRANSFORMS_EXPORT ROMol *	fragmentOnBRICSBonds (const ROMol &mol)
	Fragments a molecule by breaking all BRICS bonds.
RDKIT_CHEMTRANSFORMS_EXPORT void	constructFragmenterAtomTypes (std::istream *inStream, std::map< unsigned int, std::string > &defs, const std::string &comment="//", bool validate=true, std::map< unsigned int, ROMOL_SPTR > *environs=nullptr)
RDKIT_CHEMTRANSFORMS_EXPORT void	constructFragmenterAtomTypes (const std::string &str, std::map< unsigned int, std::string > &defs, const std::string &comment="//", bool validate=true, std::map< unsigned int, ROMOL_SPTR > *environs=nullptr)
RDKIT_CHEMTRANSFORMS_EXPORT void	constructBRICSAtomTypes (std::map< unsigned int, std::string > &defs, std::map< unsigned int, ROMOL_SPTR > *environs=nullptr)
RDKIT_CHEMTRANSFORMS_EXPORT void	constructFragmenterBondTypes (std::istream *inStream, const std::map< unsigned int, std::string > &atomTypes, std::vector< FragmenterBondType > &defs, const std::string &comment="//", bool validate=true, bool labelByConnector=true)
RDKIT_CHEMTRANSFORMS_EXPORT void	constructFragmenterBondTypes (const std::string &str, const std::map< unsigned int, std::string > &atomTypes, std::vector< FragmenterBondType > &defs, const std::string &comment="//", bool validate=true, bool labelByConnector=true)
RDKIT_CHEMTRANSFORMS_EXPORT void	constructBRICSBondTypes (std::vector< FragmenterBondType > &defs)

Function Documentation

constructBRICSAtomTypes()

RDKIT_CHEMTRANSFORMS_EXPORT void RDKit::MolFragmenter::constructBRICSAtomTypes	(	std::map< unsigned int, std::string > &	defs,
		std::map< unsigned int, ROMOL_SPTR > *	environs = nullptr
	)

constructBRICSBondTypes()

RDKIT_CHEMTRANSFORMS_EXPORT void RDKit::MolFragmenter::constructBRICSBondTypes

(

std::vector< FragmenterBondType > &

defs

)

constructFragmenterAtomTypes() [1/2]

RDKIT_CHEMTRANSFORMS_EXPORT void RDKit::MolFragmenter::constructFragmenterAtomTypes	(	const std::string &	str,
		std::map< unsigned int, std::string > &	defs,
		const std::string &	comment = "//",
		bool	validate = true,
		std::map< unsigned int, ROMOL_SPTR > *	environs = nullptr
	)

constructFragmenterAtomTypes() [2/2]

RDKIT_CHEMTRANSFORMS_EXPORT void RDKit::MolFragmenter::constructFragmenterAtomTypes	(	std::istream *	inStream,
		std::map< unsigned int, std::string > &	defs,
		const std::string &	comment = "//",
		bool	validate = true,
		std::map< unsigned int, ROMOL_SPTR > *	environs = nullptr
	)

constructFragmenterBondTypes() [1/2]

RDKIT_CHEMTRANSFORMS_EXPORT void RDKit::MolFragmenter::constructFragmenterBondTypes	(	const std::string &	str,
		const std::map< unsigned int, std::string > &	atomTypes,
		std::vector< FragmenterBondType > &	defs,
		const std::string &	comment = "//",
		bool	validate = true,
		bool	labelByConnector = true
	)

constructFragmenterBondTypes() [2/2]

RDKIT_CHEMTRANSFORMS_EXPORT void RDKit::MolFragmenter::constructFragmenterBondTypes	(	std::istream *	inStream,
		const std::map< unsigned int, std::string > &	atomTypes,
		std::vector< FragmenterBondType > &	defs,
		const std::string &	comment = "//",
		bool	validate = true,
		bool	labelByConnector = true
	)

fragmentOnBonds() [1/2]

RDKIT_CHEMTRANSFORMS_EXPORT ROMol * RDKit::MolFragmenter::fragmentOnBonds	(	const ROMol &	mol,
		const std::vector< FragmenterBondType > &	bondPatterns,
		const std::map< unsigned int, ROMOL_SPTR > *	atomEnvirons = nullptr,
		std::vector< unsigned int > *	nCutsPerAtom = nullptr
	)

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

fragmentOnBonds() [2/2]

RDKIT_CHEMTRANSFORMS_EXPORT ROMol * RDKit::MolFragmenter::fragmentOnBonds	(	const ROMol &	mol,
		const std::vector< unsigned int > &	bondIndices,
		bool	addDummies = true,
		const std::vector< std::pair< unsigned int, unsigned int > > *	dummyLabels = nullptr,
		const std::vector< Bond::BondType > *	bondTypes = nullptr,
		std::vector< unsigned int > *	nCutsPerAtom = nullptr
	)

Fragments a molecule by breaking a set of bonds.

Parameters

mol	- the molecule to be modified
bondIndices	- indices of the bonds to be broken

optional:

Parameters

addDummies	- toggles addition of dummy atoms to indicate where bonds were broken
dummyLabels	- used to provide the labels to be used for the dummies. the first element in each pair is the label for the dummy that replaces the bond's beginAtom, the second is for the dummy that replaces the bond's endAtom. If not provided, the dummies are labeled with atom indices.
bondTypes	- used to provide the bond type to use between the fragments and the dummy atoms. If not provided, defaults to single.
nCutsPerAtom	- used to return the number of bonds that were cut at each atom. Should be nAtoms long.

Returns

a new ROMol with the modifications The client is responsible for deleting this molecule.

fragmentOnBRICSBonds()

RDKIT_CHEMTRANSFORMS_EXPORT ROMol * RDKit::MolFragmenter::fragmentOnBRICSBonds

(

const ROMol &

mol

)

Fragments a molecule by breaking all BRICS bonds.

Returns

a new ROMol with the modifications The client is responsible for deleting this molecule.

fragmentOnSomeBonds()

RDKIT_CHEMTRANSFORMS_EXPORT void RDKit::MolFragmenter::fragmentOnSomeBonds	(	const ROMol &	mol,
		const std::vector< unsigned int > &	bondIndices,
		std::vector< ROMOL_SPTR > &	resMols,
		unsigned int	maxToCut = 1,
		bool	addDummies = true,
		const std::vector< std::pair< unsigned int, unsigned int > > *	dummyLabels = nullptr,
		const std::vector< Bond::BondType > *	bondTypes = nullptr,
		std::vector< std::vector< unsigned int > > *	nCutsPerAtom = nullptr
	)