NAME
GLStrGen.pl - Generate structures for Glycerolipids (GL)
SYNOPSIS
GLStrGen.pl GLAbbrev|GLAbbrevFileName ...
GLStrGen.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 Glycerolipids (GL) 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 -m, --mode option to control the type of command line arguments.
A SD file, containing structures for all GL abbreviations along with ontological information, is generated as an output.
SUPPORTED ABBREVIATIONS
Current support for GL structure generation include these main classes and sub classes:
o Monoradylglycerols
. Monoalkylglycerols
. Mono-(1Z-alkenyl)-glycerol
o Diradylglycerols
. Alkyl, acylglycerols
. Dialkylglycerols
. 1Z-alkenyl, acylglycerols
o Triradylglycerols
. Alkyl, diacylglycerols
. Dialkyl, monoacylglycerols
. 1Z-alkenyl, diacylglycerols
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: MG(16:0/0:0/0:0) DG(18:1(11E)/16:0/0:0)
TG(16:0/16:0/18:1(9Z))
Specific structures: MG(O-16:0/0:0/0:0) DG(P-16:0/16:0/0:0)
TG(O-20:0/16:0/18:1(9Z))
Specific possibilities: DG(18:*/16:0/0:0) DG(18:1(*)/16:0/0:0)
DG(*:*(9Z)/16:0/0:0)
DG(*:*(9Z)/*:*(11E)/0:0)
All TG possibilities: *(*:*/*:*/*:*) or *(*/*/*)
All MG, DG and TG possibilities: "MG(*:*/0:0/0:0)" "DG(*:*/*:*/0:0)"
"DG(*.*/0:0/*:*)" "TG(*:*/*:*/*:*)"
Along 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: TG(*+:*/*-:*/*:*)
Odd and even number chains at sn1 and sn2 with length longer than
10 and 20: TG(*+>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:
MG(16:0/0:0/0:0)[rac] - racemic mixture
DG(18:1(11E)/16:0/0:0)[S] - sn2 stereochemistry is S instead of default R
TG(16:0/16:0/18:1(9Z))[U] - sn2 stereochemistry is unknown
To generate all isomers for specific chains in DG and TG, use of iso designation is also supported. Stereochemistry specification support is not available with isomeric structure generation. Examples:
DG(18:1(11E)/16:0/0:0)[iso2] - Two isomeric structures
TG(16:0/16:0/18:1(9Z))[iso3] - Three isomeric structures
TG(16:0/18:0/18:1(9Z))[iso6] - Six isomeric structures
Additionally, all isomeric structures can also be generated by explicit specification of chains at different positions:
DG(18:1(11E)/16:0/0:0) DG(16:0/18:1(11E)/0:0)
TG(16:0/16:0/18:1(9Z)) TG(16:0/18:1(9Z)/16:0)
TG(18:1(9Z)/16:0/16:0/)
Wild card chain abbreviations are supported with sn2 stereochemistry but not with isomer abbreviation.
- -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: GLAbbrev.sdf, <AbbrevFilenName>.sdf, or <FirstAbbrevFileName>1To<Count>.sdf.
- -w, --workingdir dirname
-
Location of working directory. Default: current directory
EXAMPLES
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: MG(O-16:0/0:0/0:0) DG(P-16:0/16:0/0:0) TG(O-20:0/16:0/18:1(9Z))
Specific possibilities: DG(18:*/16:0/0:0) DG(18:1(*)/16:0/0:0) DG(*:*(9Z)/16:0/0:0) DG(*:*(9Z)/*:*(11E)/0:0)
All TG possibilities: *(*:*/*:*/*:*) or *(*/*/*)
All MG, DG and TG possibilities: "MG(*:*/0:0/0:0)" "DG(*:*/*:*/0:0)" "DG(*.*/0:0/*:*)" "TG(*:*/*:*/*:*)"
Along 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 with length longer than
10 and 20: TG(*+>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:
DG(18:1(11E)/16:0/0:0)[S] - sn2 stereochemistry is S instead of default R
TG(16:0/16:0/18:1(9Z))[U] - sn2 stereochemistry is unknown
To generate all isomers for specific chains in DG and TG, use of iso designation is also supported. Stereochemistry specification support is not available with isomeric structure generation. Examples:
TG(16:0/16:0/18:1(9Z))[iso3] - Three isomeric structures
TG(16:0/18:0/18:1(9Z))[iso6] - Six isomeric structures
Additionally, all isomeric structures can also be generated by explicit specification of chains at different positions:
TG(16:0/16:0/18:1(9Z)) TG(16:0/18:1(9Z)/16:0)
TG(18:1(9Z)/16:0/16:0/)
Wild card chain abbreviations are supported with sn2 stereochemistry but not with isomer abbreviation.
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: GLAbbrev.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 GLStructures.sdf file containing a structure specified by a command line GL abbreviation, type:
To generate a GLStructures.sdf file containing structures specified by a command line GL abbreviations, type:
To generate a GLStructures.sdf file containing structures specified by a command line GL abbreviations with specific stereochemistry, type:
To generate a GLStructures.sdf file containing all isomeric structures specified by a command line GL abbreviations, type:
To enumerate all possible GL structures and generate a GLStructures.sdf file, type:
or
or
To enumerate all possible Monoradylglycerols structures and generate a MonoGLStructures.sdf file, type:
To enumerate all possible Diradylglycerols structures and generate a DiGLStructures.sdf file, type:
To enumerate all possible Monoradylglycerols structures with one double bond on acyl chain and generate a GLStructures.sdf file, type:
To enumerate all possible Monoradylglycerols structures with even chain lengths and generate a GLStructures.sdf file, type:
To enumerate all possible Diradylglycerols structures with odd chains longer than 10 at sn1 and even chains longer than 18 at sn2, and generate a DiGLStructures.sdf file, type:
AUTHOR
CONTRIBUTOR
SEE ALSO
CLStrGen.pl, FAStrGen.pl, GPStrGen.pl, SPStrGen.pl, STStrGen.pl,
COPYRIGHT
Copyright (C) 2006-2017. The Regents of the University of California. All Rights Reserved.
LICENSE
Modified BSD License