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<h1>Source code for MMTK.Deformation</h1><div class="highlight"><pre>
<span class="c"># Deformation energy module</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 energies in proteins</span>
<span class="sd">This module implements deformational energies for use in the analysis</span>
<span class="sd">of motions and conformational changes in macromolecules. A description</span>
<span class="sd">of the techniques can be found in the following articles:</span>
<span class="sd"> | K. Hinsen</span>
<span class="sd"> | Analysis of domain motions by approximate normal mode calculations</span>
<span class="sd"> | Proteins 33 (1998): 417-429</span>
<span class="sd"> | K. Hinsen, A. Thomas, M.J. Field</span>
<span class="sd"> | Analysis of domain motions in large proteins</span>
<span class="sd"> | Proteins 34 (1999): 369-382</span>
<span class="sd">"""</span>
<span class="n">__docformat__</span> <span class="o">=</span> <span class="s">'restructuredtext'</span>
<span class="k">try</span><span class="p">:</span>
<span class="kn">from</span> <span class="nn">MMTK_forcefield</span> <span class="kn">import</span> <span class="n">NonbondedList</span>
<span class="kn">from</span> <span class="nn">MMTK_deformation</span> <span class="kn">import</span> <span class="n">deformation</span><span class="p">,</span> <span class="n">reduceDeformation</span><span class="p">,</span> \
<span class="n">reduceFiniteDeformation</span>
<span class="k">except</span> <span class="ne">ImportError</span><span class="p">:</span>
<span class="k">pass</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="n">ParticleProperties</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"># Deformation energy evaluations</span>
<span class="c">#</span>
<span class="k">class</span> <span class="nc">DeformationEvaluationFunction</span><span class="p">(</span><span class="nb">object</span><span class="p">):</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">universe</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="n">form</span> <span class="o">=</span> <span class="s">'exponential'</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">universe</span> <span class="o">=</span> <span class="n">universe</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="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="bp">self</span><span class="o">.</span><span class="n">pairs</span> <span class="o">=</span> <span class="n">NonbondedList</span><span class="p">(</span><span class="n">nothing</span><span class="p">,</span> <span class="n">nothing</span><span class="p">,</span> <span class="n">nothing</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">cutoff</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">pairs</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">universe</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span><span class="o">.</span><span class="n">array</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">normalize</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">try</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">version</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">forms</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">form</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"unknown functional form"</span><span class="p">)</span>
<span class="n">forms</span> <span class="o">=</span> <span class="p">[</span><span class="s">'exponential'</span><span class="p">,</span> <span class="s">'calpha'</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">newConfiguration</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">pairs</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span><span class="o">.</span><span class="n">array</span><span class="p">)</span>
<div class="viewcode-block" id="DeformationFunction"><a class="viewcode-back" href="../../modules.html#MMTK.Deformation.DeformationFunction">[docs]</a><span class="k">class</span> <span class="nc">DeformationFunction</span><span class="p">(</span><span class="n">DeformationEvaluationFunction</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Infinite-displacement deformation function</span>
<span class="sd"> The default values are appropriate for a |C_alpha| model of a protein</span>
<span class="sd"> with the global scaling described in the reference cited above.</span>
<span class="sd"> A DeformationFunction object must be called with a single parameter,</span>
<span class="sd"> which is a ParticleVector object containing the infinitesimal displacements</span>
<span class="sd"> of the atoms for which the deformation is to be evaluated.</span>
<span class="sd"> The return value is a ParticleScalar object containing the</span>
<span class="sd"> deformation value for each atom.</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">universe</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="n">form</span> <span class="o">=</span> <span class="s">'exponential'</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param universe: the universe for which the deformation function</span>
<span class="sd"> is defined</span>
<span class="sd"> :type universe: :class:`~MMTK.Universe.Universe`</span>
<span class="sd"> :param fc_length: the range parameter r_0 in the pair interaction term</span>
<span class="sd"> :type fc_length: float</span>
<span class="sd"> :param cutoff: the cutoff used in the deformation calculation</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"> :param form: the functional form ('exponential' or 'calpha')</span>
<span class="sd"> :type form: str</span>
<span class="sd"> """</span>
<span class="n">DeformationEvaluationFunction</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="n">universe</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">form</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">):</span>
<span class="n">conf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="n">r</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="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="p">)</span>
