RDKit::Abbreviations Namespace Reference

Namespaces
namespace	common_properties
namespace	Utils

Classes
struct	AbbreviationDefinition
struct	AbbreviationMatch

Functions
RDKIT_ABBREVIATIONS_EXPORT std::vector< AbbreviationMatch >	findApplicableAbbreviationMatches (const ROMol &mol, const std::vector< AbbreviationDefinition > &abbrevs, double maxCoverage=0.4)
	returns all matches for the abbreviations across the molecule
RDKIT_ABBREVIATIONS_EXPORT void	applyMatches (RWMol &mol, const std::vector< AbbreviationMatch > &matches)
RDKIT_ABBREVIATIONS_EXPORT void	labelMatches (RWMol &mol, const std::vector< AbbreviationMatch > &matches)
	creates "SUP" SubstanceGroups on the molecule describing the abbreviation
RDKIT_ABBREVIATIONS_EXPORT void	condenseMolAbbreviations (RWMol &mol, const std::vector< AbbreviationDefinition > &abbrevs, double maxCoverage=0.4, bool sanitize=true)
RDKIT_ABBREVIATIONS_EXPORT void	labelMolAbbreviations (RWMol &mol, const std::vector< AbbreviationDefinition > &abbrevs, double maxCoverage=0.4)
RDKIT_ABBREVIATIONS_EXPORT void	condenseAbbreviationSubstanceGroups (RWMol &mol)

Function Documentation

applyMatches()

RDKIT_ABBREVIATIONS_EXPORT void RDKit::Abbreviations::applyMatches	(	RWMol &	mol,
		const std::vector< AbbreviationMatch > &	matches
	)

applies the abbreviation matches to a molecule, modifying it in place. the modified molecule is not sanitized

condenseAbbreviationSubstanceGroups()

RDKIT_ABBREVIATIONS_EXPORT void RDKit::Abbreviations::condenseAbbreviationSubstanceGroups

(

RWMol &

mol

)

collapses abbreviation (i.e. "SUP") substance groups the modified molecule is not sanitized

condenseMolAbbreviations()

RDKIT_ABBREVIATIONS_EXPORT void RDKit::Abbreviations::condenseMolAbbreviations	(	RWMol &	mol,
		const std::vector< AbbreviationDefinition > &	abbrevs,
		double	maxCoverage = 0.4,
		bool	sanitize = true
	)

convenience function for finding and applying abbreviations the modified molecule is not sanitized

findApplicableAbbreviationMatches()

RDKIT_ABBREVIATIONS_EXPORT std::vector< AbbreviationMatch > RDKit::Abbreviations::findApplicableAbbreviationMatches	(	const ROMol &	mol,
		const std::vector< AbbreviationDefinition > &	abbrevs,
		double	maxCoverage = 0.4
	)

returns all matches for the abbreviations across the molecule

Parameters

abbrevs	the abbreviations to look for. This list is used in order.
maxCoverage	any abbreviation that covers than more than this fraction of the molecule's atoms (not counting dummies) will not be returned.

labelMatches()

RDKIT_ABBREVIATIONS_EXPORT void RDKit::Abbreviations::labelMatches	(	RWMol &	mol,
		const std::vector< AbbreviationMatch > &	matches
	)

creates "SUP" SubstanceGroups on the molecule describing the abbreviation

labelMolAbbreviations()

RDKIT_ABBREVIATIONS_EXPORT void RDKit::Abbreviations::labelMolAbbreviations	(	RWMol &	mol,
		const std::vector< AbbreviationDefinition > &	abbrevs,
		double	maxCoverage = 0.4
	)

convenience function for finding and labeling abbreviations as SUP SubstanceGroups