hps_polymer_model.html 53.16 KiB
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<h1>Source code for arbdmodel.hps_polymer_model</h1><div class="highlight"><pre>
<span></span><span class="c1"># -*- coding: utf-8 -*-</span>
<span class="c1">## Test with `python -m arbdmodel.hps_polymer_model`</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
<span class="c1">## Local imports</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">.logger</span><span class="w"> </span><span class="kn">import</span> <span class="n">logger</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">ParticleType</span><span class="p">,</span> <span class="n">PointParticle</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">.polymer</span><span class="w"> </span><span class="kn">import</span> <span class="n">PolymerBeads</span><span class="p">,</span> <span class="n">PolymerModel</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">.interactions</span><span class="w"> </span><span class="kn">import</span> <span class="n">AbstractPotential</span><span class="p">,</span> <span class="n">HarmonicBond</span>
<span class="sd">"""Define particle types"""</span>
<span class="n">_types</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
<span class="n">A</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"ALA"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">71.08</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">5.04</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.72973</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">R</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"ARG"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">156.2</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">6.56</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.0</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">N</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"ASN"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">114.1</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">5.68</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.432432</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">D</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"ASP"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">115.1</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">5.58</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.378378</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">C</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"CYS"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">103.1</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">5.48</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.594595</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">Q</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"GLN"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">128.1</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">6.02</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.513514</span><span class="p">,</span> <span class="p">),</span>
<span class="n">E</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"GLU"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">129.1</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">5.92</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.459459</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">G</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"GLY"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">57.05</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">4.5</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.648649</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">H</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"HIS"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">137.1</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="mf">0.5</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">6.08</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.513514</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">I</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"ILE"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">113.2</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">6.18</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.972973</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">L</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"LEU"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">113.2</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">6.18</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.972973</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">K</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"LYS"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">128.2</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">6.36</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.513514</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">M</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"MET"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">131.2</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">6.18</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.837838</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">F</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"PHE"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">147.2</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">6.36</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">1.0</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">P</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"PRO"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">97.12</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">5.56</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">1.0</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">S</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"SER"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">87.08</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">5.18</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.594595</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">T</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"THR"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">101.1</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">5.62</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.675676</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">W</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"TRP"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">186.2</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">sigma</span> <span class="o">=</span> <span class="mf">6.78</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.945946</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">Y</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"TYR"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">163.2</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">6.46</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.864865</span><span class="p">,</span>
