NAME
    FAStrGen.pl - Generate structures for Fatty Acyls (FA)

SYNOPSIS
    FAStrGen.pl FAAbbrev|FAAbbrevFileName ...

    FAStrGen.pl [-h, --help] [-m, --mode *Abbrev | AbbrevFileName*] [-p,
    --ProcessMode *WriteSDFile | CountOnly*] [-o, --overwrite] [-r, --root
    rootname] [-w, --workingdir dirname] <arguments>...

DESCRIPTION
    Generate Fatty Acyls (FA) 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 SP abbreviations along with
    ontological information, is generated as an output.

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

    o Fatty Acids and Conjugates

        . Straight chain fatty acids
        . Methyl branched fatty acids
        . Unsaturated fatty acids
        . Hydroperoxy fatty acids
        . Hydroxy fatty acids
        . Oxo fatty acids
        . Epoxy fatty acids
        . Methoxy fatty acids
        . Halogenated fatty acids
        . Amino fatty acids
        . Cyano fatty acids
        . Nitro fatty acids
        . Thia fatty acids

    o Eicosanoids

        . Prostaglandins

    o Fatty alcohols

    o Fatty aldehydes

    o Fatty amides

        . Primary amides

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
        to generate straight chain and unsaturated fatty acids.

        Examples:

            Specific structures: "18:0" "20:4(5Z,8Z,11Z,14Z)"
                                 "28:1(12Z)(2Me,4Me,6Me)"
                                 "18:3(6Z,9Z,11E)(13OOH[S])"
                                 "18:2(9E,11E)(13OH)"
                                 "18:1(10E)(9Ke,10Ep)"
                                 "16:1(5Z)(2OMe)" "7:1(2Z)(3Br)"
                                 "18:2(9Z,12Z)(10NO2)" "16:2(10E,12Z)(1OH)"
                                 "6:0(1CHO)" "12:0(1NH2)"
                                 "20:2(5Z,13E)(9OH[S],11OH[R],15OH[S]){8a,12b}"
            All possibilites: *:* or *

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

            Odd number chains: "*-:*"
            Even number chains: "*+:*"
            Odd number chains with chain length longer than 18: "*->18:*"
            Even number chains with chain length longer than 14: "*+>14:*"

    -o, --overwrite
        Overwrite existing files

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

    -p, --ProcessMode *WriteSDFile|CountOnly*
        Specify how abbreviations are processed: generate structures for
        specified abbreviations along with generating a SD file or just
        count the number of structures corresponding to specified
        abbreviations without generating any SD file. Possible values:
        *WriteSDFile or CountOnly*. Default: *WriteSDFile*.

        It can take substantial amount of time for generating all the
        structures and writing out a SD file for abbreviations containing
        wild cards. *CountOnly* value of --ProcessMode option can be used to
        get a quick count of number of structures to be generated without
        writing out any SD file.

    -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 FAStrGen.pl*; however, all the examples assume direct invocation of
    command line script works.

    To generate a FAStructures.sdf file containing a structure specified by
    a command line FA abbreviation for straight chain fatty acids, type:

        % FAStrGen.pl -r FAStructures -o "18:0" "9:0"

    To generate a FAStructures.sdf file containing a structure specified by
    a command line FA abbreviation for methyl branched fatty acids, type:

        % FAStrGen.pl -r FAStructures -o "8:0(6Me)" "18:1(6Z)(17Me)"
        "28:1(12Z)(2Me,4Me,6Me)"

    To generate a FAStructures.sdf file containing a structure specified by
    a command line FA abbreviation for unsaturated fatty acids, type:

        % FAStrGen.pl -r FAStructures -o "20:4(5Z,8Z,11Z,14Z)" "8:1(5E)"

    To generate a FAStructures.sdf file containing a structure specified by
    a command line FA abbreviation for hydroperoxy fatty acids, type:

        % FAStrGen.pl -r FAStructures -o "18:2(9E,11E)(13OOH)"
        "18:3(6Z,9Z,11E)(13OOH[S])"

    To generate a FAStructures.sdf file containing a structure specified by
    a command line FA abbreviation for hydroxy fatty acids, type:

        % FAStrGen.pl -r FAStructures -o "10:0(10OH)" "15:0(2OH,15OH)"
         "18:2(9E,11E)(13OH)" "4:0(3OH[R])"

    To generate a FAStructures.sdf file containing a structure specified by
    a command line FA abbreviation for oxo fatty acids, type:

        % FAStrGen.pl -r FAStructures -o "10:0(2Ke)" "18:1(10E)(9Ke,10Ep)"

    To generate a FAStructures.sdf file containing a structure specified by
    a command line FA abbreviation for epoxy fatty acids, type:

        % FAStrGen.pl -r FAStructures -o "18:0(6Ep)"

    To generate a FAStructures.sdf file containing a structure specified by
    a command line FA abbreviation for methoxy fatty acids, type:

        % FAStrGen.pl -r FAStructures -o "18:1(9E)(12OH,13OH,11OMe)"
        "16:1(5Z)(2OMe)"

    To generate a FAStructures.sdf file containing a structure specified by
    a command line FA abbreviation for halogenated fatty acids, type:

        % FAStrGen.pl -r FAStructures -o "7:1(2Z)(3Br)" "26:2(5Z,9Z)(2Br)"

    To generate a FAStructures.sdf file containing a structure specified by
    a command line FA abbreviation for amino fatty acids, type:

        % FAStrGen.pl -r FAStructures -o "13:0(2NH2[S])" "4:0(2NH2,4CN)"

    To generate a FAStructures.sdf file containing a structure specified by
    a command line FA abbreviation for Cyano fatty acids, type:

        % FAStrGen.pl -r FAStructures -o "4:0(4CN)"

    To generate a FAStructures.sdf file containing a structure specified by
    a command line FA abbreviation for nitro fatty acids, type:

        % FAStrGen.pl -r FAStructures -o "18:2(9Z,12Z)(10NO2)"

    To generate a FAStructures.sdf file containing a structure specified by
    a command line FA abbreviation for prostaglanins, type:

        % FAStrGen.pl -r FAStructures -o "20:2(5Z,13E)(9OH[S],11OH[R],
        15OH[S]){8a,12b}"

    To generate a FAStructures.sdf file containing a structure specified by
    a command line FA abbreviation for fatty alcohols, type:

        % FAStrGen.pl -r FAStructures -o "26:0(1OH)" "16:2(10E,12Z)(1OH)"
        "11:0(1OH,2Me,2Me,9Me,9Me,10OH)"

    To generate a FAStructures.sdf file containing a structure specified by
    a command line FA abbreviation for fatty aldehydes, type:

        % FAStrGen.pl -r FAStructures -o "6:0(1CHO)" "16:2(2E,4E)(1CHO,6OH)"

    To generate a FAStructures.sdf file containing a structure specified by
    a command line FA abbreviation for primary amides, type:

        % FAStrGen.pl -r FAStructures -o "12:0(1NH2)"

    To enumerate straight chain and unsaturated fatty acids with commonly
    occuring chain lengths and generate FAStructures.sdf file, type:

        % FAStrGen.pl -r FAStructures -o "*"

    or

        % FAStrGen.pl -r SPStructures -o "*:*"

AUTHOR
    Manish Sud

CONTRIBUTOR
    Eoin Fahy

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

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

LICENSE
    Modified BSD License

