NAME
    LMAPSStr - Glycerolipids (GL) structure generation methods

SYNOPSIS
    use LMAPSStr;

    use LMAPSStr qw(:all);

DESCRIPTION
    LMAPSStr module provides these methods:

        GenerateCmpdAtomLine - Generate SD file atom data line
        GenerateCmpdBondLine - Generate SD file bond data line
        GenerateCmpdCountsLine - Generate SD file count data line
        GenerateCmpdMiscInfoLine - Generate SD file misc data line
        ParseCmpdAtomLine - Parse SD file atom data line
        ParseCmpdBondLine - Parse SD file bond data line
        ParseCmpdCountsLine - Parse SD file count data line
        RoundToNextInteger - Round up to next integer
        SetupCmpdAbbrevs - Setup lipid abbreviations
        SetupSDFileName - Setup SD file name
        StandardizeStereochemistrySpec - Standardize stereochemistry
        StandardizeStereochemistrySpec - Standardize ring stereochemistry

METHODS
    GenerateCmpdAtomLine
            $Line = GenerateCmpdAtomLine($AtomX, $AtomY, $AtomZ, $AtomSymbol);

        Return a formatted atom data line for SD file.

    GenerateCmpdBondLine
            $Line = GenerateCmpdBondLine($FirstAtomNum, $SecondAtomNum,
                    $BondType, [$BondStereo]);

        Return a formatted bond data line for SD file.

    GenerateCmpdCountsLine
            $Line = GenerateCmpdCountsLine($AtomCount, $BondCount,
                    [$ChiralFlag, $PropertyCount, $Version]);

        Return a formatted count data line for SD file.

    GenerateCmpdMiscInfoLine
            $Line = GenerateCmpdMiscInfoLine();

        Return a formatted miscellaneous data line for SD file. In addition
        to a time stamp, LipdMAPS name is used as the program name.

    ParseCmpdAtomLine
            ($AtomX, $AtomY, $AtomZ, $AtomSymbol) = ParseCmpdAtomLine($Line);

        Parse SD file atom data line and return a list with these values:
        atom coordinates and element symbol.

    ParseCmpdBondLine
            ($FirstAtomNum, $SecondAtomNum, $BondType, $BondStereo) =
                ParseCmpdBondLine($Line);

        Parse SD file atom bond data line and return a list containing these
        values: bond atom numbers and bond type.

    ParseCmpdCountsLine
            ($AtomCount, $BondCount, $ChiralFlag, $PropertyCount, $Version) =
                 ParseCmpdCountsLine($Line);

        Parse SD file count data line and return a list containing these
        values: atom/bond count and other miscellaneous count information.

    RoundToNextInteger
            $IntegerValue = RoundToNextInteger($Number);

        Return an integer by rounding the number off to next integer.

    SetupCmpdAbbrevs
            $AbbrebArrayRef = SetupCmpdAbbrevs($CmdLineOptionsRef);

        Return a reference to an array containing specified compound
        abbreviations by parsing command line arguments or processing files
        containing specified abbreviations.

    SetupSDFileName
            $SDFilename = SetupSDFileName($LipidCategory, $CmdLineOptionsRef);

        Return a SD file name by processing a specified *-r, --root* option
        or using default values.

    StandardizeStereochemistrySpec
            $StandardizeSpec = StandardizeStereochemistrySpec($StereochemistrySpec);

        Return a standardize stereochemistry specification containg R/S
        instead of a/b or alpha/beta.

    StandardizeRingStereochemistrySpec
            $StandardizeSpec = StandardizeRingStereochemistrySpec($StereochemistrySpec);

        Return a standardize stereochemistry specification containg
        alpha/beta instead of a/b or alpha/beta.

AUTHOR
    Manish Sud

CONTRIBUTOR
    Eoin Fahy

SEE ALSO
    ChainAbbrev.pm, ChainStr.pm

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

LICENSE
    Modified BSD License