<span class="n">l</span> <span class="o">=</span> <span class="n">deformation</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">vector</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">pairs</span><span class="p">,</span>
<span class="bp">None</span><span class="p">,</span> <span class="n">r</span><span class="o">.</span><span class="n">array</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">fc_length</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="bp">self</span><span class="o">.</span><span class="n">normalize</span><span class="p">,</span> <span class="mi">0</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="n">r</span>
</div>
<div class="viewcode-block" id="NormalizedDeformationFunction"><a class="viewcode-back" href="../../modules.html#MMTK.Deformation.NormalizedDeformationFunction">[docs]</a><span class="k">class</span> <span class="nc">NormalizedDeformationFunction</span><span class="p">(</span><span class="n">DeformationFunction</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Normalized infinite-displacement deformation function</span>
<span class="sd"> The default values are appropriate for a |C_alpha| model of a protein</span>
<span class="sd"> with the global scaling described in the reference cited above.</span>
<span class="sd"> The normalization is defined by equation 10 of reference 1 (see above).</span>
<span class="sd"> </span>
<span class="sd"> A NormalizedDeformationFunction object must be called with a single</span>
<span class="sd"> parameter, which is a ParticleVector object containing the infinitesimal</span>
<span class="sd"> displacements of the atoms for which the deformation is to be evaluated.</span>
<span class="sd"> The return value is a ParticleScalar object containing the</span>
<span class="sd"> deformation value for each atom.</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">universe</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="n">form</span> <span class="o">=</span> <span class="s">'exponential'</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param universe: the universe for which the deformation function</span>
<span class="sd"> is defined</span>
<span class="sd"> :type universe: :class:`~MMTK.Universe.Universe`</span>
<span class="sd"> :param fc_length: the range parameter r_0 in the pair interaction term</span>
<span class="sd"> :type fc_length: float</span>
<span class="sd"> :param cutoff: the cutoff used in the deformation calculation</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"> :param form: the functional form ('exponential' or 'calpha')</span>
<span class="sd"> :type form: str</span>
<span class="sd"> """</span>
<span class="n">DeformationFunction</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="n">universe</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">form</span><span class="p">)</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="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="nb">apply</span><span class="p">(</span><span class="n">DeformationFunction</span><span class="o">.</span><span class="n">__init__</span><span class="p">,</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="p">)</span> <span class="o">+</span> <span class="n">args</span><span class="p">,</span> <span class="n">kwargs</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">normalize</span> <span class="o">=</span> <span class="mi">1</span>
</div>
<div class="viewcode-block" id="FiniteDeformationFunction"><a class="viewcode-back" href="../../modules.html#MMTK.Deformation.FiniteDeformationFunction">[docs]</a><span class="k">class</span> <span class="nc">FiniteDeformationFunction</span><span class="p">(</span><span class="n">DeformationEvaluationFunction</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Finite-displacement deformation function</span>
<span class="sd"> The default values are appropriate for a |C_alpha| model of a protein</span>
<span class="sd"> with the global scaling described in the reference cited above.</span>
<span class="sd"> A FiniteDeformationFunction object must be called with a single parameter,</span>
<span class="sd"> which is a Configuration or a ParticleVector object containing the</span>
<span class="sd"> alternate configuration of the universe for which the deformation is to be</span>
<span class="sd"> evaluated. The return value is a ParticleScalar object containing the</span>
<span class="sd"> deformation value for each atom.</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">universe</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="n">form</span> <span class="o">=</span> <span class="s">'exponential'</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param universe: the universe for which the deformation function</span>
<span class="sd"> is defined</span>
<span class="sd"> :type universe: :class:`~MMTK.Universe.Universe`</span>
<span class="sd"> :param fc_length: the range parameter r_0 in the pair interaction term</span>
<span class="sd"> :type fc_length: float</span>
<span class="sd"> :param cutoff: the cutoff used in the deformation calculation</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"> :param form: the functional form ('exponential' or 'calpha')</span>
<span class="sd"> :type form: str</span>
<span class="sd"> """</span>
<span class="n">DeformationEvaluationFunction</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="n">universe</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">form</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">):</span>
<span class="n">conf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="n">vector</span> <span class="o">=</span> <span class="n">vector</span><span class="o">-</span><span class="n">conf</span>
<span class="n">r</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="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="p">)</span>
<span class="n">l</span> <span class="o">=</span> <span class="n">deformation</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">vector</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">pairs</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="n">r</span><span class="o">.</span><span class="n">array</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">fc_length</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="mi">0</span><span class="p">,</span> <span class="mi">1</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="n">r</span>
