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<h1>Source code for MMTK.ForceFields.Restraints</h1><div class="highlight"><pre>
<span class="c"># Harmonic restraint terms that can be added to a 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">Harmonic restraint terms that can be added to any force field</span>
<span class="sd">Example::</span>
<span class="sd"> from MMTK import *</span>
<span class="sd"> from MMTK.ForceFields import Amber99ForceField</span>
<span class="sd"> from MMTK.ForceFields.Restraints import HarmonicDistanceRestraint</span>
<span class="sd"> </span>
<span class="sd"> universe = InfiniteUniverse()</span>
<span class="sd"> universe.protein = Protein('bala1')</span>
<span class="sd"> force_field = Amber99ForceField() + \</span>
<span class="sd"> HarmonicDistanceRestraint(universe.protein[0][1].peptide.N,</span>
<span class="sd"> universe.protein[0][1].peptide.O,</span>
<span class="sd"> 0.5, 10.)</span>
<span class="sd"> universe.setForceField(force_field)</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.ChemicalObjects</span> <span class="kn">import</span> <span class="n">isChemicalObject</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="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">HarmonicDistanceTerm</span><span class="p">,</span> <span class="n">HarmonicAngleTerm</span><span class="p">,</span> \
<span class="n">CosineDihedralTerm</span>
<span class="kn">from</span> <span class="nn">MMTK_restraints</span> <span class="kn">import</span> <span class="n">HarmonicCMTrapTerm</span><span class="p">,</span> <span class="n">HarmonicCMDistanceTerm</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="HarmonicDistanceRestraint"><a class="viewcode-back" href="../../../modules.html#MMTK.ForceFields.Restraints.HarmonicDistanceRestraint">[docs]</a><span class="k">class</span> <span class="nc">HarmonicDistanceRestraint</span><span class="p">(</span><span class="n">ForceField</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Harmonic distance restraint between two atoms</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">obj1</span><span class="p">,</span> <span class="n">obj2</span><span class="p">,</span> <span class="n">distance</span><span class="p">,</span> <span class="n">force_constant</span><span class="p">,</span>
<span class="n">nb_exclusion</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param obj1: the object defining center-of-mass 1</span>
<span class="sd"> :type obj1: :class:`~MMTK.Collections.GroupOfAtoms`</span>
<span class="sd"> :param obj2: the object defining center-of-mass 2</span>
<span class="sd"> :type obj2: :class:`~MMTK.Collections.GroupOfAtoms`</span>
<span class="sd"> :param distance: the distance between cm 1 and cm2 at which</span>
<span class="sd"> the restraint is zero</span>
<span class="sd"> :type distance: float</span>
<span class="sd"> :param force_constant: the force constant of the restraint term.</span>
<span class="sd"> The functional form of the restraint is</span>
<span class="sd"> force_constant*((cm1-cm2).length()-distance)**2,</span>
<span class="sd"> where cm1 and cm2 are the centrer-of-mass</span>
<span class="sd"> positions of the two objects.</span>
<span class="sd"> :type force_constant: float</span>
<span class="sd"> :param nb_exclussion: if True, non-bonded interactions between</span>
<span class="sd"> the restrained atoms are suppressed, as</span>
<span class="sd"> for a chemical bond</span>
<span class="sd"> :type nb_exclussion: bool</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">obj1</span><span class="p">,</span> <span class="nb">int</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">obj2</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
<span class="c"># Older MMTK versions admitted only single atoms and</span>
<span class="c"># stored single indices. Support this mode for opening</span>
<span class="c"># trajectories made with those versions</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_1</span> <span class="o">=</span> <span class="p">[</span><span class="n">obj1</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_2</span> <span class="o">=</span> <span class="p">[</span><span class="n">obj2</span><span class="p">]</span>
<span class="k">if</span> <span class="n">isChemicalObject</span><span class="p">(</span><span class="n">obj1</span><span class="p">):</span>
<span class="n">obj1</span> <span class="o">=</span> <span class="n">obj1</span><span class="o">.</span><span class="n">atomList</span><span class="p">()</span>
<span class="k">if</span> <span class="n">isChemicalObject</span><span class="p">(</span><span class="n">obj2</span><span class="p">):</span>
<span class="n">obj2</span> <span class="o">=</span> <span class="n">obj2</span><span class="o">.</span><span class="n">atomList</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_1</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">getAtomParameterIndices</span><span class="p">(</span><span class="n">obj1</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">getAtomParameterIndices</span><span class="p">(</span><span class="n">obj2</span><span class="p">)</span>
<span class="k">if</span> <span class="n">nb_exclusion</span> <span class="ow">and</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_1</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span>
<span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_2</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"Non-bonded exclusion possible only "</span>
<span class="s">"between single-atom objects"</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="bp">self</span><span class="o">.</span><span class="n">atom_indices_1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_2</span><span class="p">,</span>
