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<h1>Source code for MMTK.ProteinFriction</h1><div class="highlight"><pre>
<span class="c"># Friction constants for protein C-alpha models</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">A friction constant model for |C_alpha| models of proteins</span>
<span class="sd">"""</span>
<span class="n">__docformat__</span> <span class="o">=</span> <span class="s">'restructuredtext'</span>
<span class="kn">import</span> <span class="nn">MMTK.ParticleProperties</span>
<span class="kn">from</span> <span class="nn">Scientific</span> <span class="kn">import</span> <span class="n">N</span>
<div class="viewcode-block" id="calphaFrictionConstants"><a class="viewcode-back" href="../../modules.html#MMTK.ProteinFriction.calphaFrictionConstants">[docs]</a><span class="k">def</span> <span class="nf">calphaFrictionConstants</span><span class="p">(</span><span class="n">protein</span><span class="p">,</span> <span class="nb">set</span><span class="o">=</span><span class="mi">2</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param protein: a |C_alpha| model protein</span>
<span class="sd"> :type protein: :class:`~MMTK.Proteins.Protein`</span>
<span class="sd"> :param set: the number of a friction constant set (1, 2, 3, or 4)</span>
<span class="sd"> :return: the estimated friction constants for the atoms in the protein</span>
<span class="sd"> :rtype: :class:`~MMTK.ParticleProperties.ParticleScalar`</span>
<span class="sd"> """</span>
<span class="n">radius</span> <span class="o">=</span> <span class="mf">1.5</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="n">protein</span><span class="o">.</span><span class="n">atomCollection</span><span class="p">()</span>
<span class="n">f</span> <span class="o">=</span> <span class="n">MMTK</span><span class="o">.</span><span class="n">ParticleProperties</span><span class="o">.</span><span class="n">ParticleScalar</span><span class="p">(</span><span class="n">protein</span><span class="o">.</span><span class="n">universe</span><span class="p">())</span>
<span class="k">for</span> <span class="n">chain</span> <span class="ow">in</span> <span class="n">protein</span><span class="p">:</span>
<span class="k">for</span> <span class="n">residue</span> <span class="ow">in</span> <span class="n">chain</span><span class="p">:</span>
<span class="n">a</span> <span class="o">=</span> <span class="n">residue</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C_alpha</span>
<span class="n">m</span> <span class="o">=</span> <span class="n">atoms</span><span class="o">.</span><span class="n">selectShell</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">position</span><span class="p">(),</span> <span class="n">radius</span><span class="p">)</span><span class="o">.</span><span class="n">mass</span><span class="p">()</span>
<span class="n">d</span> <span class="o">=</span> <span class="mf">3.</span><span class="o">*</span><span class="n">m</span><span class="o">/</span><span class="p">(</span><span class="mf">4.</span><span class="o">*</span><span class="n">N</span><span class="o">.</span><span class="n">pi</span><span class="o">*</span><span class="n">radius</span><span class="o">**</span><span class="mi">3</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">set</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span> <span class="c"># linear fit to initial slope</span>
<span class="n">f</span><span class="p">[</span><span class="n">a</span><span class="p">]</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="mf">1000.</span><span class="p">,</span> <span class="mf">121.2</span><span class="o">*</span><span class="n">d</span><span class="o">-</span><span class="mi">8600</span><span class="p">)</span>
<span class="k">elif</span> <span class="nb">set</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span> <span class="c"># exponential fit 400 steps</span>
<span class="n">f</span><span class="p">[</span><span class="n">a</span><span class="p">]</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="mf">1000.</span><span class="p">,</span> <span class="mf">68.2</span><span class="o">*</span><span class="n">d</span><span class="o">-</span><span class="mi">5160</span><span class="p">)</span>
<span class="k">elif</span> <span class="nb">set</span> <span class="o">==</span> <span class="mi">3</span><span class="p">:</span> <span class="c"># exponential fit 200 steps</span>
<span class="n">f</span><span class="p">[</span><span class="n">a</span><span class="p">]</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="mf">1000.</span><span class="p">,</span> <span class="mf">38.2</span><span class="o">*</span><span class="n">d</span><span class="o">-</span><span class="mi">2160</span><span class="p">)</span>
<span class="k">elif</span> <span class="nb">set</span> <span class="o">==</span> <span class="mi">4</span><span class="p">:</span> <span class="c"># expansion fit 50 steps</span>
<span class="n">f</span><span class="p">[</span><span class="n">a</span><span class="p">]</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="mf">1000.</span><span class="p">,</span> <span class="mf">20.4</span><span class="o">*</span><span class="n">d</span><span class="o">-</span><span class="mf">500.</span><span class="p">)</span>
<span class="k">return</span> <span class="n">f</span></div>
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