RDKit
Open-source cheminformatics and machine learning.
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 More...
 
void parseFinalAtomAttribs (Atom *atom, bool doingQuery)
 
void parseBondAttribs (Bond *bond, AttribListType attribs, bool doingQuery)
 parses the attributes provided for a bond and sets More...
 
void parseFinalBondAttribs (Bond *bond, bool doingQuery)
 
void parseMolAttribs (ROMol *mol, AttribListType attribs)
 parses the attributes provided for a ctab and sets More...
 
void adjustAtomChiralities (RWMol *mol)
 
void finalizeQueryMol (ROMol *mol, bool mergeHs)
 
template<typename AtomType >
int startMol (std::vector< RWMol * > &molList, AtomType *firstAtom, bool doingQuery)
 initialize a molecule More...
 
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 More...
 
template<typename AtomType >
void addAtomToMol (std::vector< RWMol * > &molList, unsigned int idx, AtomType *atom, bool doingQuery)
 
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 More...
 
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 More...
 
template<typename T >
std::string convertToString (T val)
 convenience function to convert the argument to a string More...
 
void CleanupAfterParseError (RWMol *mol)
 

Typedef Documentation

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

Definition at line 65 of file SLNAttribs.h.

Enumeration Type Documentation

Enumerator
AttribLowPriAnd 
AttribOr 
AttribAnd 
AttribNot 

Definition at line 46 of file SLNAttribs.h.

Function Documentation

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 113 of file SLNParseOps.h.

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

Referenced by addAtomToMol().

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 143 of file SLNParseOps.h.

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

template<typename BondType >
int RDKit::SLNParse::addBranchToMol ( std::vector< RWMol * > &  molList,
unsigned int  molIdx,
unsigned int  branchIdx,
BondType *&  bond 
)
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 279 of file SLNParseOps.h.

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

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

Definition at line 288 of file SLNParseOps.h.

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

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

Definition at line 301 of file SLNParseOps.h.

References PRECONDITION.

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

Definition at line 154 of file SLNParseOps.h.

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

Referenced by addBranchToMol(), and closeRingBond().

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 186 of file SLNParseOps.h.

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

template<typename T >
std::string RDKit::SLNParse::convertToString ( val)

convenience function to convert the argument to a string

Definition at line 296 of file SLNParseOps.h.

void 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,
bool  doingQuery 
)

initialize a molecule

Definition at line 87 of file SLNParseOps.h.

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