<span class="p">),</span>
<span class="n">V</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"VAL"</span><span class="p">,</span>
<span class="n">mass</span> <span class="o">=</span> <span class="mf">99.07</span><span class="p">,</span>
<span class="n">charge</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">5.86</span><span class="p">,</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.891892</span><span class="p">,</span>
<span class="p">)</span>
<span class="p">)</span>
<span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">t</span> <span class="ow">in</span> <span class="n">_types</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="n">t</span><span class="o">.</span><span class="n">resname</span> <span class="o">=</span> <span class="n">t</span><span class="o">.</span><span class="n">name</span>
<div class="viewcode-block" id="HpsNonbonded">
<a class="viewcode-back" href="../../api/polymer_modeling/hps_polymer_model.html#arbdmodel.hps_polymer_model.HpsNonbonded">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">HpsNonbonded</span><span class="p">(</span><span class="n">AbstractPotential</span><span class="p">):</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">debye_length</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">resolution</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span> <span class="n">range_</span><span class="o">=</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="kc">None</span><span class="p">)):</span>
<span class="n">AbstractPotential</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resolution</span><span class="o">=</span><span class="n">resolution</span><span class="p">,</span> <span class="n">range_</span><span class="o">=</span><span class="n">range_</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">debye_length</span> <span class="o">=</span> <span class="n">debye_length</span>
<span class="bp">self</span><span class="o">.</span><span class="n">max_force</span> <span class="o">=</span> <span class="mi">50</span>
<div class="viewcode-block" id="HpsNonbonded.potential">
<a class="viewcode-back" href="../../api/polymer_modeling/hps_polymer_model.html#arbdmodel.hps_polymer_model.HpsNonbonded.potential">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">potential</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="n">types</span><span class="p">):</span>
<span class="w"> </span><span class="sd">""" Electrostatics """</span>
<span class="n">typeA</span><span class="p">,</span><span class="n">typeB</span> <span class="o">=</span> <span class="n">types</span>
<span class="n">ld</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">debye_length</span>
<span class="n">q1</span> <span class="o">=</span> <span class="n">typeA</span><span class="o">.</span><span class="n">charge</span>
<span class="n">q2</span> <span class="o">=</span> <span class="n">typeB</span><span class="o">.</span><span class="n">charge</span>
<span class="n">D</span> <span class="o">=</span> <span class="mi">80</span> <span class="c1"># dielectric of water</span>
<span class="c1">## units "e**2 / (4 * pi * epsilon0 AA)" kcal_mol</span>
<span class="n">A</span> <span class="o">=</span> <span class="mf">332.06371</span>
<span class="n">u_elec</span> <span class="o">=</span> <span class="p">(</span><span class="n">A</span><span class="o">*</span><span class="n">q1</span><span class="o">*</span><span class="n">q2</span><span class="o">/</span><span class="n">D</span><span class="p">)</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="n">r</span><span class="o">/</span><span class="n">ld</span><span class="p">)</span> <span class="o">/</span> <span class="n">r</span>
<span class="w"> </span>
<span class="w"> </span><span class="sd">""" Hydrophobicity scale model """</span>
<span class="n">lambda_</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">typeA</span><span class="o">.</span><span class="n">lambda_</span> <span class="o">+</span> <span class="n">typeB</span><span class="o">.</span><span class="n">lambda_</span><span class="p">)</span>
<span class="n">sigma</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">typeA</span><span class="o">.</span><span class="n">sigma</span> <span class="o">+</span> <span class="n">typeB</span><span class="o">.</span><span class="n">sigma</span><span class="p">)</span>
<span class="n">epsilon</span> <span class="o">=</span> <span class="mf">0.2</span>
<span class="n">r6</span> <span class="o">=</span> <span class="p">(</span><span class="n">sigma</span><span class="o">/</span><span class="n">r</span><span class="p">)</span><span class="o">**</span><span class="mi">6</span>
<span class="n">r12</span> <span class="o">=</span> <span class="n">r6</span><span class="o">**</span><span class="mi">2</span>
<span class="n">u_lj</span> <span class="o">=</span> <span class="mi">4</span> <span class="o">*</span> <span class="n">epsilon</span> <span class="o">*</span> <span class="p">(</span><span class="n">r12</span><span class="o">-</span><span class="n">r6</span><span class="p">)</span>
<span class="n">u_hps</span> <span class="o">=</span> <span class="n">lambda_</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">u_lj</span><span class="p">)</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">r</span><span class="o"><=</span><span class="n">sigma</span><span class="o">*</span><span class="mi">2</span><span class="o">**</span><span class="p">(</span><span class="mi">1</span><span class="o">/</span><span class="mi">6</span><span class="p">)</span>
