|
0
|
1 <html>
|
|
|
2 <head>
|
|
|
3 <title>MayaChemTools:Documentation:MolFilesToSD.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="./ModifyTextFilesFormat.html" title="ModifyTextFilesFormat.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./PathLengthFingerprints.html" title="PathLengthFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>MolFilesToSD.pl</strong></td><td width="33%" align="right"><a href="././code/MolFilesToSD.html" title="View source code">Code</a> | <a href="./../pdf/MolFilesToSD.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/MolFilesToSD.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/MolFilesToSD.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/MolFilesToSD.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>MolFilesToSD.pl - Generate a SD file from MDLMOL File(s)</p>
|
|
|
22 <p>
|
|
|
23 </p>
|
|
|
24 <h2>SYNOPSIS</h2>
|
|
|
25 <p>MolFilesToSD.pl MDLMOLFile(s)...</p>
|
|
|
26 <p>MolFilesToSD.pl [<strong>-c, --compoundid</strong> usefileprefix | idlabel] [<strong>-d, --datafieldlabel</strong> fieldlabel]
|
|
|
27 [<strong>-h, --help</strong>] [<strong>-m, --mode</strong> molnameline | datafield | both | none] [<strong>-o, --overwrite</strong>]
|
|
|
28 [<strong>-r, --root</strong> rootname] [<strong>-w, --workingdir</strong> dirname] MDLMOLFile(s)...</p>
|
|
|
29 <p>
|
|
|
30 </p>
|
|
|
31 <h2>DESCRIPTION</h2>
|
|
|
32 <p>Generate a SD file from <em>MDLMOL File(s)</em>. Multiple file names are separated by spaces.
|
|
|
33 The valid file extension is <em>.mol</em>. All other file names are ignored. All the files in a current
|
|
|
34 directory can be specified by <em>*.mol</em>, or the current directory name.</p>
|
|
|
35 <p>
|
|
|
36 </p>
|
|
|
37 <h2>OPTIONS</h2>
|
|
|
38 <dl>
|
|
|
39 <dt><strong><strong>-c, --compoundid</strong> <em>usefileprefix | idlabel</em></strong></dt>
|
|
|
40 <dd>
|
|
|
41 <p>Specify how to generate compound IDs: use MOL filename prefix or generate
|
|
|
42 a new compound ID by combining <em>idlabel</em> with compound number. Possible
|
|
|
43 values: <em>usefileprefix | idlabel</em>. By default, <em>Cmd</em> is used as a <em>idlabel</em> to generate
|
|
|
44 these types of compound IDs: Cmpd1, Cmpd2 and so on.</p>
|
|
|
45 <p>Example: To generate compound IDs like Mol_ID1, Mol_ID2 and so on, specify
|
|
|
46 "MolID" value for this option.</p>
|
|
|
47 </dd>
|
|
|
48 <dt><strong><strong>-d, --datafieldlabel</strong> <em>fieldlabel</em></strong></dt>
|
|
|
49 <dd>
|
|
|
50 <p>Specify data field label for adding compound ID field into SD file during <em>datafield | both</em>
|
|
|
51 values of <strong>-m, --mode</strong> option. Default: <Cmpd_ID>.</p>
|
|
|
52 </dd>
|
|
|
53 <dt><strong><strong>-h, --help</strong></strong></dt>
|
|
|
54 <dd>
|
|
|
55 <p>Print this help message.</p>
|
|
|
56 </dd>
|
|
|
57 <dt><strong><strong>-m, --mode</strong> <em>molnameline | datafield | both | none</em></strong></dt>
|
|
|
58 <dd>
|
|
|
59 <p>Specify how to add compopund ID into SD file: relplace the molname line,
|
|
|
60 add a new data field, replace the molname line and add data field, or do
|
|
|
61 nothing. Possible values: <em>molnameline | datafield | both | none</em>.
|
|
|
62 Default: <em>nothing</em>.</p>
|
|
|
63 <p>Use <strong>-c, --compoundid</strong> to specify compound ID generation process.</p>
|
|
|
64 </dd>
|
|
|
65 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
|
|
|
66 <dd>
|
|
|
67 <p>Overwrite existing files.</p>
|
|
|
68 </dd>
|
|
|
69 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
|
|
|
70 <dd>
|
|
|
71 <p>New SD file name is generated using the root: <Root>.sdf. Default new file
|
|
|
72 name: <InitialMOLFileName>1To<Count>.sdf.</p>
|
|
|
73 </dd>
|
|
|
74 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt>
|
|
|
75 <dd>
|
|
|
76 <p>Location of working directory. Default: current directory.</p>
|
|
|
77 </dd>
|
|
|
78 </dl>
|
|
|
79 <p>
|
|
|
80 </p>
|
|
|
81 <h2>EXAMPLES</h2>
|
|
|
82 <p>To generate NewSample.sdf file from Sample*.mol files, type:</p>
|
|
|
83 <div class="ExampleBox">
|
|
|
84 % MolFilesToSD.pl -r NewSample -o Sample*.mol</div>
|
|
|
85 <p>To generate NewSample.sdf with Cmpd1, Cmpd2 and so on as compound ID in
|
|
|
86 MolName line and Cmpd_ID datafield from Sample*.mol files, type:</p>
|
|
|
87 <div class="ExampleBox">
|
|
|
88 % MolFilesToSD.pl -r NewSample -m both -o Sample*.mol</div>
|
|
|
89 <p>
|
|
|
90 </p>
|
|
|
91 <h2>AUTHOR</h2>
|
|
|
92 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
|
|
|
93 <p>
|
|
|
94 </p>
|
|
|
95 <h2>SEE ALSO</h2>
|
|
|
96 <p><a href="./InfoSDFiles.html">InfoSDFiles.pl</a>, <a href="./SDToMolFiles.html">SDToMolFiles.pl</a>
|
|
|
97 </p>
|
|
|
98 <p>
|
|
|
99 </p>
|
|
|
100 <h2>COPYRIGHT</h2>
|
|
|
101 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
|
|
|
102 <p>This file is part of MayaChemTools.</p>
|
|
|
103 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
104 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
105 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
106 any later version.</p>
|
|
|
107 <p> </p><p> </p><div class="DocNav">
|
|
|
108 <table width="100%" border=0 cellpadding=0 cellspacing=2>
|
|
|
109 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ModifyTextFilesFormat.html" title="ModifyTextFilesFormat.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./PathLengthFingerprints.html" title="PathLengthFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MolFilesToSD.pl</strong></td></tr>
|
|
|
110 </table>
|
|
|
111 </div>
|
|
|
112 <br />
|
|
|
113 <center>
|
|
|
114 <img src="../../images/h2o2.png">
|
|
|
115 </center>
|
|
|
116 </body>
|
|
|
117 </html>
|
