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NAME

CLStrGen.pl - Generate structures for Glycerophosphoglycerophosphoglycerols (Cardiolipins)

SYNOPSIS

CLStrGen.pl CLAbbrev|CLAbbrevFileName ...

CLStrGen.pl [-h, --help] [-o, --overwrite] [-r, --root rootname] [-w, --workingdir dirname] <arguments>...

DESCRIPTION

Generate Cardiolipins (CL) 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 CL abbreviations along with ontological information, is generated as an output.

SUPPORTED ABBREVIATIONS

Current support for CL structure generation include these main classes and sub classes:

o Glycerophosphoglycerophosphoglycerols (Cardiolipins)

. Diacylglycerophosphoglycerophosphodiradylglycerols
. Diacylglycerophosphoglycerophosphomonoradylglycerols
. 1-alkyl,2-acylglycerophosphoglycerophosphodiradylglycerols
. 1-alkyl,2-acylglycerophosphoglycerophosphomonoradylglycerols
. 1Z-alkenyl,2-acylglycerophosphoglycerophosphodiradylglycerols
. 1Z-alkenyl,2-acylglycerophosphoglycerophosphomonoradylglycerols
. Monoacylglycerophosphoglycerophosphomonoradylglycerols
. 1-alkyl glycerophosphoglycerophosphodiradylglycerols
. 1-alkyl glycerophosphoglycerophosphomonoradylglycerols
. 1Z-alkenylglycerophosphoglycerophosphodiradylglycerols
. 1Z-alkenylglycerophosphoglycerophosphomonoradylglycerols

OPTIONS

-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: CL(1'-[18:2(9Z,12Z)/18:2(9Z,12Z)], 3'-[18:2(9Z,12Z)/18:2(9Z,12Z)])
All possibilites: *(1'-[*:*/*:*],3'-[*:*/*:*]) or *(1'-[*/*],3'-[*/*]); 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/even number chains at sn1/sn3 and sn2/sn4: *(1'-[*+:*/*-:*], 3'-[*+:*/*-:*])
Odd/even number chains at sn1/sn3 and sn2/sn4 with length longer
than 20 and 22: *(1'-[*+>20:*/*->22:*],3'-[*+>20:*/*->22:*])
-o, --overwrite: Overwrite existing files
-r, --root rootname: New file name is generated using the root: <Root>.sdf. Default for new file names: CLAbbrev.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 CLStructures.sdf file containing a structure specified by a command line CL abbreviation for Diacylglycerophosphoglycerophosphodiradylglycerols, type:

% CLStrGen.pl -r CLStructures -o "CL(1'-[18:2(9Z,12Z)/18:2(9Z,12Z)], 3'-[18:2(9Z,12Z)/18:2(9Z,12Z)])"

To generate a CLStructures.sdf file containing a structure specified by a command line CL abbreviation for Diacylglycerophosphoglycerophosphomonoradylglycerols, type:

% CLStrGen.pl -r CLStructures -o "CL(1'-[18:2(9Z,12Z)/18:2(9Z,12Z)], 3'-[18:2(9Z,12Z)/0:0])"

To generate a CLStructures.sdf file containing a structure specified by a command line CL abbreviation for 1-alkyl,2-acylglycerophosphoglycerophosphodiradylglycerols, type:

% CLStrGen.pl -r CLStructures -o "CL(1'-[O-16:0/18:2(9Z,12Z)], 3'-[18:2(9Z,12Z)/18:2(9Z,12Z)])"

To generate a CLStructures.sdf file containing a structure specified by a command line CL abbreviation for 1-alkyl,2-acylglycerophosphoglycerophosphomonoradylglycerols, type:

% CLStrGen.pl -r CLStructures -o "CL(1'-[O-16:0/18:2(9Z,12Z)], 3'-[18:2(9Z,12Z)/0:0])"

To generate a CLStructures.sdf file containing a structure specified by a command line CL abbreviation for 1Z-alkenyl,2-acylglycerophosphoglycerophosphodiradylglycerols, type:

% CLStrGen.pl -r CLStructures -o "CL(1'-[O-16:1(1Z)/18:2(9Z,12Z)], 3'-[18:2(9Z,12Z)/18:2(9Z,12Z)])"

To generate a CLStructures.sdf file containing a structure specified by a command line CL abbreviation for 1Z-alkenyl,2-acylglycerophosphoglycerophosphomonoradylglycerols, type:

% CLStrGen.pl -r CLStructures -o "CL(1'-[O-16:1(1Z)/18:2(9Z,12Z)], 3'-[18:2(9Z,12Z)/0:0])"

To generate a CLStructures.sdf file containing a structure specified by a command line CL abbreviation for Monoacylglycerophosphoglycerophosphomonoradylglycerols, type:

% CLStrGen.pl -r CLStructures -o "CL(1'-[18:2(9Z,12Z)/0:0], 3'-[18:2(9Z,12Z)/0:0])"

To generate a CLStructures.sdf file containing a structure specified by a command line CL abbreviation for 1-alkyl glycerophosphoglycerophosphodiradylglycerols, type:

% CLStrGen.pl -r CLStructures -o "CL(1'-[O-16:0/0:0], 3'-[18:2(9Z,12Z)/18:2(9Z,12Z)])"

To generate a CLStructures.sdf file containing a structure specified by a command line CL abbreviation for 1-alkyl glycerophosphoglycerophosphomonoradylglycerols, type:

% CLStrGen.pl -r CLStructures -o "CL(1'-[O-16:0/0:0], 3'-[18:2(9Z,12Z)/0:0])"

To generate a CLStructures.sdf file containing a structure specified by a command line CL abbreviation for 1Z-alkenylglycerophosphoglycerophosphodiradylglycerols, type:

% CLStrGen.pl -r CLStructures -o "CL(1'-[O-16:1(1Z)/0:0], 3'-[18:2(9Z,12Z)/18:2(9Z,12Z)])"

To generate a CLStructures.sdf file containing a structure specified by a command line CL abbreviation for 1Z-alkenylglycerophosphoglycerophosphomonoradylglycerols, type:

% CLStrGen.pl -r CLStructures -o "CL(1'-[O-16:1(1Z)/0:0], 3'-[18:2(9Z,12Z)/0:0])"

To enumerate all possible CL structures and generate a CLStructures.sdf file, type:

% CLStrGen.pl -r CLStructures -o "*(1'-[*/*],3'-[*/*])"

% CLStrGen.pl -r CLStructures -o "*(1'-[*:*/*:*],3'-[*:*/*:*])"

% CLStrGen.pl -r CLStructures -o "*(1'-[*:*(*)/*:*(*)], 3'-[*:*(*)/*:*(*)])"

AUTHOR

Manish Sud

CONTRIBUTOR

Eoin Fahy