NAME
ElementalAnalysisSDFiles.pl - Perform elemental analysis using formula data field in SDFile(s)
SYNOPSIS
ElementalAnalysisSDFiles.pl SDFile(s)...
ElementalAnalysisSDFiles.pl [-d, --detail infolevel] [--fast]
[-f, --formulafield SD data field name]
[-m, --mode All | ''ElementalAnalysis, [MolecularWeight, ExactMass]''] [-h, --help]
[-o, --overwrite] [-r, --root rootname] [-v --valuefieldnames Name, Label, [Name, Label,...]]
[-w, --workingdir dirname] SDFile(s)...
DESCRIPTION
Perform elemental analysis using molecular formula specified by a data field name in
SDFile(s).
In addition to straightforward molecular formulas - H2O, HCl, C3H7O2N -
other supported variations are: Ca3(PO4)2, [PCl4]+, [Fe(CN)6]4-, C37H42N2O6+2, Na2CO3.10H2O,
8H2S.46H2O, and so on. Charges are simply ignored. Isotope symbols in formulas specification, including
D and T, are not supported.
The file names are separated by space.The valid file extensions are .sdf and .sd.
All other file names are ignored. All the SD files in a current directory can be specified
either by *.sdf or the current directory name.
OPTIONS
- -d, --detail infolevel
-
Level of information to print about compound records being ignored. Default: 1. Possible
values: 1, 2 or 3
- --fast
-
In this mode, the formula data field specified using -f, --formulafield option is assumed
to contain valid molecular formula data and initial formula validation check is skipped.
- -f, --formulafield SD data field name
-
SDFile(s) data field name containing molecular formulas used for performing
elemental analysis. Default value: SD data field containing the word formula in its name.
- -m, --mode All | ''ElementalAnalysis,[MolecularWeight,ExactMass]''
-
Specify what values to calculate using molecular formula data field in TextFile(s): calculate
all supported values or specify a comma delimited list of values. Possible values: All | ''ElementalAnalysis,
[MolecularWeight, ExactMass]''. Default: All
- -h, --help
-
Print this help message
- -o, --overwrite
-
Overwrite existing files
- -p, --precision number
-
Precision of calculated values in the output file. Default: up to 2 decimal places.
Valid values: positive integers.
- -r, --root rootname
-
New SD file name is generated using the root: <Root>.<Ext>. Default new file
name: <InitialSDFileName>ElementalAnalysis.<Ext>. This option is ignored for multiple
input files.
- -v --valuefieldnames Name,Label,[Name,Label,...]
-
Specify SD data field names to use for calculated values. In general, it's a comma delimited
list of value name and SD field name pairs. Supported value names: ElementalAnalysis,
MolecularWeight, and ExactMass. Default labels: ElementalAnalysis, MolecularWeight,
and ExactMass.
- -w, --workingdir dirname
-
Location of working directory. Default: current directory
EXAMPLES
To perform elemental analysis, calculate molecular weight and exact mass using SD
field name value with the word Formula in its name and generate a new SD file
NewSample1.sdf, type:
% ElementalAnalysisSDFiles.pl -o -r NewSample1 Sample1.sdf
To perform elemental analysis using formulas in SD field name Formula, use field name
Analysis for calculated data, and generate a new SD file NewSample1.sdf, type:
% ElementalAnalysisSDFiles.pl --m ElementalAnalysis --formulafield
Formula --valuefieldnames "ElementalAnalysis,Analysis" -o
-r NewSample1 Sample1.sdf
To calculate molecular weight, using formulas in SD field name Formula, with four decimal
precision and generate a new SD file NewSample1.sdf, type
% ElementalAnalysisSDFiles.pl --m MolecularWeight --formulafield
Formula --precision 4 -o -r NewSample1 Sample1.sdf
AUTHOR
Manish Sud
SEE ALSO
AnalyzeSDFilesData.pl, InfoSDFiles.pl, ExtractFromSDFiles.pl
COPYRIGHT
Copyright (C) 2004-2008 Manish Sud. All rights reserved.
This file is part of MayaChemTools.
MayaChemTools is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by the Free
Software Foundation; either version 3 of the License, or (at your option)
any later version.
