RDKit::SGroupParsing Namespace Reference

Typedefs
typedef std::map< int, SubstanceGroup >	IDX_TO_SGROUP_MAP
typedef std::map< int, STR_VECT >	IDX_TO_STR_VECT_MAP

Functions
unsigned int	ParseSGroupIntField (const std::string &text, unsigned int line, unsigned int &pos, bool isFieldCounter=false)
unsigned int	ParseSGroupIntField (bool &ok, bool strictParsing, const std::string &text, unsigned int line, unsigned int &pos, bool isFieldCounter=false)
double	ParseSGroupDoubleField (const std::string &text, unsigned int line, unsigned int &pos)
double	ParseSGroupDoubleField (bool &ok, bool strictParsing, const std::string &text, unsigned int line, unsigned int &pos)
SubstanceGroup *	FindSgIdx (IDX_TO_SGROUP_MAP &sGroupMap, int sgIdx, unsigned int line)
template<class Exc = FileParseException>
void	SGroupWarnOrThrow (bool strictParsing, const std::string &msg)
void	ParseSGroupV2000STYLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
void	ParseSGroupV2000VectorDataLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
void	ParseSGroupV2000SDILine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
void	ParseSGroupV2000SSTLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
void	ParseSGroupV2000SMTLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
void	ParseSGroupV2000SLBLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
void	ParseSGroupV2000SCNLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
void	ParseSGroupV2000SDSLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
void	ParseSGroupV2000SBVLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
void	ParseSGroupV2000SDTLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
void	ParseSGroupV2000SDDLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
void	ParseSGroupV2000SCDSEDLine (IDX_TO_SGROUP_MAP &sGroupMap, IDX_TO_STR_VECT_MAP &dataFieldsMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing, unsigned int &counter, unsigned int &lastDataSGroup, std::ostringstream &currentDataField)
void	ParseSGroupV2000SPLLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
void	ParseSGroupV2000SNCLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
void	ParseSGroupV2000SAPLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
void	ParseSGroupV2000SCLLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
void	ParseSGroupV2000SBTLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
template<class T >
RDKIT_FILEPARSERS_EXPORT std::vector< T >	ParseV3000Array (std::stringstream &stream, int maxV=-1, bool strictParsing=false)
template<class T >
std::vector< T >	ParseV3000Array (const std::string &s, int maxV=-1, bool strictParsing=false)
void	ParseV3000CStateLabel (RWMol *mol, SubstanceGroup &sgroup, std::stringstream &stream, unsigned int line, bool strictParsing=true)
void	ParseV3000SAPLabel (RWMol *mol, SubstanceGroup &sgroup, std::stringstream &stream, bool strictParsing=true)
std::string	ParseV3000StringPropLabel (std::stringstream &stream)
std::string	ParseV3000SGroupsBlock (std::istream *inStream, unsigned int line, unsigned int nSgroups, RWMol *mol, bool strictParsing)

Typedef Documentation

IDX_TO_SGROUP_MAP

typedef std::map<int, SubstanceGroup> RDKit::SGroupParsing::IDX_TO_SGROUP_MAP

Definition at line 20 of file MolSGroupParsing.h.

IDX_TO_STR_VECT_MAP

typedef std::map<int, STR_VECT> RDKit::SGroupParsing::IDX_TO_STR_VECT_MAP

Definition at line 21 of file MolSGroupParsing.h.

Function Documentation

FindSgIdx()

SubstanceGroup * RDKit::SGroupParsing::FindSgIdx	(	IDX_TO_SGROUP_MAP &	sGroupMap,
		int	sgIdx,
		unsigned int	line
	)

ParseSGroupDoubleField() [1/2]

double RDKit::SGroupParsing::ParseSGroupDoubleField	(	bool &	ok,
		bool	strictParsing,
		const std::string &	text,
		unsigned int	line,
		unsigned int &	pos
	)

ParseSGroupDoubleField() [2/2]

double RDKit::SGroupParsing::ParseSGroupDoubleField	(	const std::string &	text,
		unsigned int	line,
		unsigned int &	pos
	)

