![]() |
LIPID Metabolites And Pathways Strategy |
STStrGen.pl - Generate structures for Sterols (ST)
STStrGen.pl FAAbbrev|FAAbbrevFileName ...
STStrGen.pl [-h, --help] [-o, --overwrite] [-r, --root rootname] [-w, --workingdir dirname] <arguments>...
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.
Current support for ST structure generation include these main classes and sub classes:
o Sterols
Print this help message
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:
Overwrite existing files
New file name is generated using the root: <Root>.sdf. Default for new file names: STAbbrev.sdf, <AbbrevFilenName>.sdf, or <FirstAbbrevFileName>1To<Count>.sdf.
Location of working directory. Default: current directory
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:
To generate a STStructures.sdf file containing a structure specified by a command line abbreviation for 5alpha-cholestane, type:
To generate a STStructures.sdf file containing a structure specified by a command line abbreviation for 25-hydroxy-cholesterol, type:
To generate a STStructures.sdf file containing a structure specified by a command line abbreviation for 24S-hydroxy-cholesterol, type:
To generate a STStructures.sdf file containing a structure specified by a command line abbreviation for 5,6beta-epoxy-cholesterol, type:
To generate a STStructures.sdf file containing a structure specified by a command line abbreviation for cholestenone, type:
To generate a STStructures.sdf file containing a structure specified by a command line abbreviation for desmostero;, type:
CLStrGen.pl, FAStrGen.pl, GLStrGen.pl, GPStrGen.pl, SPStrGen.pl, 
Copyright (C) 2006-2017. The Regents of the University of California. All Rights Reserved.
Modified BSD License