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, 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, bool expectMacroAtoms=false)
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, typename U>
void	applyMolListProp (ROMol &mol, const std::string &pn, const std::string &prefix, const std::string &missingValueMarker, size_t nItems, U getter)
	applies a particular property to the atoms as an atom property list
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, typename U>
void	applyMolListProps (ROMol &mol, const std::string &prefix, size_t nItems, U getter, const std::string missingValueMarker="n/a")
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, typename U>
std::string	getPropertyList (U getter, const std::string &propName, std::string missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
template<typename T>
std::string	getAtomPropertyList (ROMol &mol, const std::string &atomPropName, std::string missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
template<typename T, typename U>
void	createPropertyList (ROMol &mol, U getter, const std::string &prefix, const std::string &typeMarker, const std::string &propName, const std::string &missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
void	createAtomIntPropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
void	createAtomDoublePropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
void	createAtomBoolPropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
void	createAtomStringPropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
void	createBondIntPropertyList (ROMol &mol, const std::string &bondPropName, const std::string &missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
void	createBondDoublePropertyList (ROMol &mol, const std::string &bondPropName, const std::string &missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
void	createBondBoolPropertyList (ROMol &mol, const std::string &bondPropName, const std::string &missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
void	createBondStringPropertyList (ROMol &mol, const std::string &bondPropName, const std::string &missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
RDKIT_FILEPARSERS_EXPORT void	moveAdditionalPropertiesToSGroups (RWMol &mol)

Variables
static constexpr std::string_view	atomPropPrefixView = "atom."
static constexpr size_t	atomPropPrefixLength = atomPropPrefixView.length()
static const std::string	atomPropPrefix = std::string(atomPropPrefixView)
static constexpr std::string_view	bondPropPrefixView = "bond."
static constexpr size_t	bondPropPrefixLength = bondPropPrefixView.length()
static const std::string	bondPropPrefix = std::string(bondPropPrefixView)
static constexpr unsigned int	DEFAULT_LINESIZE = 190

Function Documentation

applyMolListProp()

template<typename T, typename U>

void RDKit::FileParserUtils::applyMolListProp	(	ROMol &	mol,
		const std::string &	pn,
		const std::string &	prefix,
		const std::string &	missingValueMarker,
		size_t	nItems,
		U	getter )

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

Definition at line 114 of file FileParserUtils.h.

References BOOST_LOG, RDKit::RDProps::getProp(), and rdWarningLog.

Referenced by applyMolListProps(), applyMolListPropsToAtoms(), applyMolListPropToAtoms(), and processMolPropertyList().

applyMolListProps()

template<typename T, typename U>

void RDKit::FileParserUtils::applyMolListProps	(	ROMol &	mol,
		const std::string &	prefix,
		size_t	nItems,
		U	getter,
		const std::string	missingValueMarker = "n/a" )

Definition at line 167 of file FileParserUtils.h.

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

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 180 of file FileParserUtils.h.

References applyMolListProp(), RDKit::ROMol::getAtomWithIdx(), RDKit::ROMol::getNumAtoms(), and 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 158 of file FileParserUtils.h.

References applyMolListProp(), RDKit::ROMol::getAtomWithIdx(), and RDKit::ROMol::getNumAtoms().

createAtomBoolPropertyList()

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

inline

Definition at line 323 of file FileParserUtils.h.

References RDKit::ROMol::atoms(), createPropertyList(), and DEFAULT_LINESIZE.

createAtomDoublePropertyList()

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

inline

Definition at line 315 of file FileParserUtils.h.

References RDKit::ROMol::atoms(), createPropertyList(), and DEFAULT_LINESIZE.

createAtomIntPropertyList()

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

inline

Definition at line 307 of file FileParserUtils.h.

References RDKit::ROMol::atoms(), createPropertyList(), and DEFAULT_LINESIZE.

createAtomStringPropertyList()

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

inline

Definition at line 331 of file FileParserUtils.h.

References RDKit::ROMol::atoms(), createPropertyList(), and DEFAULT_LINESIZE.

createBondBoolPropertyList()

void RDKit::FileParserUtils::createBondBoolPropertyList ( ROMol & mol, const std::string & bondPropName, const std::string & missingValueMarker = "", unsigned int lineSize = DEFAULT_LINESIZE )

inline

Definition at line 356 of file FileParserUtils.h.

References RDKit::ROMol::bonds(), createPropertyList(), and DEFAULT_LINESIZE.

createBondDoublePropertyList()

void RDKit::FileParserUtils::createBondDoublePropertyList ( ROMol & mol, const std::string & bondPropName, const std::string & missingValueMarker = "", unsigned int lineSize = DEFAULT_LINESIZE )

inline

Definition at line 348 of file FileParserUtils.h.

References RDKit::ROMol::bonds(), createPropertyList(), and DEFAULT_LINESIZE.

createBondIntPropertyList()

void RDKit::FileParserUtils::createBondIntPropertyList ( ROMol & mol, const std::string & bondPropName, const std::string & missingValueMarker = "", unsigned int lineSize = DEFAULT_LINESIZE )

inline

Definition at line 340 of file FileParserUtils.h.

References RDKit::ROMol::bonds(), createPropertyList(), and DEFAULT_LINESIZE.

createBondStringPropertyList()

void RDKit::FileParserUtils::createBondStringPropertyList ( ROMol & mol, const std::string & bondPropName, const std::string & missingValueMarker = "", unsigned int lineSize = DEFAULT_LINESIZE )

inline

Definition at line 364 of file FileParserUtils.h.