ParseSGroupIntField() [1/2]

unsigned int RDKit::SGroupParsing::ParseSGroupIntField	(	bool &	ok,
		bool	strictParsing,
		const std::string &	text,
		unsigned int	line,
		unsigned int &	pos,
		bool	isFieldCounter = false
	)

ParseSGroupIntField() [2/2]

unsigned int RDKit::SGroupParsing::ParseSGroupIntField	(	const std::string &	text,
		unsigned int	line,
		unsigned int &	pos,
		bool	isFieldCounter = false
	)

ParseSGroupV2000SAPLine()

void RDKit::SGroupParsing::ParseSGroupV2000SAPLine	(	IDX_TO_SGROUP_MAP &	sGroupMap,
		RWMol *	mol,
		const std::string &	text,
		unsigned int	line,
		bool	strictParsing = true
	)

if the SAP line is malformed and has no lvIdx and no id, lvIdx is set to mol->getNumAtoms() and id is set to " " the user is responsible for replacing lvIdx with the correct index: if d_bonds.size() == 1, and one of the bond atom indices is aIdx, the other can be safely assigned to lvIdx

ParseSGroupV2000SBTLine()

void RDKit::SGroupParsing::ParseSGroupV2000SBTLine	(	IDX_TO_SGROUP_MAP &	sGroupMap,
		RWMol *	mol,
		const std::string &	text,
		unsigned int	line,
		bool	strictParsing = true
	)

ParseSGroupV2000SBVLine()

void RDKit::SGroupParsing::ParseSGroupV2000SBVLine	(	IDX_TO_SGROUP_MAP &	sGroupMap,
		RWMol *	mol,
		const std::string &	text,
		unsigned int	line,
		bool	strictParsing = true
	)

ParseSGroupV2000SCDSEDLine()

void RDKit::SGroupParsing::ParseSGroupV2000SCDSEDLine	(	IDX_TO_SGROUP_MAP &	sGroupMap,
		IDX_TO_STR_VECT_MAP &	dataFieldsMap,
		RWMol *	mol,
		const std::string &	text,
		unsigned int	line,
		bool	strictParsing,
		unsigned int &	counter,
		unsigned int &	lastDataSGroup,
		std::ostringstream &	currentDataField
	)

ParseSGroupV2000SCLLine()

void RDKit::SGroupParsing::ParseSGroupV2000SCLLine	(	IDX_TO_SGROUP_MAP &	sGroupMap,
		RWMol *	mol,
		const std::string &	text,
		unsigned int	line,
		bool	strictParsing = true
	)

ParseSGroupV2000SCNLine()

void RDKit::SGroupParsing::ParseSGroupV2000SCNLine	(	IDX_TO_SGROUP_MAP &	sGroupMap,
		RWMol *	mol,
		const std::string &	text,
		unsigned int	line,
		bool	strictParsing = true
	)

ParseSGroupV2000SDDLine()

void RDKit::SGroupParsing::ParseSGroupV2000SDDLine	(	IDX_TO_SGROUP_MAP &	sGroupMap,
		RWMol *	mol,
		const std::string &	text,
		unsigned int	line,
		bool	strictParsing = true
	)

ParseSGroupV2000SDILine()

void RDKit::SGroupParsing::ParseSGroupV2000SDILine	(	IDX_TO_SGROUP_MAP &	sGroupMap,
		RWMol *	mol,
		const std::string &	text,
		unsigned int	line,
		bool	strictParsing = true
	)

ParseSGroupV2000SDSLine()

void RDKit::SGroupParsing::ParseSGroupV2000SDSLine	(	IDX_TO_SGROUP_MAP &	sGroupMap,
		RWMol *	mol,
		const std::string &	text,
		unsigned int	line,
		bool	strictParsing = true
	)

ParseSGroupV2000SDTLine()

void RDKit::SGroupParsing::ParseSGroupV2000SDTLine	(	IDX_TO_SGROUP_MAP &	sGroupMap,
		RWMol *	mol,
		const std::string &	text,
		unsigned int	line,
		bool	strictParsing = true
	)

