RDKit::SLNParse Namespace Reference

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)
	parses the attributes provided for an atom and sets
void	parseFinalAtomAttribs (Atom *atom, bool doingQuery)
void	parseBondAttribs (Bond *bond, AttribListType attribs, bool doingQuery)
	parses the attributes provided for a bond and sets
void	parseFinalBondAttribs (Bond *bond, bool doingQuery)
void	parseMolAttribs (ROMol *mol, AttribListType attribs)
	parses the attributes provided for a ctab and sets
void	adjustAtomChiralities (RWMol *mol)
RWMol *	finalizeQueryMol (ROMol *mol, bool mergeHs)
void	bookmarkAtomID (RWMol *mp, Atom *atom)
	set a bookmark in the molecule if the atom has an associated ID:
template<typename BondType>
void	addBondToMol (RWMol *mp, BondType *bond)
	adds a bond, being careful to handle aromaticity properly
template<typename AtomType>
int	startMol (std::vector< RWMol * > &molList, AtomType *firstAtom)
	initialize a molecule
template<typename AtomType, typename BondType>
void	addAtomToMol (std::vector< RWMol * > &molList, unsigned int idx, AtomType *atom, BondType *bond)
	adds an atom to a molecule
template<typename AtomType>
void	addAtomToMol (std::vector< RWMol * > &molList, unsigned int idx, AtomType *atom)
template<typename BondType>
void	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
void	closeRingBond (std::vector< RWMol * > &molList, unsigned int molIdx, unsigned int ringIdx)
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)
int	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
template<typename T>
std::string	convertToString (T val)
	convenience function to convert the argument to a string
void	CleanupAfterParseError (RWMol *mol)

---

Typedef Documentation

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

Definition at line 63 of file SLNAttribs.h.

---

Enumeration Type Documentation

enum RDKit::SLNParse::AttribCombineOp

Enumerator:

AttribLowPriAnd
AttribOr
AttribAnd
AttribNot

Definition at line 46 of file SLNAttribs.h.

---

Function Documentation

template<typename AtomType>

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

Definition at line 138 of file SLNParseOps.h.

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

template<typename AtomType, typename BondType>

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

adds an atom to a molecule

Definition at line 110 of file SLNParseOps.h.

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

Referenced by addAtomToMol().

template<typename BondType>

void RDKit::SLNParse::@66::addBondToMol	(	RWMol *	mp,
		BondType *	bond
	)			[inline, static]

adds a bond, being careful to handle aromaticity properly

Definition at line 70 of file SLNParseOps.h.

References RDKit::RWMol::addBond(), RDKit::Bond::AROMATIC, and PRECONDITION.

Referenced by addAtomToMol(), addBranchToMol(), and closeRingBond().

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

Definition at line 264 of file SLNParseOps.h.

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

template<typename BondType>

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

Definition at line 186 of file SLNParseOps.h.

References addBondToMol(), CHECK_INVARIANT, closeRingBond(), RDKit::Bond::getEndAtomIdx(), RDKit::Bond::IONIC, PRECONDITION, RDKit::Bond::setEndAtomIdx(), and RDKit::Bond::setOwningMol().

Referenced by addBranchToMol(), and 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 271 of file SLNParseOps.h.

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

void RDKit::SLNParse::adjustAtomChiralities

(

RWMol *

mol

)

void RDKit::SLNParse::@66::bookmarkAtomID	(	RWMol *	mp,
		Atom *	atom
	)			[static]

set a bookmark in the molecule if the atom has an associated ID:

Definition at line 48 of file SLNParseOps.h.

References RDKit::Atom::getProp(), RDKit::ROMol::hasAtomBookmark(), RDKit::ROMol::hasBondBookmark(), RDKit::Atom::hasProp(), PRECONDITION, and RDKit::ROMol::setAtomBookmark().

Referenced by addAtomToMol(), and startMol().

void RDKit::SLNParse::CleanupAfterParseError

(

RWMol *

mol

)

Definition at line 283 of file SLNParseOps.h.

References PRECONDITION.

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

Definition at line 179 of file SLNParseOps.h.

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

template<typename BondType>

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

closes an indexed ring in a molecule using the bond provided

Definition at line 148 of file SLNParseOps.h.

References addBondToMol(), CHECK_INVARIANT, and PRECONDITION.

Referenced by addBranchToMol(), and closeRingBond().

template<typename T>

std::string RDKit::SLNParse::convertToString

(

T

val

)

[inline]

convenience function to convert the argument to a string

Definition at line 278 of file SLNParseOps.h.

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

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

parses the attributes provided for an atom and sets

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

parses the attributes provided for a bond and sets

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

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

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

parses the attributes provided for a ctab and sets

template<typename AtomType>

int RDKit::SLNParse::startMol	(	std::vector< RWMol * > &	molList,
		AtomType *	firstAtom
	)			[inline]

initialize a molecule

Definition at line 87 of file SLNParseOps.h.

References RDKit::RWMol::addAtom(), RDKit::RWMol::addBond(), bookmarkAtomID(), PRECONDITION, and RDKit::Bond::SINGLE.