<span class="n">distance</span><span class="p">,</span> <span class="n">force_constant</span><span class="p">,</span> <span class="n">nb_exclusion</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">distance</span> <span class="o">=</span> <span class="n">distance</span>
<span class="bp">self</span><span class="o">.</span><span class="n">force_constant</span> <span class="o">=</span> <span class="n">force_constant</span>
<span class="bp">self</span><span class="o">.</span><span class="n">nb_exclusion</span> <span class="o">=</span> <span class="n">nb_exclusion</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">'harmonic distance restraint'</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">declareDependencies</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="n">global_data</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s">'nb_exclusions'</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">evaluatorParameters</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="k">if</span> <span class="n">universe</span><span class="o">.</span><span class="n">is_periodic</span> <span class="ow">and</span> \
<span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_1</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_1</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"Center-of-mass restraints not implemented"</span>
<span class="s">" for periodic universes"</span><span class="p">)</span>
<span class="n">ok</span> <span class="o">=</span> <span class="bp">False</span>
<span class="k">for</span> <span class="n">s1</span><span class="p">,</span> <span class="n">s2</span> <span class="ow">in</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="p">(</span><span class="n">subset2</span><span class="p">,</span> <span class="n">subset1</span><span class="p">)]:</span>
<span class="k">if</span> <span class="n">s1</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">s1</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">ok</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">break</span>
<span class="n">s1</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">s1</span><span class="o">.</span><span class="n">atomIterator</span><span class="p">())</span>
<span class="n">diff1</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_1</span><span class="p">)</span><span class="o">.</span><span class="n">difference</span><span class="p">(</span><span class="n">s1</span><span class="p">)</span>
<span class="n">s2</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">s2</span><span class="o">.</span><span class="n">atomIterator</span><span class="p">())</span>
<span class="n">diff2</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_2</span><span class="p">)</span><span class="o">.</span><span class="n">difference</span><span class="p">(</span><span class="n">s2</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">diff1</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">diff2</span><span class="p">:</span>
<span class="c"># Each object is in one of the subsets</span>
<span class="n">ok</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">break</span>
<span class="k">if</span> <span class="p">(</span><span class="n">diff1</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">diff1</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_1</span><span class="p">))</span> \
<span class="ow">or</span> <span class="p">(</span><span class="n">diff2</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">diff2</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_2</span><span class="p">)):</span>
<span class="c"># The subset contains some but not all of the</span>
<span class="c"># restrained atoms.</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"Restrained atoms partially "</span>
<span class="s">"in a subset"</span><span class="p">)</span>
<span class="n">global_data</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s">'initialized'</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">ok</span><span class="p">:</span>
<span class="c"># The objects are not in the subsets, so there is no</span>
<span class="c"># contribution to the total energy.</span>
<span class="k">return</span> <span class="p">{</span><span class="s">'harmonic_distance_cm'</span><span class="p">:</span> <span class="p">[]}</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">nb_exclusion</span><span class="p">:</span>
<span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_1</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span>
<span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_2</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span>
<span class="n">i1</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_1</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">i2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_2</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">global_data</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s">'excluded_pairs'</span><span class="p">,</span> <span class="n">Utility</span><span class="o">.</span><span class="n">normalizePair</span><span class="p">((</span><span class="n">i1</span><span class="p">,</span> <span class="n">i2</span><span class="p">)))</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_1</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_2</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="c"># Keep the old format for the single-atom case for best</span>
<span class="c"># compatibility with older MMTK versions.</span>
<span class="k">return</span> <span class="p">{</span><span class="s">'harmonic_distance_term'</span><span class="p">:</span>
