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NAME

GPStrGen.pl - Generate structures for Glycerophospholipids (GP)

SYNOPSIS

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>...

DESCRIPTION

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.

SUPPORTED ABBREVIATIONS

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

OPTIONS

-c, --ChainAbbrevMode MostLikely|Arbitrary

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.

-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.

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]
-p, --ProcessMode WriteSDFile|CountOnly

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.

-o, --overwrite

Overwrite existing files

-r, --root rootname

New file name is generated using the root: <Root>.sdf. Default for new file names: GPAbbrev.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 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 "*(*:*/*:*)"

or

% 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:*)"

AUTHOR

Manish Sud

CONTRIBUTOR

Eoin Fahy

SEE ALSO

CLStrGen.plFAStrGen.plGLStrGen.plSPStrGen.plSTStrGen.pl

COPYRIGHT

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

LICENSE

Modified BSD License

 

logo LIPID MAPS is funded by a Wellcome Trust.