NAME
    ChainStr - Fatty Acyls (FA), Glycerolipids (GL) and Glycerophospholipids
    (GP) structure data generation methods

SYNOPSIS
    use ChainStr;

    use ChainStr qw(:all);

DESCRIPTION
    ChainStr module provides these methods:

        AssignSubstituentStereoChemistry - Assign stereochemistry to substituents
        GenerateAtomBlockLines - Generate SD file atom data lines
        GenerateBondBlockLines - Generate SD file bond data lines
        GenerateChainStrData - Generate structure data for chains
        GenerateCmpdCountsLine - Generate SD file count data line
        IsAnySubstituentSpecifiedWithStereoChemistry - Check stereochemistry of
                                                       substituents
        SetupTemplateDataMap - Set up template data for a compound abbreviation

METHODS
    AssignSubstituentStereoChemistry
            AssignSubstituentStereoChemistry($CmpdAbbrevTemplateDataMapRef,
                $CmdDataLinesRef);

        Assign stereochemistry to substituents using structure and
        stereochemistry data available via $CmpdAbbrevTemplateDataMapRef and
        $CmdDataLinesRef. And add new lines to existing structure data using
        $CmdDataLinesRef.

    GenerateAtomBlockLines
            $AtomDataLines = GenerateAtomBlockLines($CmpdAbbrevTemplateDataMapRef,
                $Sn1AtomLinesRef, $Sn2AtomLinesRef, $Sn3AtomLinesRef);

        Return atom data lines suitable for writing to SD file. Atom data
        for all approrpriate chains is merged into a single string using new
        line character as delimiter.

    GenerateBondBlockLines
            $BondDataLines = GenerateBondBlockLines($CmpdAbbrevTemplateDataMapRef,
                $Sn1BondLinesRef, $Sn2AtomLinesRef, $Sn3AtomLinesRef);

        Return bond data lines suitable for writing to SD file. Bond data
        for all approrpriate chains is merged into a single string using new
        line character as delimiter.

    GenerateChainStrData
            ($AtomLinesArrayRef, $BondLinesArrayRef) = GenerateChainStrData($ChainType,
                $CmpdAbbrevTemplateDataMapRef);

        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.

    GenerateCmpdCountsLine
            $RetValue = GenerateCmpdCountsLine($CmpdAbbrevTemplateDataMapRef);

        Return a formatted count data line for SD file.

    IsAnySubstituentSpecifiedWithStereoChemistry
            $Status = IsAnySubstituentSpecifiedWithStereoChemistry(
                $CmpdAbbrevTemplateDataMapRef);

        Return 1 or 0 based on whether stereochemistry is specifed for any
        substituent.

    SetupTemplateDataMap
            SetupTemplateDataMap($TemplateType, $AbbrevTemplateDataMapRef,
                $TemplateData);

        Setup compound abbreviation template data using a supported
        template.

AUTHOR
    Manish Sud

CONTRIBUTOR
    Eoin Fahy

SEE ALSO
    FAStr.pm, GLStr.pm, GPStr.pm, LMAPSStr.pm, SPStr.pm

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

LICENSE
    Modified BSD License