<span class="p">[(</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_1</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">atom_indices_2</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">distance</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">force_constant</span><span class="p">)]}</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="p">{</span><span class="s">'harmonic_distance_cm'</span><span class="p">:</span>
<span class="p">[(</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">atom_indices_2</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">distance</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">force_constant</span><span class="p">)]}</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">params</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">evaluatorParameters</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="k">if</span> <span class="n">params</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'harmonic_distance_term'</span><span class="p">):</span>
<span class="n">params</span> <span class="o">=</span> <span class="n">params</span><span class="p">[</span><span class="s">'harmonic_distance_term'</span><span class="p">]</span>
<span class="k">return</span> <span class="p">[</span><span class="n">HarmonicDistanceTerm</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">N</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">p</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">array</span><span class="p">([</span><span class="n">p</span><span class="p">[</span><span class="mi">2</span><span class="p">:]]),</span>
<span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
<span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">params</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">params</span> <span class="o">=</span> <span class="n">params</span><span class="p">[</span><span class="s">'harmonic_distance_cm'</span><span class="p">]</span>
<span class="k">return</span> <span class="p">[</span><span class="n">HarmonicCMDistanceTerm</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span>
<span class="n">N</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">p</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span>
<span class="n">N</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">p</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span>
<span class="n">universe</span><span class="o">.</span><span class="n">masses</span><span class="p">()</span><span class="o">.</span><span class="n">array</span><span class="p">,</span>
<span class="n">p</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span>
<span class="n">p</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span>
<span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">params</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">description</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="s">'ForceFields.Restraints.'</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">+</span> \
<span class="sb">`self.arguments`</span>
</div>
<div class="viewcode-block" id="HarmonicAngleRestraint"><a class="viewcode-back" href="../../../modules.html#MMTK.ForceFields.Restraints.HarmonicAngleRestraint">[docs]</a><span class="k">class</span> <span class="nc">HarmonicAngleRestraint</span><span class="p">(</span><span class="n">ForceField</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Harmonic angle restraint between three atoms</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">atom1</span><span class="p">,</span> <span class="n">atom2</span><span class="p">,</span> <span class="n">atom3</span><span class="p">,</span> <span class="n">angle</span><span class="p">,</span> <span class="n">force_constant</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param atom1: first atom</span>
<span class="sd"> :type atom1: :class:`~MMTK.ChemicalObjects.Atom`</span>
<span class="sd"> :param atom2: second (central) atom</span>
<span class="sd"> :type atom2: :class:`~MMTK.ChemicalObjects.Atom`</span>
<span class="sd"> :param atom3: third atom</span>
<span class="sd"> :type atom3: :class:`~MMTK.ChemicalObjects.Atom`</span>
<span class="sd"> :param angle: the angle at which the restraint is zero</span>
<span class="sd"> :type angle: float</span>
<span class="sd"> :param force_constant: the force constant of the restraint term.</span>
<span class="sd"> The functional form of the restraint is</span>
<span class="sd"> force_constant*(phi-angle)**2, where</span>
<span class="sd"> phi is the angle atom1-atom2-atom3.</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">index1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">index2</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">index3</span> <span class="o">=</span> \
<span class="bp">self</span><span class="o">.</span><span class="n">getAtomParameterIndices</span><span class="p">((</span><span class="n">atom1</span><span class="p">,</span> <span class="n">atom2</span><span class="p">,</span> <span class="n">atom3</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="bp">self</span><span class="o">.</span><span class="n">index1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">index2</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">index3</span><span class="p">,</span>
<span class="n">angle</span><span class="p">,</span> <span class="n">force_constant</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">angle</span> <span class="o">=</span> <span class="n">angle</span>
