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.

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

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)

RDKIT_FILEPARSERS_EXPORT void	moveAdditionalPropertiesToSGroups (RWMol &mol)

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(), and RDKit::rdvalue_is().

◆ 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(), RDKit::rdvalue_is(), 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::rdvalue_is(), and 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::rdvalue_is(), and 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::rdvalue_is(), and 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::rdvalue_is(), and 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(), and RDKit::rdvalue_is().

◆ 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
	)

◆ moveAdditionalPropertiesToSGroups()

RDKIT_FILEPARSERS_EXPORT void RDKit::FileParserUtils::moveAdditionalPropertiesToSGroups ( RWMol & mol )

◆ 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, and RDKit::rdvalue_is().

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(), processMolPropertyList(), and RDKit::rdvalue_is().

◆ 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.

References RDKit::rdvalue_is().

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.

References RDKit::rdvalue_is().

◆ 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 RDKit::rdvalue_is(), and 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().

Functions

Variables

Function Documentation

◆ applyMolListPropsToAtoms()

◆ applyMolListPropToAtoms()

◆ createAtomBoolPropertyList()

◆ createAtomDoublePropertyList()

◆ createAtomIntPropertyList()

◆ createAtomStringPropertyList()

◆ finishMolProcessing()

◆ getAtomPropertyList()

◆ getV3000CTAB()

◆ getV3000Line()

◆ moveAdditionalPropertiesToSGroups()

◆ ParseV2000CTAB()

◆ ParseV3000CTAB()

◆ processMolPropertyList()

◆ processMolPropertyLists()

◆ replaceAtomWithQueryAtom()

◆ strip()

◆ stripSpacesAndCast() [1/2]

◆ stripSpacesAndCast() [2/2]

◆ toDouble() [1/2]

◆ toDouble() [2/2]

◆ toInt() [1/2]

◆ toInt() [2/2]

◆ toUnsigned() [1/2]

◆ toUnsigned() [2/2]

Variable Documentation

◆ atomPropPrefix