SmilesParseOps Namespace Reference

Functions
void	CheckRingClosureBranchStatus (RDKit::Atom *atom, RDKit::RWMol *mp)
void	ReportParseError (const char *message, bool throwIt=true)
void	CleanupAfterParseError (RDKit::RWMol *mol)
void	AddFragToMol (RDKit::RWMol *mol, RDKit::RWMol *frag, RDKit::Bond::BondType bondOrder=RDKit::Bond::UNSPECIFIED, RDKit::Bond::BondDir bondDir=RDKit::Bond::NONE, bool closeRings=false, bool doingQuery=false)
RDKit::Bond::BondType	GetUnspecifiedBondType (const RDKit::RWMol *mol, const RDKit::Atom *atom1, const RDKit::Atom *atom2)
void	CloseMolRings (RDKit::RWMol *mol, bool toleratePartials)
void	SetUnspecifiedBondTypes (RDKit::RWMol *mol)
void	AdjustAtomChiralityFlags (RDKit::RWMol *mol)
void	CleanupAfterParsing (RDKit::RWMol *mol)
void	parseCXExtensions (RDKit::RWMol &mol, const std::string &extText, std::string::const_iterator &pos)
void	ClearAtomChemicalProps (RDKit::Atom *atom)
	removes formal charge, isotope, etc. Primarily useful for QueryAtoms More...

Function Documentation

AddFragToMol()

void SmilesParseOps::AddFragToMol	(	RDKit::RWMol *	mol,
		RDKit::RWMol *	frag,
		RDKit::Bond::BondType	bondOrder = RDKit::Bond::UNSPECIFIED,
		RDKit::Bond::BondDir	bondDir = RDKit::Bond::NONE,
		bool	closeRings = false,
		bool	doingQuery = false
	)

AdjustAtomChiralityFlags()

void SmilesParseOps::AdjustAtomChiralityFlags

(

RDKit::RWMol *

mol

)

CheckRingClosureBranchStatus()

void SmilesParseOps::CheckRingClosureBranchStatus	(	RDKit::Atom *	atom,
		RDKit::RWMol *	mp
	)

CleanupAfterParseError()

void SmilesParseOps::CleanupAfterParseError

(

RDKit::RWMol *

mol

)

CleanupAfterParsing()

void SmilesParseOps::CleanupAfterParsing

(

RDKit::RWMol *

mol

)

ClearAtomChemicalProps()

void SmilesParseOps::ClearAtomChemicalProps

(

RDKit::Atom *

atom

)

removes formal charge, isotope, etc. Primarily useful for QueryAtoms

CloseMolRings()

void SmilesParseOps::CloseMolRings	(	RDKit::RWMol *	mol,
		bool	toleratePartials
	)

GetUnspecifiedBondType()

RDKit::Bond::BondType SmilesParseOps::GetUnspecifiedBondType	(	const RDKit::RWMol *	mol,
		const RDKit::Atom *	atom1,
		const RDKit::Atom *	atom2
	)

parseCXExtensions()

void SmilesParseOps::parseCXExtensions	(	RDKit::RWMol &	mol,
		const std::string &	extText,
		std::string::const_iterator &	pos
	)

ReportParseError()

void SmilesParseOps::ReportParseError	(	const char *	message,
		bool	throwIt = true
	)

SetUnspecifiedBondTypes()

void SmilesParseOps::SetUnspecifiedBondTypes

(

RDKit::RWMol *

mol

)