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ElementalAnalysisSDFiles.pl - Perform elemental analysis using formula data field in SDFile(s)
ElementalAnalysisSDFiles.pl SDFile(s)...
ElementalAnalysisSDFiles.pl [-d, --detail infolevel] [--fast] [--formulafield SD data field name] [-f, --formulamode DataField | StructureData] [--formulaout yes or no] [-m, --mode All | "ElementalAnalysis, [MolecularWeight, ExactMass]"] [-h, --help] [-o, --overwrite] [-r, --root rootname] [-v --valuefieldnames Name, Label, [Name, Label,...]] [-w, --workingdir dirname] SDFile(s)...
Perform elemental analysis using molecular formula specified by a data field name or generated from structure data 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.
Level of information to print about compound records being ignored. Default: 1. Possible values: 1, 2 or 3.
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.
SDFile(s) data field name containing molecular formulas used for performing elemental analysis during DataField value of -f, --formulamode option. Default value: SD data field containing the word formula in its name.
This option is ignore during StructureData value of -f, --formulamode option.
Specify source of molecular formula used for performing elemental analysis: retrieve formula using SDFile(s) data field name or generate formula from structure. Possible values: DataField or StructureData. Default value: DataField.
Specify whether to write out formula to SD file during StructureData value of -f, --formulamode option. Possible values: Yes or No. Default: No.
Specify what values to calculate using molecular formula data field or structure data from SDFile(s): calculate all supported values or specify a comma delimited list of values. Possible values: All | "ElementalAnalysis, [MolecularWeight, ExactMass]". Default: All
Print this help message.
Overwrite existing files.
Precision of calculated values in the output file. Default: up to 2 decimal places. Valid values: positive integers.
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.
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, ExactMass, and MolecularFormula. Default labels: ElementalAnalysis, MolecularWeight, ExactMass, and MolecularFormula.
MolecularFormula label is only used during StructureData value of -f, --formulamode option.
Location of working directory. Default: current directory.
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:
To perform elemental analysis, calculate molecular weight and exact mass using structure data in SD file and generate a new SD file NewSample1.sdf, type:
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:
To calculate molecular weight, using formulas in SD field name Formula, with four decimal precision and generate a new SD file NewSample1.sdf, type
AnalyzeSDFilesData.pl, InfoSDFiles.pl, ExtractFromSDFiles.pl
Copyright (C) 2024 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.