</div>
<div class="viewcode-block" id="DeformationEnergyFunction"><a class="viewcode-back" href="../../modules.html#MMTK.Deformation.DeformationEnergyFunction">[docs]</a><span class="k">class</span> <span class="nc">DeformationEnergyFunction</span><span class="p">(</span><span class="n">DeformationEvaluationFunction</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Infinite-displacement deformation energy function</span>
<span class="sd"> The deformation energy is the sum of the deformation values over</span>
<span class="sd"> all atoms of a system.</span>
<span class="sd"> The default values are appropriate for a |C_alpha| model of a protein</span>
<span class="sd"> with the global scaling described in the reference cited above.</span>
<span class="sd"> A DeformationEnergyFunction is called with one or two parameters.</span>
<span class="sd"> The first parameter is a ParticleVector object containing the</span>
<span class="sd"> infinitesimal displacements of the atoms for which the deformation</span>
<span class="sd"> energy is to be evaluated. The optional second argument can be</span>
<span class="sd"> set to a non-zero value to request the gradients of the energy</span>
<span class="sd"> in addition to the energy itself. In that case there are two</span>
<span class="sd"> return values (energy and the gradients in a ParticleVector</span>
<span class="sd"> object), otherwise only the energy is returned.</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">universe</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="n">form</span> <span class="o">=</span> <span class="s">'exponential'</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param universe: the universe for which the deformation function</span>
<span class="sd"> is defined</span>
<span class="sd"> :type universe: :class:`~MMTK.Universe.Universe`</span>
<span class="sd"> :param fc_length: the range parameter r_0 in the pair interaction term</span>
<span class="sd"> :type fc_length: float</span>
<span class="sd"> :param cutoff: the cutoff used in the deformation calculation</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"> :param form: the functional form ('exponential' or 'calpha')</span>
<span class="sd"> :type form: str</span>
<span class="sd"> """</span>
<span class="n">DeformationEvaluationFunction</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="n">universe</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">form</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">,</span> <span class="n">gradients</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="n">conf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="n">g</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">if</span> <span class="n">gradients</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">if</span> <span class="n">ParticleProperties</span><span class="o">.</span><span class="n">isParticleProperty</span><span class="p">(</span><span class="n">gradients</span><span class="p">):</span>
<span class="n">g</span> <span class="o">=</span> <span class="n">gradients</span>
<span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">gradients</span><span class="p">,</span> <span class="n">N</span><span class="o">.</span><span class="n">array_type</span><span class="p">):</span>
<span class="n">g</span> <span class="o">=</span> <span class="n">ParticleProperties</span><span class="o">.</span><span class="n">ParticleVector</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="p">,</span> <span class="n">gradients</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">gradients</span><span class="p">:</span>
<span class="n">g</span> <span class="o">=</span> <span class="n">ParticleProperties</span><span class="o">.</span><span class="n">ParticleVector</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="p">)</span>
<span class="k">if</span> <span class="n">g</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">g_array</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">g_array</span> <span class="o">=</span> <span class="n">g</span><span class="o">.</span><span class="n">array</span>
<span class="n">l</span> <span class="o">=</span> <span class="n">deformation</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">vector</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">pairs</span><span class="p">,</span>
<span class="n">g_array</span><span class="p">,</span> <span class="bp">None</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">fc_length</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="bp">self</span><span class="o">.</span><span class="n">normalize</span><span class="p">,</span> <span class="mi">0</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">if</span> <span class="n">g</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">l</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">l</span><span class="p">,</span> <span class="n">g</span>
</div>
<div class="viewcode-block" id="NormalizedDeformationEnergyFunction"><a class="viewcode-back" href="../../modules.html#MMTK.Deformation.NormalizedDeformationEnergyFunction">[docs]</a><span class="k">class</span> <span class="nc">NormalizedDeformationEnergyFunction</span><span class="p">(</span><span class="n">DeformationEnergyFunction</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Normalized infinite-displacement deformation energy function</span>
<span class="sd"> The normalized deformation energy is the sum of the normalized</span>
<span class="sd"> deformation values over all atoms of a system.</span>
<span class="sd"> The default values are appropriate for a |C_alpha| model of a protein</span>
<span class="sd"> with the global scaling described in the reference cited above.</span>
<span class="sd"> The normalization is defined by equation 10 of reference 1.</span>
<span class="sd"> A NormalizedDeformationEnergyFunction is called with one or two parameters.</span>
<span class="sd"> The first parameter is a ParticleVector object containing the</span>
