|
0
|
1 <html>
|
|
|
2 <head>
|
|
|
3 <title>MayaChemTools:Documentation:ElementalAnalysisSDFiles.pl</title>
|
|
|
4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
|
|
|
5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css">
|
|
|
6 </head>
|
|
|
7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
|
|
|
8 <br/>
|
|
|
9 <center>
|
|
|
10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
|
|
|
11 </center>
|
|
|
12 <br/>
|
|
|
13 <div class="DocNav">
|
|
|
14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
|
|
|
15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ElementalAnalysis.html" title="ElementalAnalysis.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ElementalAnalysisTextFiles.html" title="ElementalAnalysisTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>ElementalAnalysisSDFiles.pl</strong></td><td width="33%" align="right"><a href="././code/ElementalAnalysisSDFiles.html" title="View source code">Code</a> | <a href="./../pdf/ElementalAnalysisSDFiles.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/ElementalAnalysisSDFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/ElementalAnalysisSDFiles.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/ElementalAnalysisSDFiles.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
|
|
|
16 </table>
|
|
|
17 </div>
|
|
|
18 <p>
|
|
|
19 </p>
|
|
|
20 <h2>NAME</h2>
|
|
|
21 <p>ElementalAnalysisSDFiles.pl - Perform elemental analysis using formula data field in SDFile(s)</p>
|
|
|
22 <p>
|
|
|
23 </p>
|
|
|
24 <h2>SYNOPSIS</h2>
|
|
|
25 <p>ElementalAnalysisSDFiles.pl SDFile(s)...</p>
|
|
|
26 <p>ElementalAnalysisSDFiles.pl [<strong>-d, --detail</strong> infolevel] [<strong>--fast</strong>]
|
|
|
27 [<strong>--formulafield</strong> SD data field name] [<strong>-f, --formulamode</strong> <em>DataField | StructureData</em>]
|
|
|
28 [<strong>--formulaout</strong> yes or no] [<strong>-m, --mode</strong> All | "ElementalAnalysis, [MolecularWeight, ExactMass]"]
|
|
|
29 [<strong>-h, --help</strong>] [<strong>-o, --overwrite</strong>] [<strong>-r, --root</strong> rootname]
|
|
|
30 [<strong>-v --valuefieldnames</strong> Name, Label, [Name, Label,...]] [<strong>-w, --workingdir</strong> dirname] SDFile(s)...</p>
|
|
|
31 <p>
|
|
|
32 </p>
|
|
|
33 <h2>DESCRIPTION</h2>
|
|
|
34 <p>Perform elemental analysis using molecular formula specified by a data field name or generated
|
|
|
35 from structure data in <em>SDFile(s)</em>.</p>
|
|
|
36 <p>In addition to straightforward molecular formulas - H2O, HCl, C3H7O2N -
|
|
|
37 other supported variations are: Ca3(PO4)2, [PCl4]+, [Fe(CN)6]4-, C37H42N2O6+2, Na2CO3.10H2O,
|
|
|
38 8H2S.46H2O, and so on. Charges are simply ignored. Isotope symbols in formulas specification, including
|
|
|
39 D and T, are not supported.</p>
|
|
|
40 <p>The file names are separated by space.The valid file extensions are <em>.sdf</em> and <em>.sd</em>.
|
|
|
41 All other file names are ignored. All the SD files in a current directory can be specified
|
|
|
42 either by <em>*.sdf</em> or the current directory name.</p>
|
|
|
43 <p>
|
|
|
44 </p>
|
|
|
45 <h2>OPTIONS</h2>
|
|
|
46 <dl>
|
|
|
47 <dt><strong><strong>-d, --detail</strong> <em>infolevel</em></strong></dt>
|
|
|
48 <dd>
|
|
|
49 <p>Level of information to print about compound records being ignored. Default: <em>1</em>. Possible
|
|
|
50 values: <em>1, 2 or 3</em>.</p>
|
|
|
51 </dd>
|
|
|
52 <dt><strong><strong>--fast</strong></strong></dt>
|
|
|
53 <dd>
|
|
|
54 <p>In this mode, the formula data field specified using <strong>-f, --formulafield</strong> option is assumed
|
|
|
55 to contain valid molecular formula data and initial formula validation check is skipped.</p>
|
|
|
56 </dd>
|
|
|
57 <dt><strong><strong>--formulafield</strong> <em>SD data field name</em></strong></dt>
|
|
|
58 <dd>
|
|
|
59 <p><em>SDFile(s)</em> data field name containing molecular formulas used for performing
|
|
|
60 elemental analysis during <em>DataField</em> value of <strong>-f, --formulamode</strong> option.
