RDKit::FileParserUtils Namespace Reference

Functions
RDKIT_FILEPARSERS_EXPORT std::string_view	strip (std::string_view orig, std::string stripChars=" \t\r\n")
template<typename T >
T	stripSpacesAndCast (std::string_view input, bool acceptSpaces=false)
template<typename T >
T	stripSpacesAndCast (const std::string &input, bool acceptSpaces=false)
RDKIT_FILEPARSERS_EXPORT int	toInt (const std::string &input, bool acceptSpaces=true)
RDKIT_FILEPARSERS_EXPORT unsigned int	toUnsigned (const std::string &input, bool acceptSpaces=true)
RDKIT_FILEPARSERS_EXPORT double	toDouble (const std::string &input, bool acceptSpaces=true)
RDKIT_FILEPARSERS_EXPORT int	toInt (const std::string_view input, bool acceptSpaces=true)
RDKIT_FILEPARSERS_EXPORT unsigned int	toUnsigned (std::string_view input, bool acceptSpaces=true)
RDKIT_FILEPARSERS_EXPORT double	toDouble (const std::string_view input, bool acceptSpaces=true)
RDKIT_FILEPARSERS_EXPORT std::string	getV3000CTAB (const ROMol &tmol, int confId=-1)
RDKIT_FILEPARSERS_EXPORT std::string	getV3000Line (std::istream *inStream, unsigned int &line)
RDKIT_FILEPARSERS_EXPORT bool	ParseV3000CTAB (std::istream *inStream, unsigned int &line, RWMol *mol, Conformer *&conf, bool &chiralityPossible, unsigned int &nAtoms, unsigned int &nBonds, bool strictParsing=true, bool expectMEND=true)
RDKIT_FILEPARSERS_EXPORT bool	ParseV2000CTAB (std::istream *inStream, unsigned int &line, RWMol *mol, Conformer *&conf, bool &chiralityPossible, unsigned int &nAtoms, unsigned int &nBonds, bool strictParsing=true)
RDKIT_FILEPARSERS_EXPORT void	finishMolProcessing (RWMol *res, bool chiralityPossible, bool sanitize, bool removeHs)
RDKIT_FILEPARSERS_EXPORT Atom *	replaceAtomWithQueryAtom (RWMol *mol, Atom *atom)
	Deprecated, please use QueryOps::replaceAtomWithQueryAtom instead. More...
template<typename T >
void	applyMolListPropToAtoms (ROMol &mol, const std::string &pn, const std::string &prefix, const std::string &missingValueMarker="n/a")
	applies a particular property to the atoms as an atom property list More...
template<typename T >
void	applyMolListPropsToAtoms (ROMol &mol, const std::string &prefix, const std::string missingValueMarker="n/a")
void	processMolPropertyList (ROMol &mol, const std::string pn, const std::string &missingValueMarker="n/a")
void	processMolPropertyLists (ROMol &mol, const std::string &missingValueMarker="n/a")
template<typename T >
std::string	getAtomPropertyList (ROMol &mol, const std::string &atomPropName, std::string missingValueMarker="", unsigned int lineSize=190)
void	createAtomIntPropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=190)
void	createAtomDoublePropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=190)
void	createAtomBoolPropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=190)
void	createAtomStringPropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=190)

Variables
static const std::string	atomPropPrefix = "atom."

Function Documentation

applyMolListPropsToAtoms()

template<typename T >

void RDKit::FileParserUtils::applyMolListPropsToAtoms	(	ROMol &	mol,
		const std::string &	prefix,
		const std::string	missingValueMarker = "n/a"
	)

applies all properties matching a particular prefix as an atom property list

Definition at line 141 of file FileParserUtils.h.

References RDKit::RDProps::getPropList().

applyMolListPropToAtoms()

template<typename T >

void RDKit::FileParserUtils::applyMolListPropToAtoms	(	ROMol &	mol,
		const std::string &	pn,
		const std::string &	prefix,
		const std::string &	missingValueMarker = "n/a"
	)

applies a particular property to the atoms as an atom property list

Definition at line 98 of file FileParserUtils.h.

References BOOST_LOG, RDKit::ROMol::getAtomWithIdx(), RDKit::ROMol::getNumAtoms(), RDKit::RDProps::getProp(), rdWarningLog, and RDKit::RDProps::setProp().

createAtomBoolPropertyList()

void RDKit::FileParserUtils::createAtomBoolPropertyList ( ROMol &  mol, const std::string &  atomPropName, const std::string &  missingValueMarker = "", unsigned int  lineSize = 190  )

inline

Definition at line 236 of file FileParserUtils.h.

References RDKit::RDProps::setProp().

createAtomDoublePropertyList()

void RDKit::FileParserUtils::createAtomDoublePropertyList ( ROMol &  mol, const std::string &  atomPropName, const std::string &  missingValueMarker = "", unsigned int  lineSize = 190  )

inline

Definition at line 228 of file FileParserUtils.h.

References RDKit::RDProps::setProp().

createAtomIntPropertyList()

void RDKit::FileParserUtils::createAtomIntPropertyList ( ROMol &  mol, const std::string &  atomPropName, const std::string &  missingValueMarker = "", unsigned int  lineSize = 190  )

inline

Definition at line 220 of file FileParserUtils.h.