ParseSGroupV2000SLBLine()

void RDKit::SGroupParsing::ParseSGroupV2000SLBLine	(	IDX_TO_SGROUP_MAP &	sGroupMap,
		RWMol *	mol,
		const std::string &	text,
		unsigned int	line,
		bool	strictParsing = true
	)

ParseSGroupV2000SMTLine()

void RDKit::SGroupParsing::ParseSGroupV2000SMTLine	(	IDX_TO_SGROUP_MAP &	sGroupMap,
		RWMol *	mol,
		const std::string &	text,
		unsigned int	line,
		bool	strictParsing = true
	)

ParseSGroupV2000SNCLine()

void RDKit::SGroupParsing::ParseSGroupV2000SNCLine	(	IDX_TO_SGROUP_MAP &	sGroupMap,
		RWMol *	mol,
		const std::string &	text,
		unsigned int	line,
		bool	strictParsing = true
	)

ParseSGroupV2000SPLLine()

void RDKit::SGroupParsing::ParseSGroupV2000SPLLine	(	IDX_TO_SGROUP_MAP &	sGroupMap,
		RWMol *	mol,
		const std::string &	text,
		unsigned int	line,
		bool	strictParsing = true
	)

ParseSGroupV2000SSTLine()

void RDKit::SGroupParsing::ParseSGroupV2000SSTLine	(	IDX_TO_SGROUP_MAP &	sGroupMap,
		RWMol *	mol,
		const std::string &	text,
		unsigned int	line,
		bool	strictParsing = true
	)

ParseSGroupV2000STYLine()

void RDKit::SGroupParsing::ParseSGroupV2000STYLine	(	IDX_TO_SGROUP_MAP &	sGroupMap,
		RWMol *	mol,
		const std::string &	text,
		unsigned int	line,
		bool	strictParsing = true
	)

ParseSGroupV2000VectorDataLine()

void RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine	(	IDX_TO_SGROUP_MAP &	sGroupMap,
		RWMol *	mol,
		const std::string &	text,
		unsigned int	line,
		bool	strictParsing = true
	)

ParseV3000Array() [1/2]

template<class T >

std::vector< T > RDKit::SGroupParsing::ParseV3000Array	(	const std::string &	s,
		int	maxV = -1,
		bool	strictParsing = false
	)

Definition at line 141 of file MolSGroupParsing.h.

References RDKit::rdvalue_is().

ParseV3000Array() [2/2]

template<class T >

RDKIT_FILEPARSERS_EXPORT std::vector< T > RDKit::SGroupParsing::ParseV3000Array	(	std::stringstream &	stream,
		int	maxV = -1,
		bool	strictParsing = false
	)

ParseV3000CStateLabel()

void RDKit::SGroupParsing::ParseV3000CStateLabel	(	RWMol *	mol,
		SubstanceGroup &	sgroup,
		std::stringstream &	stream,
		unsigned int	line,
		bool	strictParsing = true
	)

ParseV3000SAPLabel()

void RDKit::SGroupParsing::ParseV3000SAPLabel	(	RWMol *	mol,
		SubstanceGroup &	sgroup,
		std::stringstream &	stream,
		bool	strictParsing = true
	)

ParseV3000SGroupsBlock()

std::string RDKit::SGroupParsing::ParseV3000SGroupsBlock	(	std::istream *	inStream,
		unsigned int	line,
		unsigned int	nSgroups,
		RWMol *	mol,
		bool	strictParsing
	)

ParseV3000StringPropLabel()

std::string RDKit::SGroupParsing::ParseV3000StringPropLabel

(

std::stringstream &

stream

)

SGroupWarnOrThrow()

template<class Exc = FileParseException>

void RDKit::SGroupParsing::SGroupWarnOrThrow	(	bool	strictParsing,
		const std::string &	msg
	)

Definition at line 45 of file MolSGroupParsing.h.

References BOOST_LOG, RDKit::rdvalue_is(), and rdWarningLog.