NAME
    LMStrGen.pl - Generate arbitrary LIPID MAPS structures

SYNOPSIS
    LMStrGen.pl LMAbbrev|LMAbbrevFileName ...

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

DESCRIPTION
    Generate arbitrary LIPID MAPS (LM) 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 mode option to control the type
    of command line arguments.

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

SUPPORTED ABBREVIATIONS
    Current support for LM structure generation include these headgroups and
    acyl chains:

       o DIMAXX - sn1, sn2 and sn3
       o DIMA20 - sn1 and sn2
       o DIMA22 - sn1 and sn2
       o DIMA20Me - sn1 and sn2
       o DIMA22Me - sn1 and sn2
       o DIMB20 - sn1 and sn2
       o DIMB22 - sn1 and sn2
       o DIB20Me - sn1 and sn2
       o DIB22Me - sn1 and sn2
       o PIM1 - sn1 and sn2
       o PIM2 - sn1 and sn2
       o PIM3 - sn1 and sn2
       o PIM4 - sn1 and sn2
       o PIM5 - sn1 and sn2
       o PIM6 - sn1 and sn2
       o DAT - sn1 and sn2
       o CoA - sn1

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 not supported in compound abbreviations.

        Examples:

            Specific structures: DIMA20(12:0/13:0) DIMB20(17:1(9Z)/18:0)
                                 CoA(16:0) PIM1(21:0/22:0)

    -o, --overwrite
        Overwrite existing files

    -r, --root *rootname*
        New file name is generated using the root: <Root>.sdf. Default for
        new file names: LMAbbrev.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 LMStrGen.pl*; however, all the examples assume direct invocation of
    command line script works.

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

        % LMStrGen.pl -r LMStructures -o "DIMA20(12:0/13:0)"

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

        % LMStrGen.pl -r LMStructures -o "DIMA22(16:0/18:0)" "DIMA22Me(18:1(11E)/16:0)"

AUTHOR
    Manish Sud

CONTRIBUTOR
    Eoin Fahy

SEE ALSO
    CLStrGen.pl, FAStrGen.pl, GLStrGen.pl, SPStrGen.pl, STStrGen.pl

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

LICENSE
    Modified BSD License