|
|
|
61 Default value: <em>SD data field containing the word formula in its name</em>.</p>
|
|
|
62 <p>This option is ignore during <em>StructureData</em> value of <strong>-f, --formulamode</strong> option.</p>
|
|
|
63 </dd>
|
|
|
64 <dt><strong><strong>-f, --formulamode</strong> <em>DataField | StructureData</em></strong></dt>
|
|
|
65 <dd>
|
|
|
66 <p>Specify source of molecular formula used for performing elemental analysis: retrieve
|
|
|
67 formula using <em>SDFile(s)</em> data field name or generate formula from structure. Possible
|
|
|
68 values: <em>DataField or StructureData</em>. Default value: <em>DataField</em>.</p>
|
|
|
69 </dd>
|
|
|
70 <dt><strong><strong>--formulaout</strong> <em>yes or no</em></strong></dt>
|
|
|
71 <dd>
|
|
|
72 <p>Specify whether to write out formula to SD file during <em>StructureData</em> value of
|
|
|
73 <strong>-f, --formulamode</strong> option. Possible values: <em>Yes or No</em>. Default: <em>No</em>.</p>
|
|
|
74 </dd>
|
|
|
75 <dt><strong><strong>-m, --mode</strong> <em>All | "ElementalAnalysis,[MolecularWeight,ExactMass]"</em></strong></dt>
|
|
|
76 <dd>
|
|
|
77 <p>Specify what values to calculate using molecular formula data field or structure data from
|
|
|
78 <em>SDFile(s)</em>: calculate all supported values or specify a comma delimited list of values.
|
|
|
79 Possible values: <em>All | "ElementalAnalysis, [MolecularWeight, ExactMass]"</em>. Default: <em>All</em></p>
|
|
|
80 </dd>
|
|
|
81 <dt><strong><strong>-h, --help</strong></strong></dt>
|
|
|
82 <dd>
|
|
|
83 <p>Print this help message.</p>
|
|
|
84 </dd>
|
|
|
85 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
|
|
|
86 <dd>
|
|
|
87 <p>Overwrite existing files.</p>
|
|
|
88 </dd>
|
|
|
89 <dt><strong><strong>-p, --precision</strong> <em>number</em></strong></dt>
|
|
|
90 <dd>
|
|
|
91 <p>Precision of calculated values in the output file. Default: up to <em>2</em> decimal places.
