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, const boost::dynamic_bitset<> &wasAromatic, int confId=-1, unsigned int precision=6)

std::string	getV3000CTAB (const ROMol &tmol, int confId=-1, unsigned int precision=6)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

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, const v2::FileParsers::MolFileParserParams &ps)

void	finishMolProcessing (RWMol *res, bool chiralityPossible, bool sanitize, bool removeHs)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

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 156 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 113 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 251 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 243 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 235 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 259 of file FileParserUtils.h.

References RDKit::rdvalue_is(), and RDKit::RDProps::setProp().

◆ finishMolProcessing() [1/2]

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

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 100 of file FileParserUtils.h.

References finishMolProcessing(), RDKit::rdvalue_is(), and RDKit::v2::FileParsers::MolFileParserParams::sanitize.

◆ finishMolProcessing() [2/2]

RDKIT_FILEPARSERS_EXPORT void RDKit::FileParserUtils::finishMolProcessing	(	RWMol *	res,
		bool	chiralityPossible,
		const v2::FileParsers::MolFileParserParams &	ps
	)

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

Referenced by finishMolProcessing().

◆ 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 202 of file FileParserUtils.h.

References RDKit::ROMol::atoms(), and RDKit::rdvalue_is().

◆ getV3000CTAB() [1/2]

RDKIT_FILEPARSERS_EXPORT std::string RDKit::FileParserUtils::getV3000CTAB	(	const ROMol &	tmol,
		const boost::dynamic_bitset<> &	wasAromatic,
		int	confId = `-1`,
		unsigned int	precision = `6`
	)

Referenced by getV3000CTAB().

◆ getV3000CTAB() [2/2]

std::string RDKit::FileParserUtils::getV3000CTAB	(	const ROMol &	tmol,
		int	confId = `-1`,
		unsigned int	precision = `6`
	)

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 73 of file FileParserUtils.h.

References getV3000CTAB(), and RDKit::rdvalue_is().

◆ 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 167 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 195 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 164 of file FileParserUtils.h.

Referenced by processMolPropertyList().

Functions

Variables

Function Documentation

◆ applyMolListPropsToAtoms()

◆ applyMolListPropToAtoms()

◆ createAtomBoolPropertyList()

◆ createAtomDoublePropertyList()

◆ createAtomIntPropertyList()

◆ createAtomStringPropertyList()

◆ finishMolProcessing() [1/2]

◆ finishMolProcessing() [2/2]

◆ getAtomPropertyList()

◆ getV3000CTAB() [1/2]

◆ getV3000CTAB() [2/2]

◆ 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