GPStrGen.pl - Generate structures for Glycerophospholipids (GP)
GPStrGen.pl GPAbbrev|GPAbbrevFileName ...
GPStrGen.pl [-c, --ChainAbbrevMode MostLikely | Arbitrary] [-h, --help] [-m, --mode Abbrev | AbbrevFileName] [-p, --ProcessMode WriteSDFile | CountOnly] [-o, --overwrite] [-r, --root rootname] [-w, --workingdir dirname] <arguments>...
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.
Current support for GP structure generation include these main classes and sub classes:
o Glycerophosphocholines (PC)
o Glycerophosphoethanolamines (PE)
o Glycerophosphoserines (PS)
o Glycerophosphoglycerols (PG)
o Glycerophosphoglycerophosphates (PGP)
o Glycerophosphoinositols (PI)
o Glycerophosphoinositol monophosphates (PIP)
o Glycerophosphates (PA)
o Glyceropyrophosphates (PPA)
o Glycerophosphonocholines (PnC)
o Glycerophosphonoethanolamines (PnE)
Specify what types of acyl chain abbreviations are allowed during processing of complete abbreviations: allow most likely chain abbreviations containing specific double bond geometry specifications; allow any acyl chain abbreviation with valid chain length and double bond geometry specificatios. Possible values: MostLikely or Arbitrary. Default value: MostLikely.
Arbitrary value of -c, --ChainAbbrevMode option is not allowed during processing of abbreviations containing wild cards.
During MostLikely value of -c, --ChainAbbrevMode option, only the most likely acyl chain abbreviations specified in ChainAbbrev.pm module are allowed. However, during Arbitrary value of -c, --ChainAbbrevMode option, any acyl chain abbreviations with valid chain length and double bond geometry can be specified. The current release of lipidmapstools support chain lengths from 2 to 50 as specified in ChainAbbev.pm module.
In addition to double bond geometry specifications, valid substituents can be specified for in the acyl chain abbreviations.
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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.
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:
Default sn2 stereochemistry is R. However, abbreviation format also supports these additional stereochemistry specifications for sn2 position: S; U - unknown; rac - racemic mixture. Examples:
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.
Overwrite existing files
New file name is generated using the root: <Root>.sdf. Default for new file names: GPAbbrev.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 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:
To generate a GPStructures.sdf file containing structures specified by a command line GL abbreviations, type:
To generate a GPStructures.sdf file containing structures specified by a command line GP abbreviations with specific stereochemistry, type:
To enumerate all possible GP structures and generate a GPStructures.sdf file, type:
To enumerate all possible GP structures with a sn1 chain, and generate a GPStructures.sdf file, type:
To enumerate all possible GP structures with a sn1 chain containing one double bond, and generate a GPStructures.sdf file, type:
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:
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:
Copyright (C) 2006-2017. The Regents of the University of California. All Rights Reserved.
Modified BSD License