|
|
|
92 Valid values: positive integers.</p>
|
|
|
93 </dd>
|
|
|
94 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
|
|
|
95 <dd>
|
|
|
96 <p>New SD file name is generated using the root: <Root>.<Ext>. Default new file
|
|
|
97 name: <InitialSDFileName>ElementalAnalysis.<Ext>. This option is ignored for multiple
|
|
|
98 input files.</p>
|
|
|
99 </dd>
|
|
|
100 <dt><strong><strong>-v --valuefieldnames</strong> <em>Name,Label,[Name,Label,...]</em></strong></dt>
|
|
|
101 <dd>
|
|
|
102 <p>Specify SD data field names to use for calculated values. In general, it's a comma delimited
|
|
|
103 list of value name and SD field name pairs. Supported value names: <em>ElementalAnalysis,
|
|
|
104 MolecularWeight, ExactMass, and MolecularFormula</em>. Default labels: <em>ElementalAnalysis,
|
|
|
105 MolecularWeight, ExactMass, and MolecularFormula</em>.</p>
|
|
|
106 <p><em>MolecularFormula</em> label is only used during <em>StructureData</em> value of
|
|
|
107 <strong>-f, --formulamode</strong> option.</p>
|
|
|
108 </dd>
|
|
|
109 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt>
|
|
|
110 <dd>
|
|
|
111 <p>Location of working directory. Default: current directory.</p>
|
|
|
112 </dd>
|
|
|
113 </dl>
|
|
|
114 <p>
|
|
|
115 </p>
|
|
|
116 <h2>EXAMPLES</h2>
|
|
|
117 <p>To perform elemental analysis, calculate molecular weight and exact mass using SD
|
|
|
118 field name value with the word Formula in its name and generate a new SD file
|
|
|
119 NewSample1.sdf, type:</p>
|
|
|
120 <div class="ExampleBox">
|
|
|
121 % ElementalAnalysisSDFiles.pl -o -r NewSample1 Sample1.sdf</div>
|
|
|
122 <p>To perform elemental analysis, calculate molecular weight and exact mass using
|
|
|
123 structure data in SD file and generate a new SD file NewSample1.sdf, type:</p>
|
|
|
124 <div class="ExampleBox">
|
|
|
125 % ElementalAnalysisSDFiles.pl --formulamode StructureData -o
|
|
|
126 -r NewSample1 Sample1.sdf</div>
|
|
|
127 <p>To perform elemental analysis using formulas in SD field name Formula, use field name
|
|
|
128 Analysis for calculated data, and generate a new SD file NewSample1.sdf, type:</p>
|
|
|
129 <div class="ExampleBox">
|
|
|
130 % ElementalAnalysisSDFiles.pl --m ElementalAnalysis --formulafield
|
|
|
131 Formula --valuefieldnames "ElementalAnalysis,Analysis" -o
|
|
|
132 -r NewSample1 Sample1.sdf</div>
|
|
|
133 <p>To calculate molecular weight, using formulas in SD field name Formula, with four decimal
|
|
|
134 precision and generate a new SD file NewSample1.sdf, type</p>
|
|
|
135 <div class="ExampleBox">
|
|
|
136 % ElementalAnalysisSDFiles.pl --m MolecularWeight --formulafield
|
|
|
137 Formula --precision 4 -o -r NewSample1 Sample1.sdf</div>
|
|
|
138 <p>
|
|
|
139 </p>
|
|
|
140 <h2>AUTHOR</h2>
|
|
|
141 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
|
|
|
142 <p>
|
|
|
143 </p>
|
|
|
144 <h2>SEE ALSO</h2>
|
|
|
145 <p><a href="./AnalyzeSDFilesData.html">AnalyzeSDFilesData.pl</a>, <a href="./InfoSDFiles.html">InfoSDFiles.pl</a>, <a href="./ExtractFromSDFiles.html">ExtractFromSDFiles.pl</a>
|
|
|
146 </p>
|
|
|
147 <p>
|
|
|
148 </p>
|
|
|
149 <h2>COPYRIGHT</h2>
|
|
|
150 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
|
|
|
151 <p>This file is part of MayaChemTools.</p>
|
|
|
152 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
153 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
154 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
155 any later version.</p>
|
|
|
156 <p> </p><p> </p><div class="DocNav">
|
|
|
157 <table width="100%" border=0 cellpadding=0 cellspacing=2>
|
|
|
158 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ElementalAnalysis.html" title="ElementalAnalysis.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ElementalAnalysisTextFiles.html" title="ElementalAnalysisTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>ElementalAnalysisSDFiles.pl</strong></td></tr>
|
|
|
159 </table>
|
|
|
160 </div>
|
|
|
161 <br />
|
|
|
162 <center>
|
|
|
163 <img src="../../images/h2o2.png">
|
|
|
164 </center>
|
|
|
165 </body>
|
|
|
166 </html>
|
