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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/man1/ElementalAnalysisSDFiles.1 Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,264 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +ElementalAnalysisSDFiles.pl \- Perform elemental analysis using formula data field in SDFile(s) +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +ElementalAnalysisSDFiles.pl SDFile(s)... +.PP +ElementalAnalysisSDFiles.pl [\fB\-d, \-\-detail\fR infolevel] [\fB\-\-fast\fR] +[\fB\-\-formulafield\fR \s-1SD\s0 data field name] [\fB\-f, \-\-formulamode\fR \fIDataField | StructureData\fR] +[\fB\-\-formulaout\fR yes or no] [\fB\-m, \-\-mode\fR All | \*(L"ElementalAnalysis, [MolecularWeight, ExactMass]\*(R"] +[\fB\-h, \-\-help\fR] [\fB\-o, \-\-overwrite\fR] [\fB\-r, \-\-root\fR rootname] +[\fB\-v \-\-valuefieldnames\fR Name, Label, [Name, Label,...]] [\fB\-w, \-\-workingdir\fR dirname] SDFile(s)... +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +Perform elemental analysis using molecular formula specified by a data field name or generated +from structure data in \fISDFile(s)\fR. +.PP +In addition to straightforward molecular formulas \- H2O, HCl, C3H7O2N \- +other supported variations are: Ca3(\s-1PO4\s0)2, [PCl4]+, [Fe(\s-1CN\s0)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. +.PP +The file names are separated by space.The valid file extensions are \fI.sdf\fR and \fI.sd\fR. +All other file names are ignored. All the \s-1SD\s0 files in a current directory can be specified +either by \fI*.sdf\fR or the current directory name. +.SH "OPTIONS" +.IX Header "OPTIONS" +.IP "\fB\-d, \-\-detail\fR \fIinfolevel\fR" 4 +.IX Item "-d, --detail infolevel" +Level of information to print about compound records being ignored. Default: \fI1\fR. Possible +values: \fI1, 2 or 3\fR. +.IP "\fB\-\-fast\fR" 4 +.IX Item "--fast" +In this mode, the formula data field specified using \fB\-f, \-\-formulafield\fR option is assumed +to contain valid molecular formula data and initial formula validation check is skipped. +.IP "\fB\-\-formulafield\fR \fI\s-1SD\s0 data field name\fR" 4 +.IX Item "--formulafield SD data field name" +\&\fISDFile(s)\fR data field name containing molecular formulas used for performing +elemental analysis during \fIDataField\fR value of \fB\-f, \-\-formulamode\fR option. +Default value: \fI\s-1SD\s0 data field containing the word formula in its name\fR. +.Sp +This option is ignore during \fIStructureData\fR value of \fB\-f, \-\-formulamode\fR option. +.IP "\fB\-f, \-\-formulamode\fR \fIDataField | StructureData\fR" 4 +.IX Item "-f, --formulamode DataField | StructureData" +Specify source of molecular formula used for performing elemental analysis: retrieve +formula using \fISDFile(s)\fR data field name or generate formula from structure. Possible +values: \fIDataField or StructureData\fR. Default value: \fIDataField\fR. +.IP "\fB\-\-formulaout\fR \fIyes or no\fR" 4 +.IX Item "--formulaout yes or no" +Specify whether to write out formula to \s-1SD\s0 file during \fIStructureData\fR value of +\&\fB\-f, \-\-formulamode\fR option. Possible values: \fIYes or No\fR. Default: \fINo\fR. +.ie n .IP "\fB\-m, \-\-mode\fR \fIAll | ""ElementalAnalysis,[MolecularWeight,ExactMass]""\fR" 4 +.el .IP "\fB\-m, \-\-mode\fR \fIAll | ``ElementalAnalysis,[MolecularWeight,ExactMass]''\fR" 4 +.IX Item "-m, --mode All | ElementalAnalysis,[MolecularWeight,ExactMass]" +Specify what values to calculate using molecular formula data field or structure data from +\&\fISDFile(s)\fR: calculate all supported values or specify a comma delimited list of values. +Possible values: \fIAll | \*(L"ElementalAnalysis, [MolecularWeight, ExactMass]\*(R"\fR. Default: \fIAll\fR +.IP "\fB\-h, \-\-help\fR" 4 +.IX Item "-h, --help" +Print this help message. +.IP "\fB\-o, \-\-overwrite\fR" 4 +.IX Item "-o, --overwrite" +Overwrite existing files. +.IP "\fB\-p, \-\-precision\fR \fInumber\fR" 4 +.IX Item "-p, --precision number" +Precision of calculated values in the output file. Default: up to \fI2\fR decimal places. +Valid values: positive integers. +.IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4 +.IX Item "-r, --root rootname" +New \s-1SD\s0 file name is generated using the root: <Root>.<Ext>. Default new file +name: <InitialSDFileName>ElementalAnalysis.<Ext>. This option is ignored for multiple +input files. +.IP "\fB\-v \-\-valuefieldnames\fR \fIName,Label,[Name,Label,...]\fR" 4 +.IX Item "-v --valuefieldnames Name,Label,[Name,Label,...]" +Specify \s-1SD\s0 data field names to use for calculated values. In general, it's a comma delimited +list of value name and \s-1SD\s0 field name pairs. Supported value names: \fIElementalAnalysis, +MolecularWeight, ExactMass, and MolecularFormula\fR. Default labels: \fIElementalAnalysis, +MolecularWeight, ExactMass, and MolecularFormula\fR. +.Sp +\&\fIMolecularFormula\fR label is only used during \fIStructureData\fR value of +\&\fB\-f, \-\-formulamode\fR option. +.IP "\fB\-w, \-\-workingdir\fR \fIdirname\fR" 4 +.IX Item "-w, --workingdir dirname" +Location of working directory. Default: current directory. +.SH "EXAMPLES" +.IX Header "EXAMPLES" +To perform elemental analysis, calculate molecular weight and exact mass using \s-1SD\s0 +field name value with the word Formula in its name and generate a new \s-1SD\s0 file +NewSample1.sdf, type: +.PP +.Vb 1 +\& % ElementalAnalysisSDFiles.pl \-o \-r NewSample1 Sample1.sdf +.Ve +.PP +To perform elemental analysis, calculate molecular weight and exact mass using +structure data in \s-1SD\s0 file and generate a new \s-1SD\s0 file NewSample1.sdf, type: +.PP +.Vb 2 +\& % ElementalAnalysisSDFiles.pl \-\-formulamode StructureData \-o +\& \-r NewSample1 Sample1.sdf +.Ve +.PP +To perform elemental analysis using formulas in \s-1SD\s0 field name Formula, use field name +Analysis for calculated data, and generate a new \s-1SD\s0 file NewSample1.sdf, type: +.PP +.Vb 3 +\& % ElementalAnalysisSDFiles.pl \-\-m ElementalAnalysis \-\-formulafield +\& Formula \-\-valuefieldnames "ElementalAnalysis,Analysis" \-o +\& \-r NewSample1 Sample1.sdf +.Ve +.PP +To calculate molecular weight, using formulas in \s-1SD\s0 field name Formula, with four decimal +precision and generate a new \s-1SD\s0 file NewSample1.sdf, type +.PP +.Vb 2 +\& % ElementalAnalysisSDFiles.pl \-\-m MolecularWeight \-\-formulafield +\& Formula \-\-precision 4 \-o \-r NewSample1 Sample1.sdf +.Ve +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +AnalyzeSDFilesData.pl, InfoSDFiles.pl, ExtractFromSDFiles.pl +.SH "COPYRIGHT" +.IX Header "COPYRIGHT" +Copyright (C) 2015 Manish Sud. All rights reserved. +.PP +This file is part of MayaChemTools. +.PP +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.