1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
|
<!-- manual page source format generated by PolyglotMan v3.2, -->
<!-- available at http://polyglotman.sourceforge.net/ -->
<html>
<head>
<title>obrotamer</title>
</head>
<body bgcolor='white'>
<a href='#toc'>Table of Contents</a><p>
<h2><a name='sect0' href='#toc0'>Name</a></h2>
<p>
<b>obrotamer</b> -- generate conformer/rotamer coordinates
<p>
<h2><a name='sect1' href='#toc1'><b>Synopsis</b></a></h2>
<p>
<b>obrotamer</b> <i>filename</i>
<p>
<h2><a name='sect2' href='#toc2'><b>Description</b></a></h2>
<p>
The obrotamer tool can be used as part of a conformational search by generating
random isomers based on rotating dihedral angles. These rotamers
are not conformers -- that is, obrotamer does not perform geometry optimization
after generating the rotamer structure. The obminimize tool can
do geometry optimization using molecular mechanics.
<p>
<h2><a name='sect3' href='#toc3'><b>Examples</b></a></h2>
<p>
Generate a random rotational isomer of baseconformer.sdf and write it to
rotamer1.sdf:<br>
<pre>obrotamer baseconformer.sdf >rotamer1.sdf</pre>
<p>
<h2><a name='sect4' href='#toc4'><b>See</b> <b>Also</b></a></h2>
<p>
<a href='babel.html'>babel(1)</a>
, <a href='obenergy.html'>obenergy(1)</a>
, <a href='obfit.html'>obfit(1)</a>
, <a href='obgrep.html'>obgrep(1)</a>
, <a href='obminimize.html'>obminimize(1)</a>
, <a href='obrotate.html'>obrotate(1)</a>
.
<p><p>
The web pages for Open Babel can be found at: <<b><a href="http://openbabel.org/">http://openbabel.org/</a></b>>
<p>
<h2><a name='sect5' href='#toc5'><b>Authors</b></a></h2>
<p>
Open Babel is developed by a cast of many, including currrent maintainers
Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who
have contributed fixes and additions. For more contributors to Open
Babel, see <<b><a href="http://openbabel.org/wiki/THANKS">http://openbabel.org/wiki/THANKS</a></b>>
<p>
<h2><a name='sect6' href='#toc6'><b>Copyright</b></a></h2>
<p>
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.<br>
Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison and other
contributors.
<p><p>
This program is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the
Free Software Foundation version 2 of the License.
<p><p>
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
License for more details.
<p>
<hr><p>
<a name='toc'><b>Table of Contents</b></a><p>
<ul>
<li><a name='toc0' href='#sect0'>Name</a></li>
<li><a name='toc1' href='#sect1'>Synopsis</a></li>
<li><a name='toc2' href='#sect2'>Description</a></li>
<li><a name='toc3' href='#sect3'>Examples</a></li>
<li><a name='toc4' href='#sect4'>See Also</a></li>
<li><a name='toc5' href='#sect5'>Authors</a></li>
<li><a name='toc6' href='#sect6'>Copyright</a></li>
</ul>
</body>
</html>
|
