Classes
class	AttribType

Typedefs
typedef std::vector< std::pair< AttribCombineOp, boost::shared_ptr< AttribType > > >	AttribListType

Enumerations
enum	AttribCombineOp { AttribLowPriAnd = 0 , AttribOr , AttribAnd , AttribNot }

Functions
void	parseAtomAttribs (Atom *atom, AttribListType attribs, bool doingQuery)

void	parseFinalAtomAttribs (Atom *atom, bool doingQuery)

void	parseBondAttribs (Bond *bond, AttribListType attribs, bool doingQuery)

void	parseFinalBondAttribs (Bond *bond, bool doingQuery)

void	parseMolAttribs (ROMol *mol, AttribListType attribs)

void	adjustAtomChiralities (RWMol *mol)

RDKIT_SLNPARSE_EXPORT void	finalizeQueryMol (ROMol *mol, bool mergeHs)

void	CleanupAfterParse (RWMol *mol)

template<typename AtomType >
int	startMol (std::vector< RWMol * > &molList, AtomType *firstAtom, bool doingQuery)
	initialize a molecule

template<typename AtomType , typename BondType >
void	addAtomToMol (std::vector< RWMol * > &molList, unsigned int idx, AtomType atom, BondType bond, bool doingQuery)
	adds an atom to a molecule

template<typename AtomType >
void	addAtomToMol (std::vector< RWMol * > &molList, unsigned int idx, AtomType *atom, bool doingQuery)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

template<typename BondType >
void	closeRingBond (std::vector< RWMol * > &molList, unsigned int molIdx, unsigned int ringIdx, BondType *bond, bool postponeAllowed=true)

void	closeRingBond (std::vector< RWMol * > &molList, unsigned int molIdx, unsigned int ringIdx)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

template<typename BondType >
int	addBranchToMol (std::vector< RWMol * > &molList, unsigned int molIdx, unsigned int branchIdx, BondType *&bond)

int	addBranchToMol (std::vector< RWMol * > &molList, unsigned int molIdx, unsigned int branchIdx)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

int	addFragToMol (std::vector< RWMol * > &molList, unsigned int molIdx, unsigned int fragIdx)

template<typename T >
std::string	convertToString (T val)
	convenience function to convert the argument to a string

Typedef Documentation

◆ AttribListType

typedef std::vector<std::pair<AttribCombineOp, boost::shared_ptr<AttribType> > > RDKit::SLNParse::AttribListType

Definition at line 65 of file SLNAttribs.h.

Enumeration Type Documentation

◆ AttribCombineOp

enum RDKit::SLNParse::AttribCombineOp

Enumerator
AttribLowPriAnd
AttribOr
AttribAnd
AttribNot

Definition at line 47 of file SLNAttribs.h.

Function Documentation

◆ addAtomToMol() [1/2]

template<typename AtomType , typename BondType >

void RDKit::SLNParse::addAtomToMol	(	std::vector< RWMol * > &	molList,
		unsigned int	idx,
		AtomType *	atom,
		BondType *	bond,
		bool	doingQuery
	)

adds an atom to a molecule

Definition at line 116 of file SLNParseOps.h.

References RDKit::Atom::getIdx(), PRECONDITION, RDKit::rdvalue_is(), and RDKit::Bond::SINGLE.

Referenced by addAtomToMol().

◆ addAtomToMol() [2/2]

template<typename AtomType >

void RDKit::SLNParse::addAtomToMol	(	std::vector< RWMol * > &	molList,
		unsigned int	idx,
		AtomType *	atom,
		bool	doingQuery
	)

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 146 of file SLNParseOps.h.

References addAtomToMol(), RDKit::rdvalue_is(), and RDKit::Bond::SINGLE.

◆ addBranchToMol() [1/2]

int RDKit::SLNParse::addBranchToMol	(	std::vector< RWMol * > &	molList,
		unsigned int	molIdx,
		unsigned int	branchIdx
	)

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 290 of file SLNParseOps.h.

References addBranchToMol(), RDKit::rdvalue_is(), and RDKit::Bond::SINGLE.

◆ addBranchToMol() [2/2]

template<typename BondType >

int RDKit::SLNParse::addBranchToMol	(	std::vector< RWMol * > &	molList,
		unsigned int	molIdx,
		unsigned int	branchIdx,
		BondType *&	bond
	)

Definition at line 203 of file SLNParseOps.h.

References CHECK_INVARIANT, closeRingBond(), RDKit::Bond::IONIC, PRECONDITION, and RDKit::rdvalue_is().

Referenced by addBranchToMol(), and addFragToMol().

