NAME
    GPStrGen.pl - Generate structures for Glycerophospholipids (GP)

SYNOPSIS
    GPStrGen.pl GPAbbrev|GPAbbrevFileName ...

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

DESCRIPTION
    Generate Glyceriphospholipids (GP) 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 GP abbreviations along with
    ontological information, is generated as an output.

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

    o Glycerophosphocholines (GPCho)

        . Diacylglycerophosphocholines
        . 1-alkyl,2-acylglycerophosphocholines
        . 1Z-alkenyl,2-acylglycerophosphocholines
        . Dialkylglycerophosphocholines
        . Monoacylglycerophosphocholines
        . 1-alkyl glycerophosphocholines
        . 1Z-alkenylglycerophosphocholines

    o Glycerophosphoethanolamines (GPEtn)

        . Diacylglycerophosphoethanolamines
        . 1-alkyl,2-acylglycerophosphoethanolamines
        . 1Z-alkenyl,2-acylglycerophosphoethanolamines
        . Dialkylglycerophosphoethanolamines
        . Monoacylglycerophosphoethanolamines
        . 1-alkyl glycerophosphoethanolamines
        . 1Z-alkenylglycerophosphoethanolamines

    o Glycerophosphoserines (GPSer)

        . Diacylglycerophosphoserines
        . 1-alkyl,2-acylglycerophosphoserines
        . 1Z-alkenyl,2-acylglycerophosphoserines
        . Dialkylglycerophosphoserines
        . Monoacylglycerophosphoserines
        . 1-alkyl glycerophosphoserines
        . 1Z-alkenylglycerophosphoserines

    o Glycerophosphoglycerols (GPGro)

        . Diacylglycerophosphoglycerols
        . 1-alkyl,2-acylglycerophosphoglycerols
        . 1Z-alkenyl,2-acylglycerophosphoglycerols
        . Dialkylglycerophosphoglycerols
        . Monoacylglycerophosphoglycerols
        . 1-alkyl glycerophosphoglycerols
        . 1Z-alkenylglycerophosphoglycerols

    o Glycerophosphoglycerophosphates (GPGroP)

        . Diacylglycerophosphoglycerophosphates
        . 1-alkyl,2-acylglycerophosphoglycerophosphates
        . 1Z-alkenyl,2-acylglycerophosphoglycerophosphates
        . Dialkylglycerophosphoglycerophosphates
        . Monoacylglycerophosphoglycerophosphates
        . 1-alkyl glycerophosphoglycerophosphates
        . 1Z-alkenylglycerophosphoglycerophosphates

    o Glycerophosphoinositols (GPIns)

        . Diacylglycerophosphoinositols
        . 1-alkyl,2-acylglycerophosphoinositols
        . 1Z-alkenyl,2-acylglycerophosphoinositols
        . Dialkylglycerophosphoinositols
        . Monoacylglycerophosphoinositols
        . 1-alkyl glycerophosphoinositols
        . 1Z-alkenylglycerophosphoinositols

    o Glycerophosphoinositol monophosphates (GPInsP)

        . Diacylglycerophosphoinositol monophosphates
        . 1-alkyl,2-acylglycerophosphoinositol monophosphates
        . 1Z-alkenyl,2-acylglycerophosphoinositol monophosphates
        . Dialkylglycerophosphoinositol monophosphates
        . Monoacylglycerophosphoinositol monophosphates
        . 1-alkyl glycerophosphoinositol monophosphates
        . 1Z-alkenylglycerophosphoinositol monophosphates

    o Glycerophosphates (GPA)

        . Diacylglycerophosphates
        . 1-alkyl,2-acylglycerophosphates
        . 1Z-alkenyl,2-acylglycerophosphates
        . Dialkylglycerophosphates
        . Monoacylglycerophosphates
        . 1-alkyl glycerophosphates
        . 1Z-alkenylglycerophosphates

    o Glyceropyrophosphates (GPP)

        . Diacylglyceropyrophosphates
        . Monoacylglyceropyrophosphates

    o Glycerophosphonocholines (GPnCho)

        . Diacylglycerophosphonocholines
        . 1-alkyl,2-acylglycerophosphonocholines
        . 1Z-alkenyl,2-acylglycerophosphonocholines
        . Dialkylglycerophosphonocholines
        . Monoacylglycerophosphonocholines
        . 1-alkyl glycerophosphonocholines
        . 1Z-alkenylglycerophosphonocholines

    o Glycerophosphonoethanolamines (GPnEtn)

        . Diacylglycerophosphonoethanolamines
        . 1-alkyl,2-acylglycerophosphonoethanolamines
        . 1Z-alkenyl,2-acylglycerophosphonoethanolamines
        . Dialkylglycerophosphonoethanolamines
        . Monoacylglycerophosphonoethanolamines
        . 1-alkyl glycerophosphonoethanolamines
        . 1Z-alkenylglycerophosphonoethanolamines

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: GPCho(12:0/13:0) GPCho(17:1(9Z)/0:0)
                                 GPA(13:0/0:0)
            Specific structures: GPCho(O-16:0/13:0) GPCho(O-16:1(1Z)/0:0)
            Specific possibilities: GPCho(21:0/22:*) GPA(17:*/0:0)
                                    GPEtn(O-18:0/*:*)
            All possibilites: *(*:*/*:*) or *(*/*)

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

            GPCho(12:0/13:0)[rac]
            GPCho(17:1(9Z)/14:0)[S]
            GPA(13:0/12:0)[U]

    -o, --overwrite
        Overwrite existing files

    -r, --root *rootname*
        New file name is generated using the root: <Root>.sdf. Default for
        new file names: GPAbbrev.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 GPStructures.sdf file containing a structure specified by
    a command line GP abbreviation, type:

        % GPStrGen.pl -r GPStructures -o "GPCho(16:0/0:0)"

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

        % GPStrGen.pl -r GPStructures -o "GPCho(16:0/0:0)" "GPEtn(18:1(11E)/16:0)"

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

        % GPStrGen.pl -r GPStructures -o "GPCho(16:0/0:0)[U]"
        "GPEtn(18:1(11E)/16:0)[S]"

    To enumerate all possible GP structures and generate a GPStructures.sdf
    file, type:

        % GPStrGen.pl -r GPStructures -o "*(*/*)"

    or

        % GPStrGen.pl -r GPStructures -o "*(*:*/*:*)"

    or

        % GPStrGen.pl -r GPStructures -o "*(*:*(*)/*:*(*))"

    To enumerate all possible GP structures with a sn1 chain, and generate a
    GPStructures.sdf file, type:

        % GPStrGen.pl -r GPStructures -o "*(*/0:0)"

    To enumerate all possible GP structures with a sn1 chain containing one
    double bond, and generate a GPStructures.sdf file, type:

        % GPStrGen.pl -r GPStructures -o "*(*:1/0:0)"

    To enumerate all possible GP structures with even chain length larger
    than 10 at sn1 position, and generate and generate a GPStructures.sdf
    file, type:

        % GPStrGen.pl -r GPStructures -o "*(*+:*/0:0/0:0)"

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

        % GPStrGen.pl -r GPStructures -o "*(*->10:*/*+>18:*)"

AUTHOR
    Manish Sud

CONTRIBUTOR
    Eoin Fahy

SEE ALSO
    GLStrGen.pl

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

