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
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
|
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>Compute an average structure from a trajectory — MMTK User Guide 2.7.7 documentation</title>
<link rel="stylesheet" href="../../_static/default.css" type="text/css" />
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../',
VERSION: '2.7.7',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
};
</script>
<script type="text/javascript" src="../../_static/jquery.js"></script>
<script type="text/javascript" src="../../_static/underscore.js"></script>
<script type="text/javascript" src="../../_static/doctools.js"></script>
<link rel="top" title="MMTK User Guide 2.7.7 documentation" href="../../index.html" />
</head>
<body>
<div class="related">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="../../genindex.html" title="General Index"
accesskey="I">index</a></li>
<li class="right" >
<a href="../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li><a href="../../index.html">MMTK User Guide 2.7.7 documentation</a> »</li>
</ul>
</div>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body">
<div class="section" id="compute-an-average-structure-from-a-trajectory">
<h1>Compute an average structure from a trajectory<a class="headerlink" href="#compute-an-average-structure-from-a-trajectory" title="Permalink to this headline">ΒΆ</a></h1>
<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 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</pre></div></td><td class="code"><div class="highlight"><pre><span class="c"># This program reads a trajecory and calculates the average</span>
<span class="c"># configuration, which is then visualized. This is not a particularly</span>
<span class="c"># useful operation, but it illustrates the use of trajectories and</span>
<span class="c"># configuration variables.</span>
<span class="c">#</span>
<span class="c"># Note: In order to create the trajectory file "bala1.nc" which is</span>
<span class="c"># read by this example, you must run the example</span>
<span class="c"># MolecularDynamics/protein.py!</span>
<span class="c">#</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="o">*</span>
<span class="kn">from</span> <span class="nn">MMTK.Trajectory</span> <span class="kn">import</span> <span class="n">Trajectory</span>
<span class="kn">from</span> <span class="nn">MMTK.Visualization</span> <span class="kn">import</span> <span class="n">view</span>
<span class="c"># Open the input trajectory.</span>
<span class="n">trajectory</span> <span class="o">=</span> <span class="n">Trajectory</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">'bala1.nc'</span><span class="p">)</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">trajectory</span><span class="o">.</span><span class="n">universe</span>
<span class="c"># Create a zeroed particle vector object.</span>
<span class="nb">sum</span> <span class="o">=</span> <span class="n">ParticleVector</span><span class="p">(</span><span class="n">universe</span><span class="p">)</span>
<span class="c"># Loop over all steps and add the configurations to the sum.</span>
<span class="k">for</span> <span class="n">configuration</span> <span class="ow">in</span> <span class="n">trajectory</span><span class="o">.</span><span class="n">configuration</span><span class="p">:</span>
<span class="nb">sum</span> <span class="o">=</span> <span class="nb">sum</span> <span class="o">+</span> <span class="n">configuration</span>
<span class="c"># Divide by the number of steps.</span>
<span class="nb">sum</span> <span class="o">=</span> <span class="nb">sum</span><span class="o">/</span><span class="nb">len</span><span class="p">(</span><span class="n">trajectory</span><span class="p">)</span>
<span class="c"># Visualize the average.</span>
<span class="n">view</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="nb">sum</span><span class="p">)</span>
</pre></div>
</td></tr></table></div>
</div>
</div>
</div>
</div>
<div class="sphinxsidebar">
<div class="sphinxsidebarwrapper">
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="../../_sources/Examples/Trajectories/trajectory_average.py.txt"
rel="nofollow">Show Source</a></li>
</ul>
<div id="searchbox" style="display: none">
<h3>Quick search</h3>
<form class="search" action="../../search.html" method="get">
<input type="text" name="q" />
<input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
<p class="searchtip" style="font-size: 90%">
Enter search terms or a module, class or function name.
</p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="related">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="../../genindex.html" title="General Index"
>index</a></li>
<li class="right" >
<a href="../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li><a href="../../index.html">MMTK User Guide 2.7.7 documentation</a> »</li>
</ul>
</div>
<div class="footer">
© Copyright 2010, Konrad Hinsen.
Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
</div>
</body>
</html>
|