<span class="sd"> infinitesimal displacements of the atoms for which the deformation</span>
<span class="sd"> energy is to be evaluated. The optional second argument can be</span>
<span class="sd"> set to a non-zero value to request the gradients of the energy</span>
<span class="sd"> in addition to the energy itself. In that case there are two</span>
<span class="sd"> return values (energy and the gradients in a ParticleVector</span>
<span class="sd"> object), otherwise only the energy is returned.</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">universe</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="n">form</span> <span class="o">=</span> <span class="s">'exponential'</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param universe: the universe for which the deformation function</span>
<span class="sd"> is defined</span>
<span class="sd"> :type universe: :class:`~MMTK.Universe.Universe`</span>
<span class="sd"> :param fc_length: the range parameter r_0 in the pair interaction term</span>
<span class="sd"> :type fc_length: float</span>
<span class="sd"> :param cutoff: the cutoff used in the deformation calculation</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"> :param form: the functional form ('exponential' or 'calpha')</span>
<span class="sd"> :type form: str</span>
<span class="sd"> """</span>
<span class="n">DeformationEnergyFunction</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="n">universe</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">form</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">normalize</span> <span class="o">=</span> <span class="mi">1</span>
</div>
<div class="viewcode-block" id="FiniteDeformationEnergyFunction"><a class="viewcode-back" href="../../modules.html#MMTK.Deformation.FiniteDeformationEnergyFunction">[docs]</a><span class="k">class</span> <span class="nc">FiniteDeformationEnergyFunction</span><span class="p">(</span><span class="n">DeformationEvaluationFunction</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Finite-displacement deformation energy function</span>
<span class="sd"> The deformation energy is the sum of the</span>
<span class="sd"> deformation values over all atoms of a system.</span>
<span class="sd"> The default values are appropriate for a |C_alpha| model of a protein</span>
<span class="sd"> with the global scaling described in the reference cited above.</span>
<span class="sd"> A FiniteDeformationEnergyFunction is called with one or two parameters.</span>
<span class="sd"> The first parameter is a ParticleVector object containing the</span>
<span class="sd"> alternate configuration of the universe for which the deformation</span>
<span class="sd"> energy is to be evaluated. The optional second argument can be</span>
<span class="sd"> set to a non-zero value to request the gradients of the energy</span>
<span class="sd"> in addition to the energy itself. In that case there are two</span>
<span class="sd"> return values (energy and the gradients in a ParticleVector</span>
<span class="sd"> object), otherwise only the energy is returned.</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">universe</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="n">form</span> <span class="o">=</span> <span class="s">'exponential'</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param universe: the universe for which the deformation function</span>
<span class="sd"> is defined</span>
<span class="sd"> :type universe: :class:`~MMTK.Universe.Universe`</span>
<span class="sd"> :param fc_length: the range parameter r_0 in the pair interaction term</span>
<span class="sd"> :type fc_length: float</span>
<span class="sd"> :param cutoff: the cutoff used in the deformation calculation</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"> :param form: the functional form ('exponential' or 'calpha')</span>
<span class="sd"> :type form: str</span>
<span class="sd"> """</span>
<span class="n">DeformationEvaluationFunction</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="n">universe</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">form</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">,</span> <span class="n">gradients</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="n">conf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="n">g</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">if</span> <span class="n">gradients</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">if</span> <span class="n">ParticleProperties</span><span class="o">.</span><span class="n">isParticleProperty</span><span class="p">(</span><span class="n">gradients</span><span class="p">):</span>
<span class="n">g</span> <span class="o">=</span> <span class="n">gradients</span>
<span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">gradients</span><span class="p">,</span> <span class="n">N</span><span class="o">.</span><span class="n">array_type</span><span class="p">):</span>
<span class="n">g</span> <span class="o">=</span> <span class="n">ParticleProperties</span><span class="o">.</span><span class="n">ParticleVector</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="p">,</span> <span class="n">gradients</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">gradients</span><span class="p">:</span>
<span class="n">g</span> <span class="o">=</span> <span class="n">ParticleProperties</span><span class="o">.</span><span class="n">ParticleVector</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="p">)</span>
<span class="k">if</span> <span class="n">g</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">g_array</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">g_array</span> <span class="o">=</span> <span class="n">g</span><span class="o">.</span><span class="n">array</span>
<span class="n">l</span> <span class="o">=</span> <span class="n">deformation</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">vector</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">pairs</span><span class="p">,</span> <span class="n">g_array</span><span class="p">,</span> <span class="bp">None</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">fc_length</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="mi">0</span><span class="p">,</span> <span class="mi">1</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">if</span> <span class="n">g</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">l</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">l</span><span class="p">,</span> <span class="n">g</span>
