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<h1>Source code for MMTK.ForceFields.CalphaFF</h1><div class="highlight"><pre>
<span class="c"># C-alpha 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">C-alpha force field for protein normal mode analysis</span>
<span class="sd">(Elastic Network Model)</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">CalphaTerm</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="CalphaForceField"><a class="viewcode-back" href="../../../modules.html#MMTK.ForceFields.CalphaFF.CalphaForceField">[docs]</a><span class="k">class</span> <span class="nc">CalphaForceField</span><span class="p">(</span><span class="n">ForceField</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Effective harmonic force field for a C-alpha protein model</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">cutoff</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">scale_factor</span> <span class="o">=</span> <span class="mf">1.</span><span class="p">,</span> <span class="n">version</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
<span class="sd">"""</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 scale_factor: a global scaling factor</span>
<span class="sd"> :type scale_factor: float</span>
<span class="sd"> """</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">'calpha'</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">cutoff</span><span class="p">,)</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">scale_factor</span> <span class="o">=</span> <span class="n">scale_factor</span>
<span class="bp">self</span><span class="o">.</span><span class="n">version</span> <span class="o">=</span> <span class="n">version</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">CalphaTerm</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="n">cutoff</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">scale_factor</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">version</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>
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