NAME

GLStr - Glycerolipids (GL) structure generation methods

SYNOPSIS

use GLStr;

use GLStr qw(:all);

DESCRIPTION

GLStr module provides these methods:

GenerateCmpdOntologyData - Generate ontology data
GenerateCmpdOntologySDDataLines - Generate ontology data lines for SD file
GenerateGLChainStrData - Generate chain structure data
GenerateSDFile - Generate SD file
IsGLAbbrevSupported - Is it a supported GL abbreviation
ParseGLAbrev - Parse GL abbreviation
ProcessGLCmpdAbbrevs - Process GL abbreviation
SetupGLCmpdAbbrevTemplateDataMap - Setup template structure data map
ValidateGLAbbrev - Validate GL abbreviation

METHODS

ExpandGLCmpdAbbrevs: $ExpandedAbbrevArrayRef = ExpandGLCmpdAbbrevs($CmpdAbbrev);

Return a reference to an array containing complete GL abbreviations. Wild card characters in GL abbreviation name are expanded to generate fully qualified GL abbreviations.
GenerateCmpdOntologyData: $DataHashRef = GenerateCmpdOntologyData($CmpdDataRef);

Return a reference to a hash containing ontology data with hash keys and values corresponding to property names and values.
GenerateCmpdOntologySDDataLines: $DataLinesArrayRef = GenerateCmpdOntologySDDataLines($CmpDataRef);

Return a reference to an array containing ontology data lines suitable for generate SD file data block.
GenerateGLChainStrData: ($AtomLinesArrayRef, $BondLinesArrayRef) = GenerateGLChainStrData($ChainType, $CmpdDataRef);

Return array references containing atom and bond data lines for SD file. Appropriate atom and bond data lines are generated using chain type and abbreviation template data.
GenerateSDFile: GenerateSDFile($SDFileName, $CmdAbbrevsRef);

Generate a SD file for compound abbreviations. Structure data for specified abbreviation is generated sequentially and written to SD file.
IsGLAbbrevSupported: $Status = IsGLAbbrevSupported($Abbrev, $PrintWarning);

Return 1 or 0 based on whether GL abbreviated is supported. For unsupported GL abbreviations, a warning is printed unless PrintWarning flag is set.
ParseGLAbrev: ($GLType, $ChainsAbbrev, $AbbrevModifier) = ParseGLAbrev($Abbrev);

Parse GL abbreviation and return these values: GLType, ChainsAbbrev, AbbrevModifier.
ProcessGLCmpdAbbrevs: ProcessGLCmpdAbbrevs($CmpdAbbrevsRef, $AllowArbitraryChainAbbrev, $WriteSDFile, $SDFileName);

Process specified GL abbreviations to generate structures and write them out either a SD file or simply report number of valid abbreviations.
SetupGLCmpdAbbrevTemplateDataMap: $AbbrevTemplateDataMapRef = SetupGLCmpdAbbrevTemplateDataMap($Abbrev);

Return a reference to a hash containing template data for compound abbreviation. The template data is used to generate SD file for compound abbreviation.
ValidateGLAbbrev: $Status = ValidateGLAbbrev($Abbrev);

Return 1 or 0 based on whether a GL abbreviation is valid.

AUTHOR

Manish Sud

CONTRIBUTOR

Eoin Fahy

COPYRIGHT

LICENSE

Modified BSD License