<span class="n">u_hps</span><span class="p">[</span><span class="n">s</span><span class="p">]</span> <span class="o">=</span> <span class="n">u_lj</span><span class="p">[</span><span class="n">s</span><span class="p">]</span> <span class="o">+</span> <span class="p">(</span><span class="mi">1</span><span class="o">-</span><span class="n">lambda_</span><span class="p">)</span> <span class="o">*</span> <span class="n">epsilon</span>
<span class="n">u</span> <span class="o">=</span> <span class="n">u_elec</span> <span class="o">+</span> <span class="n">u_hps</span>
<span class="k">return</span> <span class="n">u</span></div>
</div>
<div class="viewcode-block" id="HpsBeads">
<a class="viewcode-back" href="../../api/polymer_modeling/hps_polymer_model.html#arbdmodel.hps_polymer_model.HpsBeads">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">HpsBeads</span><span class="p">(</span><span class="n">PolymerBeads</span><span class="p">):</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">polymer</span><span class="p">,</span> <span class="n">sequence</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">spring_constant</span> <span class="o">=</span> <span class="mf">2.3900574</span><span class="p">,</span>
<span class="n">rest_length</span> <span class="o">=</span> <span class="mf">3.8</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="k">if</span> <span class="n">sequence</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">NotImplementedError</span>
<span class="c1"># ... set random sequence</span>
<span class="bp">self</span><span class="o">.</span><span class="n">spring_constant</span> <span class="o">=</span> <span class="n">spring_constant</span> <span class="n">PolymerBeads</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">polymer</span><span class="p">,</span> <span class="n">sequence</span><span class="p">,</span> <span class="n">rest_length</span><span class="o">=</span><span class="n">rest_length</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
<span class="k">assert</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">monomers_per_bead_group</span> <span class="o">==</span> <span class="mi">1</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sequence</span><span class="p">)</span> <span class="o">!=</span> <span class="n">polymer</span><span class="o">.</span><span class="n">num_monomers</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Length of sequence does not match length of polymer"</span><span class="p">)</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_generate_ith_bead_group</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="n">o</span><span class="p">):</span>
<span class="n">s</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="k">return</span> <span class="n">PointParticle</span><span class="p">(</span><span class="n">_types</span><span class="p">[</span><span class="n">s</span><span class="p">],</span> <span class="n">r</span><span class="p">,</span>
<span class="n">name</span> <span class="o">=</span> <span class="n">s</span><span class="p">,</span>
<span class="n">resid</span> <span class="o">=</span> <span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_join_adjacent_bead_groups</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ids</span><span class="p">):</span>
<span class="c1">## Two consecutive nts </span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
<span class="n">b1</span><span class="p">,</span><span class="n">b2</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">ids</span><span class="p">]</span>
<span class="w"> </span><span class="sd">""" units "10 kJ/N_A" kcal_mol """</span>
<span class="n">bond</span> <span class="o">=</span> <span class="n">HarmonicBond</span><span class="p">(</span><span class="n">k</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">spring_constant</span><span class="p">,</span>
<span class="n">r0</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">rest_length</span><span class="p">,</span>
<span class="n">range_</span> <span class="o">=</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">500</span><span class="p">),</span>
<span class="n">resolution</span> <span class="o">=</span> <span class="mf">0.01</span><span class="p">,</span>
<span class="n">max_force</span> <span class="o">=</span> <span class="mi">10</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">add_bond</span><span class="p">(</span> <span class="n">i</span><span class="o">=</span><span class="n">b1</span><span class="p">,</span> <span class="n">j</span><span class="o">=</span><span class="n">b2</span><span class="p">,</span> <span class="n">bond</span> <span class="o">=</span> <span class="n">bond</span><span class="p">,</span> <span class="n">exclude</span><span class="o">=</span><span class="kc">True</span> <span class="p">)</span>
<span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span> <span class="o">==</span> <span class="mi">3</span><span class="p">:</span>
<span class="o">...</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">pass</span></div>
<div class="viewcode-block" id="HpsModel">
<a class="viewcode-back" href="../../api/polymer_modeling/hps_polymer_model.html#arbdmodel.hps_polymer_model.HpsModel">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">HpsModel</span><span class="p">(</span><span class="n">PolymerModel</span><span class="p">):</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">polymers</span><span class="p">,</span>
<span class="n">sequences</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="n">rest_length</span> <span class="o">=</span> <span class="mf">3.8</span><span class="p">,</span>
<span class="n">spring_constant</span> <span class="o">=</span> <span class="mf">2.3900574</span><span class="p">,</span>
<span class="n">debye_length</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span>
<span class="n">damping_coefficient</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span>
<span class="n">DEBUG</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
<span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="w"> </span><span class="sd">""" </span>
<span class="sd"> [debye_length]: angstroms</span>
