SmilesParseOps Namespace Reference

Namespaces
namespace	detail

Functions
RDKIT_SMILESPARSE_EXPORT void	CheckRingClosureBranchStatus (RDKit::Atom *atom, RDKit::RWMol *mp)
RDKIT_SMILESPARSE_EXPORT void	ReportParseError (const char *message, bool throwIt=true)
RDKIT_SMILESPARSE_EXPORT void	CleanupAfterParseError (RDKit::RWMol *mol)
RDKIT_SMILESPARSE_EXPORT void	AddFragToMol (RDKit::RWMol *mol, RDKit::RWMol *frag, RDKit::Bond::BondType bondOrder=RDKit::Bond::UNSPECIFIED, RDKit::Bond::BondDir bondDir=RDKit::Bond::NONE)
RDKIT_SMILESPARSE_EXPORT RDKit::Bond::BondType	GetUnspecifiedBondType (const RDKit::RWMol *mol, const RDKit::Atom *atom1, const RDKit::Atom *atom2)
RDKIT_SMILESPARSE_EXPORT void	CheckChiralitySpecifications (RDKit::RWMol *mol, bool strict)
RDKIT_SMILESPARSE_EXPORT void	CloseMolRings (RDKit::RWMol *mol, bool toleratePartials)
RDKIT_SMILESPARSE_EXPORT void	SetUnspecifiedBondTypes (RDKit::RWMol *mol)
RDKIT_SMILESPARSE_EXPORT void	AdjustAtomChiralityFlags (RDKit::RWMol *mol)
RDKIT_SMILESPARSE_EXPORT void	CleanupAfterParsing (RDKit::RWMol *mol)
RDKIT_SMILESPARSE_EXPORT void	parseCXExtensions (RDKit::RWMol &mol, const std::string &extText, std::string::const_iterator &pos, unsigned int startAtomIdx=0, unsigned int startBondIdx=0)
void	parseCXExtensions (RDKit::RWMol &mol, const std::string &extText, unsigned int startAtomIdx, unsigned int startBondIdx)
RDKIT_SMILESPARSE_EXPORT void	ClearAtomChemicalProps (RDKit::Atom *atom)
	removes formal charge, isotope, etc. Primarily useful for QueryAtoms
RDKIT_SMILESPARSE_EXPORT bool	checkChiralPermutation (int chiralTag, int permutation)
RDKIT_SMILESPARSE_EXPORT RDKit::QueryBond *	getUnspecifiedQueryBond (const RDKit::Atom *a1, const RDKit::Atom *a2)

Function Documentation

AddFragToMol()

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

AdjustAtomChiralityFlags()

RDKIT_SMILESPARSE_EXPORT void SmilesParseOps::AdjustAtomChiralityFlags

(

RDKit::RWMol *

mol

)

CheckChiralitySpecifications()

RDKIT_SMILESPARSE_EXPORT void SmilesParseOps::CheckChiralitySpecifications	(	RDKit::RWMol *	mol,
		bool	strict
	)

checkChiralPermutation()

RDKIT_SMILESPARSE_EXPORT bool SmilesParseOps::checkChiralPermutation	(	int	chiralTag,
		int	permutation
	)

returns whether or not the combination of tag and permutation provided are legal

CheckRingClosureBranchStatus()

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

CleanupAfterParseError()

RDKIT_SMILESPARSE_EXPORT void SmilesParseOps::CleanupAfterParseError

(

RDKit::RWMol *

mol

)

CleanupAfterParsing()

RDKIT_SMILESPARSE_EXPORT void SmilesParseOps::CleanupAfterParsing

(

RDKit::RWMol *

mol

)

ClearAtomChemicalProps()

RDKIT_SMILESPARSE_EXPORT void SmilesParseOps::ClearAtomChemicalProps

(

RDKit::Atom *

atom

)

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

CloseMolRings()

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

GetUnspecifiedBondType()

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

getUnspecifiedQueryBond()

RDKIT_SMILESPARSE_EXPORT RDKit::QueryBond * SmilesParseOps::getUnspecifiedQueryBond	(	const RDKit::Atom *	a1,
		const RDKit::Atom *	a2
	)

this is a bit of a hack to try and get nicer "SMILES" from a SMARTS molecule

parseCXExtensions() [1/2]

RDKIT_SMILESPARSE_EXPORT void SmilesParseOps::parseCXExtensions	(	RDKit::RWMol &	mol,
		const std::string &	extText,
		std::string::const_iterator &	pos,
		unsigned int	startAtomIdx = 0,
		unsigned int	startBondIdx = 0
	)

Referenced by parseCXExtensions().

parseCXExtensions() [2/2]

void SmilesParseOps::parseCXExtensions ( RDKit::RWMol &  mol, const std::string &  extText, unsigned int  startAtomIdx, unsigned int  startBondIdx  )

inline

Definition at line 48 of file SmilesParseOps.h.

References parseCXExtensions().

ReportParseError()

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

SetUnspecifiedBondTypes()

RDKIT_SMILESPARSE_EXPORT void SmilesParseOps::SetUnspecifiedBondTypes

(

RDKit::RWMol *

mol

)