GLStrGen.pl - Generate structures for Glycerolipids (GL)
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>...
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.
Current support for GL structure generation include these main classes and sub classes:
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.
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:
Default sn2 stereochemistry is R. However, abbreviation format also supports these additional stereochemistry specifications for sn2 position: S; U - unknown; rac - racemic mixture. Examples:
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:
Additionally, all isomeric structures can also be generated by explicit specification of chains at different positions:
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:
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:
Copyright (C) 2006-2017. The Regents of the University of California. All Rights Reserved.
Modified BSD License