<span class="c">#</span>
<span class="c"># Deformation energy minimization</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="DeformationReducer"><a class="viewcode-back" href="../../modules.html#MMTK.Deformation.DeformationReducer">[docs]</a><span class="k">class</span> <span class="nc">DeformationReducer</span><span class="p">(</span><span class="n">DeformationEvaluationFunction</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Iterative reduction of the deformation energy</span>
<span class="sd"> The default values are appropriate for a |C_alpha| model of a protein</span>
<span class="sd"> with the global scaling described in the reference cited above.</span>
<span class="sd"> A DeformationReducer is called with two arguments. The first</span>
<span class="sd"> is a ParticleVector containing the initial infinitesimal displacements</span>
<span class="sd"> for all atoms. The second is an integer indicating the number of</span>
<span class="sd"> iterations. The result is a modification of the displacements</span>
<span class="sd"> by steepest-descent minimization of the deformation energy.</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">universe</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="n">form</span> <span class="o">=</span> <span class="s">'exponential'</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param universe: the universe for which the deformation function</span>
<span class="sd"> is defined</span>
<span class="sd"> :type universe: :class:`~MMTK.Universe.Universe`</span>
<span class="sd"> :param fc_length: the range parameter r_0 in the pair interaction term</span>
<span class="sd"> :type fc_length: float</span>
<span class="sd"> :param cutoff: the cutoff used in the deformation calculation</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"> :param form: the functional form ('exponential' or 'calpha')</span>
<span class="sd"> :type form: str</span>
<span class="sd"> """</span>
<span class="n">DeformationEvaluationFunction</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="n">universe</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">form</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">,</span> <span class="n">niter</span><span class="p">):</span>
<span class="n">conf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="n">reduceDeformation</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">vector</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">pairs</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">fc_length</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="n">niter</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">version</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="FiniteDeformationReducer"><a class="viewcode-back" href="../../modules.html#MMTK.Deformation.FiniteDeformationReducer">[docs]</a><span class="k">class</span> <span class="nc">FiniteDeformationReducer</span><span class="p">(</span><span class="n">DeformationEvaluationFunction</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Iterative reduction of the finite-displacement deformation energy</span>
<span class="sd"> The default values are appropriate for a |C_alpha| model of a protein</span>
<span class="sd"> with the global scaling described in the reference cited above.</span>
<span class="sd"> A FiniteDeformationReducer is called with two arguments. The first</span>
<span class="sd"> is a ParticleVector or Configuration containing the alternate</span>
<span class="sd"> configuration for which the deformation energy is evaluated.</span>
<span class="sd"> The second is the RMS distance that defines the termination</span>
<span class="sd"> condition. The return value a configuration that differs from</span>
<span class="sd"> the input configuration by approximately the specified RMS distance,</span>
<span class="sd"> and which is obtained by iterative steepest-descent minimization of</span>
<span class="sd"> the finite-displacement deformation energy.</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">universe</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="n">form</span> <span class="o">=</span> <span class="s">'exponential'</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param universe: the universe for which the deformation function</span>
<span class="sd"> is defined</span>
<span class="sd"> :type universe: :class:`~MMTK.Universe.Universe`</span>
<span class="sd"> :param fc_length: the range parameter r_0 in the pair interaction term</span>
<span class="sd"> :type fc_length: float</span>
<span class="sd"> :param cutoff: the cutoff used in the deformation calculation</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"> :param form: the functional form ('exponential' or 'calpha')</span>
<span class="sd"> :type form: str</span>
<span class="sd"> """</span>
<span class="n">DeformationEvaluationFunction</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="n">universe</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">form</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">,</span> <span class="n">rms_reduction</span><span class="p">):</span>
<span class="n">conf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="n">vector</span> <span class="o">=</span> <span class="n">vector</span><span class="o">-</span><span class="n">conf</span>
<span class="n">reduceFiniteDeformation</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">vector</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">pairs</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">fc_length</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="n">rms_reduction</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="n">conf</span><span class="o">+</span><span class="n">vector</span></div>
</pre></div>
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