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NAME

GLStrGen.pl - Generate structures for Glycerolipids (GL)

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

COPYRIGHT

LICENSE

Modified BSD License