References RDKit::RDProps::setProp().

createAtomStringPropertyList()

void RDKit::FileParserUtils::createAtomStringPropertyList ( ROMol &  mol, const std::string &  atomPropName, const std::string &  missingValueMarker = "", unsigned int  lineSize = 190  )

inline

Definition at line 244 of file FileParserUtils.h.

References RDKit::RDProps::setProp().

finishMolProcessing()

RDKIT_FILEPARSERS_EXPORT void RDKit::FileParserUtils::finishMolProcessing	(	RWMol *	res,
		bool	chiralityPossible,
		bool	sanitize,
		bool	removeHs
	)

finishes up the processing (sanitization, etc.) of a molecule read from CTAB

getAtomPropertyList()

template<typename T >

std::string RDKit::FileParserUtils::getAtomPropertyList	(	ROMol &	mol,
		const std::string &	atomPropName,
		std::string	missingValueMarker = "",
		unsigned int	lineSize = 190
	)

Definition at line 187 of file FileParserUtils.h.

References RDKit::ROMol::atoms().

getV3000CTAB()

RDKIT_FILEPARSERS_EXPORT std::string RDKit::FileParserUtils::getV3000CTAB	(	const ROMol &	tmol,
		int	confId = -1
	)

getV3000Line()

RDKIT_FILEPARSERS_EXPORT std::string RDKit::FileParserUtils::getV3000Line	(	std::istream *	inStream,
		unsigned int &	line
	)

ParseV2000CTAB()

RDKIT_FILEPARSERS_EXPORT bool RDKit::FileParserUtils::ParseV2000CTAB	(	std::istream *	inStream,
		unsigned int &	line,
		RWMol *	mol,
		Conformer *&	conf,
		bool &	chiralityPossible,
		unsigned int &	nAtoms,
		unsigned int &	nBonds,
		bool	strictParsing = true
	)

ParseV3000CTAB()

RDKIT_FILEPARSERS_EXPORT bool RDKit::FileParserUtils::ParseV3000CTAB	(	std::istream *	inStream,
		unsigned int &	line,
		RWMol *	mol,
		Conformer *&	conf,
		bool &	chiralityPossible,
		unsigned int &	nAtoms,
		unsigned int &	nBonds,
		bool	strictParsing = true,
		bool	expectMEND = true
	)

processMolPropertyList()

void RDKit::FileParserUtils::processMolPropertyList ( ROMol &  mol, const std::string  pn, const std::string &  missingValueMarker = "n/a"  )

inline

if the property name matches our rules for atom property lists, we'll apply it to the atoms

Definition at line 152 of file FileParserUtils.h.

References atomPropPrefix.

Referenced by processMolPropertyLists().

processMolPropertyLists()

void RDKit::FileParserUtils::processMolPropertyLists ( ROMol &  mol, const std::string &  missingValueMarker = "n/a"  )

inline

loops over all properties and applies the ones that match the rules for atom property lists to the atoms

Definition at line 180 of file FileParserUtils.h.

References RDKit::RDProps::getPropList(), and processMolPropertyList().

replaceAtomWithQueryAtom()

RDKIT_FILEPARSERS_EXPORT Atom * RDKit::FileParserUtils::replaceAtomWithQueryAtom	(	RWMol *	mol,
		Atom *	atom
	)

Deprecated, please use QueryOps::replaceAtomWithQueryAtom instead.

strip()

RDKIT_FILEPARSERS_EXPORT std::string_view RDKit::FileParserUtils::strip ( std::string_view  orig, std::string  stripChars = " \t\r\n"  )

inline

Definition at line 29 of file FileParserUtils.h.

Referenced by stripSpacesAndCast().

stripSpacesAndCast() [1/2]

template<typename T >

T RDKit::FileParserUtils::stripSpacesAndCast	(	const std::string &	input,
		bool	acceptSpaces = false
	)

Definition at line 52 of file FileParserUtils.h.

stripSpacesAndCast() [2/2]

template<typename T >

T RDKit::FileParserUtils::stripSpacesAndCast	(	std::string_view	input,
		bool	acceptSpaces = false
	)

Definition at line 43 of file FileParserUtils.h.

References strip().

toDouble() [1/2]

RDKIT_FILEPARSERS_EXPORT double RDKit::FileParserUtils::toDouble	(	const std::string &	input,
		bool	acceptSpaces = true
	)

toDouble() [2/2]

RDKIT_FILEPARSERS_EXPORT double RDKit::FileParserUtils::toDouble	(	const std::string_view	input,
		bool	acceptSpaces = true
	)

toInt() [1/2]

RDKIT_FILEPARSERS_EXPORT int RDKit::FileParserUtils::toInt	(	const std::string &	input,
		bool	acceptSpaces = true
	)

toInt() [2/2]

RDKIT_FILEPARSERS_EXPORT int RDKit::FileParserUtils::toInt	(	const std::string_view	input,
		bool	acceptSpaces = true
	)

toUnsigned() [1/2]

RDKIT_FILEPARSERS_EXPORT unsigned int RDKit::FileParserUtils::toUnsigned	(	const std::string &	input,
		bool	acceptSpaces = true
	)

toUnsigned() [2/2]

RDKIT_FILEPARSERS_EXPORT unsigned int RDKit::FileParserUtils::toUnsigned	(	std::string_view	input,
		bool	acceptSpaces = true
	)

Variable Documentation

atomPropPrefix

const std::string RDKit::FileParserUtils::atomPropPrefix = "atom."

static

Definition at line 149 of file FileParserUtils.h.

Referenced by processMolPropertyList().