NAME
    GLStrGen.pl - Generate structures for Glycerolipids (GL)

SYNOPSIS
    GLStrGen.pl GLAbbrev|GLAbbrevFileName ...

    GLStrGen.pl [-h, --help] [-o, --overwrite] [-r, --root rootname] [-w,
    --workingdir dirname] <arguments>...

DESCRIPTION
    Generate Glycerolipids (GL) structures using compound abbreviations
    specified on a command line or in a CSV/TSV Text file. All the command
    line arguments represent either compound abbreviations or file name
    containing abbreviations. Use *-m, --mode* option to control the type of
    command line arguments.

    A SD file, containing structures for all GL abbreviations along with
    ontological information, is generated as an output.

SUPPORTED ABBREVIATIONS
    Current support for GL structure generation include these main classes
    and sub classes:

    o Monoradylglycerols

        . Monoacylglycerols
        . Monoalkylglycerols
        . Mono-(1Z-alkenyl)-glycerol

    o Diradylglycerols

        . Diacylglycerols
        . Alkyl, acylglycerols
        . Dialkylglycerols
        . 1Z-alkenyl, acylglycerols

    o Triradylglycerols

        . Triacylglycerols
        . Alkyl, diacylglycerols
        . Dialkyl, monoacylglycerols
        . 1Z-alkenyl, diacylglycerols

OPTIONS
    -h, --help
        Print this help message

    -m, --mode *Abbrev|AbbrevFileName*
        Controls interpretation of command line arguments. Two different
        methods are provided: specify compound abbreviations or a file name
        containing compound abbreviations. Possible values: *Abbrev or
        AbbrevFileName*. Default: *Abbrev*

        In *AbbrevFileName* mode, a single line in CSV/TSV files can contain
        multiple compound abbreviations. The file extension determines
        delimiter used to process data lines: comma for CSV and tab for TSV.
        For files with TXT extension, only one compound abbreviation per
        line is allowed.

        Wild card character, *, is also supported in compound abbreviations.

        Examples:

            Specific structures: MG(16:0/0:0/0:0) DG(18:1(11E)/16:0/0:0)
                                 TG(16:0/16:0/18:1(9Z))
            Specific structures: MG(O-16:0/0:0/0:0) DG(O-16:1(1Z)/16:0/0:0)
                                 TG(O-20:0/16:0/18:1(9Z))
            Specific possibilities: DG(18:*/16:0/0:0) DG(18:1(*)/16:0/0:0)
                                    DG(*:*(9Z)/16:0/0:0)
                                    DG(*:*(9Z)/*:*(11E)/0:0)
            All TG possibilities: *(*:*/*:*/*:*) or *(*/*/*)
            All MG, DG and TG possibilities: "MG(*:*/0:0/0:0)" "DG(*:*/*:*/0:0)"
                                             "DG(*.*/0:0/*:*)" "TG(*:*/*:*/*:*)"

        Along with wild card character, +/- can also be used for chain
        lengths to indicate even and odd lengths at sn1/sn2/sn3 positions;
        additionally > and < qualifiers are also allowed to specify length
        requirements. Examples:

            Odd and even number chains at sn1 and sn2: TG(*+:*/*-:*/*:*)
            Odd and even number chains at sn1 and sn2 with length longer than
            10 and 20: TG(*+>10:*/*->20:*/*:*)

        Default sn2 stereochemistry is R. However, abbreviation format also
        supports these additional stereochemistry specifications for sn2
        position: S; U - unknown; rac - racemic mixture. Examples:

            MG(16:0/0:0/0:0)[rac] - racemic mixture
            DG(18:1(11E)/16:0/0:0)[S] - sn2 stereochemistry is S instead of default R
            TG(16:0/16:0/18:1(9Z))[U] - sn2 stereochemistry is unknown

        To generate all isomers for specific chains in DG and TG, use of iso
        designation is also supported. Stereochemistry specification support
        is not available with isomeric structure generation. Examples:

            DG(18:1(11E)/16:0/0:0)[iso2] - Two isomeric structures
            TG(16:0/16:0/18:1(9Z))[iso3] - Three isomeric structures
            TG(16:0/18:0/18:1(9Z))[iso6] - Six isomeric structures

        Additionally, all isomeric structures can also be generated by
        explicit specification of chains at different positions:

            DG(18:1(11E)/16:0/0:0) DG(16:0/18:1(11E)/0:0)
            TG(16:0/16:0/18:1(9Z)) TG(16:0/18:1(9Z)/16:0)
            TG(18:1(9Z)/16:0/16:0/)

        Wild card chain abbreviations are supported with sn2 stereochemistry
        but not with isomer abbreviation.

    -o, --overwrite
        Overwrite existing files

    -r, --root *rootname*
        New file name is generated using the root: <Root>.sdf. Default for
        new file names: GLAbbrev.sdf, <AbbrevFilenName>.sdf, or
        <FirstAbbrevFileName>1To<Count>.sdf.

    -w, --workingdir *dirname*
        Location of working directory. Default: current directory

EXAMPLES
    On some systems, command line scripts may need to be invoked using *perl
    -s GLStrGen.pl*; however, all the examples assume direct invocation of
    command line script works.

    To generate a GLStructures.sdf file containing a structure specified by
    a command line GL abbreviation, type:

        % GLStrGen.pl -r GLStructures -o "MG(16:0/0:0/0:0)"

    To generate a GLStructures.sdf file containing structures specified by a
    command line GL abbreviations, type:

        % GLStrGen.pl -r GLStructures -o "MG(16:0/0:0/0:0)"
        "DG(18:1(11E)/16:0/0:0)" "TG(16:0/16:0/18:1(9Z))"

    To generate a GLStructures.sdf file containing structures specified by a
    command line GL abbreviations with specific stereochemistry, type:

        % GLStrGen.pl -r GLStructures -o "MG(16:0/0:0/0:0)[rac]"
        "DG(18:1(11E)/16:0/0:0)[S]" "TG(16:0/16:0/18:1(9Z))[U]"

    To generate a GLStructures.sdf file containing all isomeric structures
    specified by a command line GL abbreviations, type:

        % GLStrGen.pl -r GLStructures -o "DG(18:1(11E)/16:0/0:0)[iso2]"
        "TG(16:0/16:0/18:1(9Z))[iso3]" "TG(16:0/16:0/18:1(9Z))[iso6]"

    To enumerate all possible GL structures and generate a GLStructures.sdf
    file, type:

        % GLStrGen.pl -r GLStructures -o "*(*/*/*)"

    or

        % GLStrGen.pl -r GLStructures -o "*(*:*/*:*/*:*)"

    or

        % GLStrGen.pl -r GLStructures -o "*(*:*(*)/*:*(*)/*:*(*))"

    To enumerate all possible Monoradylglycerols structures and generate a
    MonoGLStructures.sdf file, type:

        % GLStrGen.pl -r MonoGLStructures -o "MG(*/0:0/0:0)"

    To enumerate all possible Diradylglycerols structures and generate a
    DiGLStructures.sdf file, type:

        % GLStrGen.pl -r DiGLStructures -o "DG(*/*/0:0)"

    To enumerate all possible Monoradylglycerols structures with one double
    bond on acyl chain and generate a GLStructures.sdf file, type:

        % GLStrGen.pl -r MonoGLStructures -o "MG(*:1/0:0/0:0)"

    To enumerate all possible Monoradylglycerols structures with even chain
    lengths and generate a GLStructures.sdf file, type:

        % GLStrGen.pl -r MonoGLStructures -o "MG(*+:*/0:0/0:0)"

    To enumerate all possible Diradylglycerols structures with odd chains
    longer than 10 at sn1 and even chains longer than 18 at sn2, and
    generate a DiGLStructures.sdf file, type:

        % GLStrGen.pl -r DiGLStructures -o "DG(*->10:*/*+>18:*/0:0)"

AUTHOR
    Manish Sud

CONTRIBUTOR
    Eoin Fahy

SEE ALSO
    GPStrGen.pl

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

