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
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
|
<!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>MMTK.ForceFields.DeformationFF — 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" />
<link rel="up" title="Module code" 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>
<li><a href="../../index.html" accesskey="U">Module code</a> »</li>
</ul>
</div>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body">
<h1>Source code for MMTK.ForceFields.DeformationFF</h1><div class="highlight"><pre>
<span class="c"># Deformation force field</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">Deformation force field (elastic network model)</span>
<span class="sd">For proteins, CalphaForceField is usually a better choice.</span>
<span class="sd">"""</span>
<span class="n">__docformat__</span> <span class="o">=</span> <span class="s">'restructuredtext'</span>
<span class="kn">from</span> <span class="nn">MMTK.ForceFields.ForceField</span> <span class="kn">import</span> <span class="n">ForceField</span><span class="p">,</span> <span class="n">ForceFieldData</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="n">Utility</span>
<span class="kn">from</span> <span class="nn">MMTK_forcefield</span> <span class="kn">import</span> <span class="n">NonbondedList</span><span class="p">,</span> <span class="n">NonbondedListTerm</span>
<span class="kn">from</span> <span class="nn">MMTK_deformation</span> <span class="kn">import</span> <span class="n">DeformationTerm</span>
<span class="kn">from</span> <span class="nn">Scientific</span> <span class="kn">import</span> <span class="n">N</span>
<span class="c">#</span>
<span class="c"># The deformation force field class</span>
<span class="c">#</span>
<div class="viewcode-block" id="DeformationForceField"><a class="viewcode-back" href="../../../modules.html#MMTK.ForceFields.DeformationFF.DeformationForceField">[docs]</a><span class="k">class</span> <span class="nc">DeformationForceField</span><span class="p">(</span><span class="n">ForceField</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Deformation force field for protein normal mode calculations</span>
<span class="sd"> The pair interaction force constant has the form</span>
<span class="sd"> k(r)=factor*exp(-(r**2-0.01)/range**2). The default value</span>
<span class="sd"> for range is appropriate for a C-alpha model of a protein.</span>
<span class="sd"> The offset of 0.01 is a convenience for defining factor;</span>
<span class="sd"> with this definition, factor is the force constant for a</span>
<span class="sd"> distance of 0.1nm.</span>
<span class="sd"> """</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fc_length</span> <span class="o">=</span> <span class="mf">0.7</span><span class="p">,</span> <span class="n">cutoff</span> <span class="o">=</span> <span class="mf">1.2</span><span class="p">,</span> <span class="n">factor</span> <span class="o">=</span> <span class="mf">46402.</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param fc_length: a range parameter</span>
<span class="sd"> :type fc_length: float</span>
<span class="sd"> :param cutoff: the cutoff for pair interactions, should be</span>
<span class="sd"> at least 2.5 nm. Pair interactions in periodic</span>
<span class="sd"> systems are calculated using the minimum-image</span>
<span class="sd"> convention; the cutoff should therefore never be</span>
<span class="sd"> larger than half the smallest edge length of the</span>
<span class="sd"> elementary cell.</span>
<span class="sd"> :type cutoff: float</span>
<span class="sd"> :param factor: a global scaling factor</span>
<span class="sd"> :type factor: float</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">arguments</span> <span class="o">=</span> <span class="p">(</span><span class="n">fc_length</span><span class="p">,</span> <span class="n">cutoff</span><span class="p">,</span> <span class="n">factor</span><span class="p">)</span>
<span class="n">ForceField</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">'deformation'</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">arguments</span> <span class="o">=</span> <span class="p">(</span><span class="n">fc_length</span><span class="p">,</span> <span class="n">cutoff</span><span class="p">,</span> <span class="n">factor</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fc_length</span> <span class="o">=</span> <span class="n">fc_length</span>
<span class="bp">self</span><span class="o">.</span><span class="n">cutoff</span> <span class="o">=</span> <span class="n">cutoff</span>
<span class="bp">self</span><span class="o">.</span><span class="n">factor</span> <span class="o">=</span> <span class="n">factor</span>
<span class="k">def</span> <span class="nf">ready</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">global_data</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">True</span>
<span class="k">def</span> <span class="nf">evaluatorTerms</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">universe</span><span class="p">,</span> <span class="n">subset1</span><span class="p">,</span> <span class="n">subset2</span><span class="p">,</span> <span class="n">global_data</span><span class="p">):</span>
<span class="n">nothing</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">),</span> <span class="n">N</span><span class="o">.</span><span class="n">Int</span><span class="p">)</span>
<span class="k">if</span> <span class="n">subset1</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">set1</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">index</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">subset1</span><span class="o">.</span><span class="n">atomList</span><span class="p">())</span>
<span class="n">set2</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">index</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">subset2</span><span class="o">.</span><span class="n">atomList</span><span class="p">())</span>
<span class="n">excluded_pairs</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">Utility</span><span class="o">.</span><span class="n">orderedPairs</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">set1</span><span class="o">-</span><span class="n">set2</span><span class="p">)))</span> \
<span class="o">|</span> <span class="nb">set</span><span class="p">(</span><span class="n">Utility</span><span class="o">.</span><span class="n">orderedPairs</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">set2</span><span class="o">-</span><span class="n">set1</span><span class="p">)))</span>
<span class="n">excluded_pairs</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">excluded_pairs</span><span class="p">))</span>
<span class="n">atom_subset</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">set1</span> <span class="o">|</span> <span class="n">set2</span><span class="p">)</span>
<span class="n">atom_subset</span><span class="o">.</span><span class="n">sort</span><span class="p">()</span>
<span class="n">atom_subset</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">atom_subset</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">atom_subset</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">array</span><span class="p">([],</span> <span class="n">N</span><span class="o">.</span><span class="n">Int</span><span class="p">)</span>
<span class="n">excluded_pairs</span> <span class="o">=</span> <span class="n">nothing</span>
<span class="n">nbl</span> <span class="o">=</span> <span class="n">NonbondedList</span><span class="p">(</span><span class="n">excluded_pairs</span><span class="p">,</span> <span class="n">nothing</span><span class="p">,</span> <span class="n">atom_subset</span><span class="p">,</span> <span class="n">universe</span><span class="o">.</span><span class="n">_spec</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">cutoff</span><span class="p">)</span>
<span class="n">update</span> <span class="o">=</span> <span class="n">NonbondedListTerm</span><span class="p">(</span><span class="n">nbl</span><span class="p">)</span>
<span class="n">cutoff</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">cutoff</span>
<span class="k">if</span> <span class="n">cutoff</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">cutoff</span> <span class="o">=</span> <span class="mf">0.</span>
<span class="n">ev</span> <span class="o">=</span> <span class="n">DeformationTerm</span><span class="p">(</span><span class="n">universe</span><span class="o">.</span><span class="n">_spec</span><span class="p">,</span> <span class="n">nbl</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">fc_length</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">cutoff</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">factor</span><span class="p">,</span> <span class="mf">1.</span><span class="p">)</span>
<span class="k">return</span> <span class="p">[</span><span class="n">update</span><span class="p">,</span> <span class="n">ev</span><span class="p">]</span></div>
</pre></div>
</div>
</div>
</div>
<div class="sphinxsidebar">
<div class="sphinxsidebarwrapper">
<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>
<li><a href="../../index.html" >Module code</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>
|