<span class="sd"> [damping_coefficient]: 1/ns</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="s1">'timestep'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> <span class="n">kwargs</span><span class="p">[</span><span class="s1">'timestep'</span><span class="p">]</span> <span class="o">=</span> <span class="mf">10e-6</span>
<span class="k">if</span> <span class="s1">'cutoff'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> <span class="n">kwargs</span><span class="p">[</span><span class="s1">'cutoff'</span><span class="p">]</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="mi">4</span><span class="o">*</span><span class="n">debye_length</span><span class="p">,</span><span class="mi">20</span><span class="p">)</span>
<span class="k">if</span> <span class="s1">'decomp_period'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
<span class="n">kwargs</span><span class="p">[</span><span class="s1">'decomp_period'</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1000</span>
<span class="bp">self</span><span class="o">.</span><span class="n">rest_length</span> <span class="o">=</span> <span class="n">rest_length</span>
<span class="bp">self</span><span class="o">.</span><span class="n">spring_constant</span> <span class="o">=</span> <span class="n">spring_constant</span>
<span class="w"> </span><span class="sd">""" Assign sequences """</span>
<span class="k">if</span> <span class="n">sequences</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s2">"HpsModel must be provided a sequences argument"</span><span class="p">)</span>
<span class="n">PolymerModel</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">polymers</span><span class="p">,</span> <span class="n">sequences</span><span class="p">,</span> <span class="n">monomers_per_bead_group</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
<span class="w"> </span><span class="sd">""" Update type diffusion coefficients """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">types</span> <span class="o">=</span> <span class="n">all_types</span> <span class="o">=</span> <span class="p">[</span><span class="n">t</span> <span class="k">for</span> <span class="n">key</span><span class="p">,</span><span class="n">t</span> <span class="ow">in</span> <span class="n">_types</span><span class="o">.</span><span class="n">items</span><span class="p">()]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">set_damping_coefficient</span><span class="p">(</span> <span class="n">damping_coefficient</span> <span class="p">)</span>
<span class="w"> </span><span class="sd">""" Set up nonbonded interactions """</span>
<span class="n">nonbonded</span> <span class="o">=</span> <span class="n">HpsNonbonded</span><span class="p">(</span><span class="n">debye_length</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">types</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">all_types</span><span class="p">)):</span>
<span class="n">t1</span> <span class="o">=</span> <span class="n">all_types</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="nb">len</span><span class="p">(</span><span class="n">all_types</span><span class="p">)):</span>
<span class="n">t2</span> <span class="o">=</span> <span class="n">all_types</span><span class="p">[</span><span class="n">j</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">add_nonbonded_interaction</span><span class="p">(</span> <span class="n">nonbonded</span><span class="p">,</span> <span class="n">typeA</span><span class="o">=</span><span class="n">t1</span><span class="p">,</span> <span class="n">typeB</span><span class="o">=</span><span class="n">t2</span> <span class="p">)</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_generate_polymer_beads</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">polymer</span><span class="p">,</span> <span class="n">sequence</span><span class="p">,</span> <span class="n">polymer_index</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="k">return</span> <span class="n">HpsBeads</span><span class="p">(</span><span class="n">polymer</span><span class="p">,</span> <span class="n">sequence</span><span class="p">,</span>
<span class="n">rest_length</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">rest_length</span><span class="p">,</span>
<span class="n">spring_constant</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">spring_constant</span><span class="p">,</span>
<span class="n">monomers_per_bead_group</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">monomers_per_bead_group</span><span class="p">,</span>
<span class="n">polymer_index</span> <span class="o">=</span> <span class="n">polymer_index</span>
<span class="p">)</span>
<div class="viewcode-block" id="HpsModel.set_damping_coefficient">
<a class="viewcode-back" href="../../api/polymer_modeling/hps_polymer_model.html#arbdmodel.hps_polymer_model.HpsModel.set_damping_coefficient">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">set_damping_coefficient</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">damping_coefficient</span><span class="p">):</span>
<span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">types</span><span class="p">:</span>
<span class="n">t</span><span class="o">.</span><span class="n">damping_coefficient</span> <span class="o">=</span> <span class="n">damping_coefficient</span></div>
</div>
<span class="c1"># t.diffusivity = 831447.2 * temperature / (t.mass * damping_coefficient)</span>
<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"TYPES"</span><span class="p">)</span>
<span class="k">for</span> <span class="n">n</span><span class="p">,</span><span class="n">t</span> <span class="ow">in</span> <span class="n">_types</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"</span><span class="si">{}</span><span class="se">\t</span><span class="si">{}</span><span class="se">\t</span><span class="si">{}</span><span class="se">\t</span><span class="si">{}</span><span class="se">\t</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">t</span><span class="o">.</span><span class="n">mass</span><span class="p">,</span> <span class="n">t</span><span class="o">.</span><span class="n">charge</span><span class="p">,</span> <span class="n">t</span><span class="o">.</span><span class="n">sigma</span><span class="p">,</span> <span class="n">t</span><span class="o">.</span><span class="n">lambda_</span><span class="p">))</span>
</pre></div>
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