NAME
    STStrGen.pl - Generate structures for Sterols (ST)

SYNOPSIS
    STStrGen.pl FAAbbrev|FAAbbrevFileName ...

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

DESCRIPTION
    Generate Strerol (ST) 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 ST structure generation include these main classes
    and sub classes:

    o Sterols

        . Cholesterol and derivatives
        . Ergosterols and C24-methyl derivatives
        . Stigmasterols and C24-ethyl derivatives

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.

        Examples:

            cholesterol: "CHOLESTANE(3,b,OH:5(6))"
            5alpha-cholestane: "CHOLESTANE(5,a,H)"
            25-hydroxy-cholesterol: "CHOLESTANE(3,b,OH/25,,OH:5(6))"
            5,6beta-epoxy-cholesterol: "CHOLESTANE(3,b,OH/5,b,Ep)"
            cholestenone: "CHOLESTANE(3,,Ke:4)"

            ergost-5-en-3beta-ol: "ERGOSTANE(3,b,OH:5)"

            campest-5-en-3beta-ol: "CAMPESTANE(3,b,OH:5)"

            stigmast-5,25-dien-3beta-ol: "STIGMASTANE(3,b,OH:5/25(26))"

    -o, --overwrite
        Overwrite existing files

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

    To generate a STStructures.sdf file containing a structure specified by
    a command line abbreviation for cholesterol, type:

        % STStrGen.pl -r STStructures -o "CHOLESTANE(3,b,OH:5(6))"

    To generate a STStructures.sdf file containing a structure specified by
    a command line abbreviation for 5alpha-cholestane, type:

        % STStrGen.pl -r STStructures -o "CHOLESTANE(5,a,H)"

    To generate a STStructures.sdf file containing a structure specified by
    a command line abbreviation for 25-hydroxy-cholesterol, type:

        % STStrGen.pl -r STStructures -o "CHOLESTANE(3,b,OH/25,,OH:5(6))"

    To generate a STStructures.sdf file containing a structure specified by
    a command line abbreviation for 24S-hydroxy-cholesterol, type:

        % STStrGen.pl -r STStructures -o "CHOLESTANE(3,b,OH/24,a,OH:5(6))"

    To generate a STStructures.sdf file containing a structure specified by
    a command line abbreviation for 5,6beta-epoxy-cholesterol, type:

        % STStrGen.pl -r STStructures -o "CHOLESTANE(3,b,OH/5,b,Ep)"

    To generate a STStructures.sdf file containing a structure specified by
    a command line abbreviation for cholestenone, type:

        % STStrGen.pl -r STStructures -o "CHOLESTANE(3,,Ke:4)"

    To generate a STStructures.sdf file containing a structure specified by
    a command line abbreviation for desmostero;, type:

        % STStrGen.pl -r STStructures -o "CHOLESTANE(3,b,OH:5/24)"

AUTHOR
    Manish Sud

CONTRIBUTOR
    Eoin Fahy

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

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

LICENSE
    Modified BSD License

