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)

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)

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:

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:

or

or

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:

AUTHOR

Manish Sud

CONTRIBUTOR

Eoin Fahy

SEE ALSO

CLStrGen.pl, FAStrGen.pl, GLStrGen.pl, SPStrGen.pl, STStrGen.pl

COPYRIGHT

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

LICENSE

Modified BSD License