NAME
    CLStr - Cardiolipins (CL) structure generation methods

SYNOPSIS
    use CLStr;

    use CLStr qw(:all);

DESCRIPTION
    CLStr module provides these methods:

        GenerateCmpdOntologyData - Generate ontology data
        GenerateCmpdOntologySDDataLines - Generate ontology data lines for
                                          SD file
        GenerateCLChainStrData - Generate chain structure data
        GenerateSDFile - Generate SD file
        GetCLTemplatesData - Get templates data
        GetCLSupportedHeadGroupMap - Get supported headgroups data
        GetCLTemplateID - Get templates ID
        IsCLChainsAbbrevSupported - Is it a supported CL abbreviation
        ParseCLAbbrev - Parse CL abbreviation
        ProcessCLCmpdAbbrevs - Process CL abbreviation
        SetupCLCmpdAbbrevTemplateDataMap - Setup template structure data map
        ValidateCLAbbrev - Validate CL abbreviation

METHODS
    GenerateCmpdOntologyData
            $DataHashRef = GenerateCmpdOntologyData($CmpDataRef);

        Return a reference to a hash containing ontology data with hash keys
        and values corresponding to property names and values.

    GenerateCmpdOntologySDDataLines
            $DataLinesArrayRef =
               GenerateCmpdOntologySDDataLines($CmpdDataRef);

        Return a reference to an array containing ontology data lines
        suitable for generate SD file data block.

    GenerateCLChainStrData
            ($AtomLinesArrayRef, $BondLinesArrayRef) =
               GenerateCLChainStrData($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.

    GetCLTemplatesData
            $TemplatesDataRef = GetCLTemplatesData();

        Return a reference to a hash containing CL templates data

    GetCLSupportedHeadGroupMap
            $SupportedHeadGroupDataRef = GetCLSupportedHeadGroupMap();

        Return a reference to a hash containing supported head groups data.

    GetCLTemplateID
            $HeadGroupID = GetCLTemplateID($HeadGroupAbbrev, $ChainsAbbrev);

        Return a supported template ID for compound abbreviation.

    IsCLChainsAbbrevSupported
            $Status = IsCLChainsAbbrevSupported($Abbrev, $PrintWarning);

        Return 1 or 0 based on whether CL abbreviated is supported. For
        unsupported CL abbreviations, a warning is printed unless
        PrintWarning flag is set.

    ParseCLAbbrev
            ($HeadGroup, $ChainsAbbrev, $AbbrevModifier) =
               ParseCLAbbrev($Abbrev);

        Parse CL abbreviation and return these values: HeadGroup,
        ChainsAbbrev, AbbrevModifier.

    ProcessCLCmpdAbbrevs
            ProcessCLCmpdAbbrevs($CmpdAbbrevsRef, $AllowArbitraryChainAbbrev,
                                 $WriteSDFile, $SDFileName);

        Process specified CL abbreviations to generate structures and write
        them out either a SD file or simply report number of valid
        abbreviations.

    SetupCLCmpdAbbrevTemplateDataMap
            $AbbrevTemplateDataMapRef =
               SetupCLCmpdAbbrevTemplateDataMap($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.

    ValidateCLAbbrev
            $Status = ValidateCLAbbrev($Abbrev);

        Return 1 or 0 based on whether a CL 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

