diff docs/scripts/txt/ElementalAnalysisSDFiles.txt @ 0:4816e4a8ae95 draft default tip

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+++ b/docs/scripts/txt/ElementalAnalysisSDFiles.txt	Wed Jan 20 09:23:18 2016 -0500
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+NAME
+    ElementalAnalysisSDFiles.pl - Perform elemental analysis using formula
+    data field in SDFile(s)
+
+SYNOPSIS
+    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)...
+
+DESCRIPTION
+    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.
+
+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.
+
+    --formulafield *SD data field name*
+        *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.
+
+    -f, --formulamode *DataField | StructureData*
+        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*.
+
+    --formulaout *yes or no*
+        Specify whether to write out formula to SD file during
+        *StructureData* value of -f, --formulamode option. Possible values:
+        *Yes or No*. Default: *No*.
+
+    -m, --mode *All | "ElementalAnalysis,[MolecularWeight,ExactMass]"*
+        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*
+
+    -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,
+        ExactMass, and MolecularFormula*. Default labels:
+        *ElementalAnalysis, MolecularWeight, ExactMass, and
+        MolecularFormula*.
+
+        *MolecularFormula* label is only used during *StructureData* value
+        of -f, --formulamode option.
+
+    -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, calculate molecular weight and exact mass
+    using structure data in SD file and generate a new SD file
+    NewSample1.sdf, type:
+
+        % ElementalAnalysisSDFiles.pl --formulamode StructureData -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 <[e-mail]>
+
+SEE ALSO
+    AnalyzeSDFilesData.pl, InfoSDFiles.pl, ExtractFromSDFiles.pl
+
+COPYRIGHT
+    Copyright (C) 2015 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.
+