References RDKit::ROMol::bonds(), createPropertyList(), and DEFAULT_LINESIZE.

createPropertyList()

template<typename T, typename U>

void RDKit::FileParserUtils::createPropertyList	(	ROMol &	mol,
		U	getter,
		const std::string &	prefix,
		const std::string &	typeMarker,
		const std::string &	propName,
		const std::string &	missingValueMarker = "",
		unsigned int	lineSize = DEFAULT_LINESIZE )

Definition at line 297 of file FileParserUtils.h.

References DEFAULT_LINESIZE, getPropertyList(), and RDKit::RDProps::setProp().

Referenced by createAtomBoolPropertyList(), createAtomDoublePropertyList(), createAtomIntPropertyList(), createAtomStringPropertyList(), createBondBoolPropertyList(), createBondDoublePropertyList(), createBondIntPropertyList(), and createBondStringPropertyList().

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 101 of file FileParserUtils.h.

References finishMolProcessing(), RDKit::v2::FileParsers::MolFileParserParams::removeHs, 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

References RDKIT_FILEPARSERS_EXPORT.

Referenced by finishMolProcessing().

getAtomPropertyList()

template<typename T>

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

Definition at line 289 of file FileParserUtils.h.

References RDKit::ROMol::atoms(), DEFAULT_LINESIZE, and getPropertyList().

getPropertyList()

template<typename T, typename U>

std::string RDKit::FileParserUtils::getPropertyList	(	U	getter,
		const std::string &	propName,
		std::string	missingValueMarker = "",
		unsigned int	lineSize = DEFAULT_LINESIZE )

Definition at line 255 of file FileParserUtils.h.

References DEFAULT_LINESIZE.

Referenced by createPropertyList(), and getAtomPropertyList().

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 )

References RDKIT_FILEPARSERS_EXPORT.

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 RDKit::ROMol::getNumBonds(), and getV3000CTAB().

getV3000Line()

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

References RDKIT_FILEPARSERS_EXPORT.

moveAdditionalPropertiesToSGroups()

RDKIT_FILEPARSERS_EXPORT void RDKit::FileParserUtils::moveAdditionalPropertiesToSGroups

(

RWMol &

mol

)

References RDKIT_FILEPARSERS_EXPORT.

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 )

References RDKIT_FILEPARSERS_EXPORT.

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,
		bool	expectMacroAtoms = false )

References RDKIT_FILEPARSERS_EXPORT.

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 200 of file FileParserUtils.h.

References applyMolListProp(), atomPropPrefix, atomPropPrefixLength, bondPropPrefix, bondPropPrefixLength, RDKit::ROMol::getAtomWithIdx(), RDKit::ROMol::getBondWithIdx(), RDKit::ROMol::getNumAtoms(), and RDKit::ROMol::getNumBonds().

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 and bonds

Definition at line 245 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.

References RDKIT_FILEPARSERS_EXPORT.

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_FILEPARSERS_EXPORT.

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 stripSpacesAndCast().

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().

Referenced by stripSpacesAndCast().

toDouble() [1/2]

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

References RDKIT_FILEPARSERS_EXPORT.

toDouble() [2/2]

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

References RDKIT_FILEPARSERS_EXPORT.

toInt() [1/2]

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

References RDKIT_FILEPARSERS_EXPORT.

toInt() [2/2]

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

References RDKIT_FILEPARSERS_EXPORT.

toUnsigned() [1/2]

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

References RDKIT_FILEPARSERS_EXPORT.

toUnsigned() [2/2]

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

References RDKIT_FILEPARSERS_EXPORT.

Variable Documentation

atomPropPrefix

const std::string RDKit::FileParserUtils::atomPropPrefix = std::string(atomPropPrefixView)

static

Definition at line 193 of file FileParserUtils.h.

Referenced by processMolPropertyList().

atomPropPrefixLength

size_t RDKit::FileParserUtils::atomPropPrefixLength = atomPropPrefixView.length()

staticconstexpr

Definition at line 192 of file FileParserUtils.h.

Referenced by processMolPropertyList().

atomPropPrefixView

std::string_view RDKit::FileParserUtils::atomPropPrefixView = "atom."

staticconstexpr

Definition at line 191 of file FileParserUtils.h.

bondPropPrefix

const std::string RDKit::FileParserUtils::bondPropPrefix = std::string(bondPropPrefixView)

static

Definition at line 196 of file FileParserUtils.h.

Referenced by processMolPropertyList().

bondPropPrefixLength

size_t RDKit::FileParserUtils::bondPropPrefixLength = bondPropPrefixView.length()

staticconstexpr

Definition at line 195 of file FileParserUtils.h.

Referenced by processMolPropertyList().

bondPropPrefixView

std::string_view RDKit::FileParserUtils::bondPropPrefixView = "bond."

staticconstexpr

Definition at line 194 of file FileParserUtils.h.

DEFAULT_LINESIZE

unsigned int RDKit::FileParserUtils::DEFAULT_LINESIZE = 190

staticconstexpr

Definition at line 252 of file FileParserUtils.h.

Referenced by createAtomBoolPropertyList(), createAtomDoublePropertyList(), createAtomIntPropertyList(), createAtomStringPropertyList(), createBondBoolPropertyList(), createBondDoublePropertyList(), createBondIntPropertyList(), createBondStringPropertyList(), createPropertyList(), getAtomPropertyList(), and getPropertyList().