◆ addFragToMol()

int RDKit::SLNParse::addFragToMol	(	std::vector< RWMol * > &	molList,
		unsigned int	molIdx,
		unsigned int	fragIdx
	)

adds the atoms and bonds from a fragment to the molecule, sets no bond between them

Definition at line 306 of file SLNParseOps.h.

References addBranchToMol(), RDKit::Bond::IONIC, and RDKit::rdvalue_is().

◆ adjustAtomChiralities()

void RDKit::SLNParse::adjustAtomChiralities ( RWMol * mol )

◆ CleanupAfterParse()

void RDKit::SLNParse::CleanupAfterParse ( RWMol * mol )

◆ closeRingBond() [1/2]

void RDKit::SLNParse::closeRingBond	(	std::vector< RWMol * > &	molList,
		unsigned int	molIdx,
		unsigned int	ringIdx
	)

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 189 of file SLNParseOps.h.

References closeRingBond(), RDKit::rdvalue_is(), and RDKit::Bond::SINGLE.

◆ closeRingBond() [2/2]

template<typename BondType >

void RDKit::SLNParse::closeRingBond	(	std::vector< RWMol * > &	molList,
		unsigned int	molIdx,
		unsigned int	ringIdx,
		BondType *	bond,
		bool	postponeAllowed = `true`
	)

closes an indexed ring in a molecule using the bond provided The bond is formed from the atom in the molecule with the corresponding bookmark to the active atom

Definition at line 157 of file SLNParseOps.h.

References CHECK_INVARIANT, PRECONDITION, RDKit::rdvalue_is(), and RDKit::Atom::setOwningMol().

Referenced by addBranchToMol(), and closeRingBond().

◆ convertToString()

template<typename T >

std::string RDKit::SLNParse::convertToString ( T val )

convenience function to convert the argument to a string

Definition at line 321 of file SLNParseOps.h.

References RDKit::rdvalue_is().

◆ finalizeQueryMol()

RDKIT_SLNPARSE_EXPORT void RDKit::SLNParse::finalizeQueryMol	(	ROMol *	mol,
		bool	mergeHs
	)

◆ parseAtomAttribs()

void RDKit::SLNParse::parseAtomAttribs	(	Atom *	atom,
		AttribListType	attribs,
		bool	doingQuery
	)

parses the attributes provided for an atom and sets the appropriate RD properties/queries. NOTES: 1) Some SLN query values cannot be properly set until the molecule is fully/ initialized. These are handled by parseFinalAtomAttribs()

◆ parseBondAttribs()

void RDKit::SLNParse::parseBondAttribs	(	Bond *	bond,
		AttribListType	attribs,
		bool	doingQuery
	)

parses the attributes provided for a bond and sets the appropriate RD properties/queries. NOTES: 1) Some SLN query values cannot be properly set until the molecule is fully/ initialized. These are handled by parseFinalBondAttribs()

◆ parseFinalAtomAttribs()

void RDKit::SLNParse::parseFinalAtomAttribs	(	Atom *	atom,
		bool	doingQuery
	)

◆ parseFinalBondAttribs()

void RDKit::SLNParse::parseFinalBondAttribs	(	Bond *	bond,
		bool	doingQuery
	)

◆ parseMolAttribs()

void RDKit::SLNParse::parseMolAttribs	(	ROMol *	mol,
		AttribListType	attribs
	)

parses the attributes provided for a ctab and sets the appropriate RD properties/queries.

◆ startMol()

template<typename AtomType >

int RDKit::SLNParse::startMol	(	std::vector< RWMol * > &	molList,
		AtomType *	firstAtom,
		bool	doingQuery
	)

initialize a molecule

Definition at line 90 of file SLNParseOps.h.

References PRECONDITION, RDKit::rdvalue_is(), and RDKit::Bond::SINGLE.

Classes

Typedefs

Enumerations

Functions

Typedef Documentation

◆ AttribListType

Enumeration Type Documentation

◆ AttribCombineOp

Function Documentation

◆ addAtomToMol() [1/2]

◆ addAtomToMol() [2/2]

◆ addBranchToMol() [1/2]

◆ addBranchToMol() [2/2]

◆ addFragToMol()

◆ adjustAtomChiralities()

◆ CleanupAfterParse()

◆ closeRingBond() [1/2]

◆ closeRingBond() [2/2]

◆ convertToString()

◆ finalizeQueryMol()

◆ parseAtomAttribs()

◆ parseBondAttribs()

◆ parseFinalAtomAttribs()

◆ parseFinalBondAttribs()

◆ parseMolAttribs()

◆ startMol()