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)
. Diacylglycerophosphocholines . 1-alkyl,2-acylglycerophosphocholines . 1Z-alkenyl,2-acylglycerophosphocholines . Dialkylglycerophosphocholines . Monoacylglycerophosphocholines . 1-alkyl glycerophosphocholines . 1Z-alkenylglycerophosphocholines
o Glycerophosphoethanolamines (PE)
. Diacylglycerophosphoethanolamines . 1-alkyl,2-acylglycerophosphoethanolamines . 1Z-alkenyl,2-acylglycerophosphoethanolamines . Dialkylglycerophosphoethanolamines . Monoacylglycerophosphoethanolamines . 1-alkyl glycerophosphoethanolamines . 1Z-alkenylglycerophosphoethanolamines
o Glycerophosphoserines (PS)
. Diacylglycerophosphoserines . 1-alkyl,2-acylglycerophosphoserines . 1Z-alkenyl,2-acylglycerophosphoserines . Dialkylglycerophosphoserines . Monoacylglycerophosphoserines . 1-alkyl glycerophosphoserines . 1Z-alkenylglycerophosphoserines
o Glycerophosphoglycerols (PG)
. Diacylglycerophosphoglycerols . 1-alkyl,2-acylglycerophosphoglycerols . 1Z-alkenyl,2-acylglycerophosphoglycerols . Dialkylglycerophosphoglycerols . Monoacylglycerophosphoglycerols . 1-alkyl glycerophosphoglycerols . 1Z-alkenylglycerophosphoglycerols
o Glycerophosphoglycerophosphates (PGP)
. Diacylglycerophosphoglycerophosphates . 1-alkyl,2-acylglycerophosphoglycerophosphates . 1Z-alkenyl,2-acylglycerophosphoglycerophosphates . Dialkylglycerophosphoglycerophosphates . Monoacylglycerophosphoglycerophosphates . 1-alkyl glycerophosphoglycerophosphates . 1Z-alkenylglycerophosphoglycerophosphates
o Glycerophosphoinositols (PI)
. Diacylglycerophosphoinositols . 1-alkyl,2-acylglycerophosphoinositols . 1Z-alkenyl,2-acylglycerophosphoinositols . Dialkylglycerophosphoinositols . Monoacylglycerophosphoinositols . 1-alkyl glycerophosphoinositols . 1Z-alkenylglycerophosphoinositols
o Glycerophosphoinositol monophosphates (PIP)
. Diacylglycerophosphoinositol monophosphates . 1-alkyl,2-acylglycerophosphoinositol monophosphates . 1Z-alkenyl,2-acylglycerophosphoinositol monophosphates . Dialkylglycerophosphoinositol monophosphates . Monoacylglycerophosphoinositol monophosphates . 1-alkyl glycerophosphoinositol monophosphates . 1Z-alkenylglycerophosphoinositol monophosphates
o Glycerophosphates (PA)
. Diacylglycerophosphates . 1-alkyl,2-acylglycerophosphates . 1Z-alkenyl,2-acylglycerophosphates . Dialkylglycerophosphates . Monoacylglycerophosphates . 1-alkyl glycerophosphates . 1Z-alkenylglycerophosphates
o Glyceropyrophosphates (PPA)
. Diacylglyceropyrophosphates . Monoacylglyceropyrophosphates
o Glycerophosphonocholines (PnC)
. Diacylglycerophosphonocholines . 1-alkyl,2-acylglycerophosphonocholines . 1Z-alkenyl,2-acylglycerophosphonocholines . Dialkylglycerophosphonocholines . Monoacylglycerophosphonocholines . 1-alkyl glycerophosphonocholines . 1Z-alkenylglycerophosphonocholines
o Glycerophosphonoethanolamines (PnE)
. Diacylglycerophosphonoethanolamines . 1-alkyl,2-acylglycerophosphonoethanolamines . 1Z-alkenyl,2-acylglycerophosphonoethanolamines . Dialkylglycerophosphonoethanolamines . Monoacylglycerophosphonoethanolamines . 1-alkyl glycerophosphonoethanolamines . 1Z-alkenylglycerophosphonoethanolamines
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.
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.
Wild card character, *, is also supported in compound abbreviations.
Examples:
Specific structures: PC(12:0/13:0) PC(17:1(9Z)/0:0) PA(13:0/0:0) Specific structures: PC(O-16:0/13:0) PC(P-16:0/0:0) Specific possibilities: PC(21:0/22:*) PA(17:*/0:0) PE(O-18:0/*:*) All possibilites: *(*:*/*:*) or *(*/*)
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:
Odd and even number chains at sn1 and sn2: *(*+:*/*-:*) Odd and even number chains at sn1 and sn2 with length longer than 10 and 20: *(*+>10:*/*->20:*)
Default sn2 stereochemistry is R. However, abbreviation format also supports these additional stereochemistry specifications for sn2 position: S; U - unknown; rac - racemic mixture. Examples:
PC(12:0/13:0)[rac] PC(17:1(9Z)/14:0)[S] PA(13:0/12:0)[U]
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:
% GPStrGen.pl -r GPStructures -o "PC(16:0/0:0)"
To generate a GPStructures.sdf file containing structures specified by a command line GL abbreviations, type:
% GPStrGen.pl -r GPStructures -o "PC(16:0/0:0)" "PE(18:1(11E)/16:0)"
To generate a GPStructures.sdf file containing structures specified by a command line GP abbreviations with specific stereochemistry, type:
% GPStrGen.pl -r GPStructures -o "PC(16:0/0:0)[U]" "PE(18:1(11E)/16:0)[S]"
To enumerate all possible GP structures and generate a GPStructures.sdf file, type:
% GPStrGen.pl -r GPStructures -o "*(*/*)"
or
% GPStrGen.pl -r GPStructures -o "*(*:*/*:*)"
% GPStrGen.pl -r GPStructures -o "*(*:*(*)/*:*(*))"
To enumerate all possible GP structures with a sn1 chain, and generate a GPStructures.sdf file, type:
% GPStrGen.pl -r GPStructures -o "*(*/0:0)"
To enumerate all possible GP structures with a sn1 chain containing one double bond, and generate a GPStructures.sdf file, type:
% GPStrGen.pl -r GPStructures -o "*(*:1/0:0)"
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:
% GPStrGen.pl -r GPStructures -o "*(*+>10:*/0:0)"
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:
% GPStrGen.pl -r GPStructures -o "*(*->10:*/*+>18:*)"
Manish Sud
Eoin Fahy
CLStrGen.pl, FAStrGen.pl, GLStrGen.pl, SPStrGen.pl, STStrGen.pl,
Copyright (C) 2006-2017. The Regents of the University of California. All Rights Reserved.
Modified BSD License
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