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

SEE ALSO
    ChainAbbrev.pm, ChainStr.pm, LMAPSStr.pm

COPYRIGHT
    Copyright (C) 2006-2012. The Regents of the University of California.
    All Rights Reserved.

LICENSE
    Modified BSD License