<span class="bp">self</span><span class="o">.</span><span class="n">force_constant</span> <span class="o">=</span> <span class="n">force_constant</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">'harmonic angle restraint'</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">evaluatorParameters</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="k">return</span> <span class="p">{</span><span class="s">'harmonic_angle_term'</span><span class="p">:</span>
<span class="p">[(</span><span class="bp">self</span><span class="o">.</span><span class="n">index1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">index2</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">index3</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">angle</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">force_constant</span><span class="p">)]}</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">params</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">evaluatorParameters</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="s">'harmonic_angle_term'</span><span class="p">]</span>
<span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="n">params</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span>
<span class="n">indices</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">params</span><span class="p">[</span><span class="mi">0</span><span class="p">][:</span><span class="mi">3</span><span class="p">]])</span>
<span class="n">parameters</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">params</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">3</span><span class="p">:]])</span>
<span class="k">return</span> <span class="p">[</span><span class="n">HarmonicAngleTerm</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">indices</span><span class="p">,</span> <span class="n">parameters</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)]</span>
</div>
<div class="viewcode-block" id="HarmonicDihedralRestraint"><a class="viewcode-back" href="../../../modules.html#MMTK.ForceFields.Restraints.HarmonicDihedralRestraint">[docs]</a><span class="k">class</span> <span class="nc">HarmonicDihedralRestraint</span><span class="p">(</span><span class="n">ForceField</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Harmonic dihedral angle restraint between four atoms</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">atom1</span><span class="p">,</span> <span class="n">atom2</span><span class="p">,</span> <span class="n">atom3</span><span class="p">,</span> <span class="n">atom4</span><span class="p">,</span> <span class="n">dihedral</span><span class="p">,</span> <span class="n">force_constant</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param atom1: first atom</span>
<span class="sd"> :type atom1: :class:`~MMTK.ChemicalObjects.Atom`</span>
<span class="sd"> :param atom2: second (axis) atom</span>
<span class="sd"> :type atom2: :class:`~MMTK.ChemicalObjects.Atom`</span>
<span class="sd"> :param atom3: third (axis)atom</span>
<span class="sd"> :type atom3: :class:`~MMTK.ChemicalObjects.Atom`</span>
<span class="sd"> :param atom4: fourth atom</span>
<span class="sd"> :type atom4: :class:`~MMTK.ChemicalObjects.Atom`</span>
<span class="sd"> :param dihedral: the dihedral angle at which the restraint is zero</span>
<span class="sd"> :type dihedral: float</span>
<span class="sd"> :param force_constant: the force constant of the restraint term.</span>
<span class="sd"> The functional form of the restraint is</span>
<span class="sd"> force_constant*(phi-abs(dihedral))**2, where</span>
<span class="sd"> phi is the dihedral angle</span>
<span class="sd"> atom1-atom2-atom3-atom4.</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">index1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">index2</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">index3</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">index4</span> <span class="o">=</span> \
<span class="bp">self</span><span class="o">.</span><span class="n">getAtomParameterIndices</span><span class="p">((</span><span class="n">atom1</span><span class="p">,</span> <span class="n">atom2</span><span class="p">,</span> <span class="n">atom3</span><span class="p">,</span> <span class="n">atom4</span><span class="p">))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">dihedral</span> <span class="o">=</span> <span class="n">dihedral</span>
<span class="bp">self</span><span class="o">.</span><span class="n">force_constant</span> <span class="o">=</span> <span class="n">force_constant</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="bp">self</span><span class="o">.</span><span class="n">index1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">index2</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">index3</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">index4</span><span class="p">,</span>
<span class="n">dihedral</span><span class="p">,</span> <span class="n">force_constant</span><span class="p">)</span>
<span class="n">ForceField</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">'harmonic dihedral restraint'</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">evaluatorParameters</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="k">return</span> <span class="p">{</span><span class="s">'cosine_dihedral_term'</span><span class="p">:</span> <span class="p">[(</span><span class="bp">self</span><span class="o">.</span><span class="n">index1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">index2</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">index3</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">index4</span><span class="p">,</span>
<span class="mf">0.</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dihedral</span><span class="p">,</span>
<span class="mf">0.</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">force_constant</span><span class="p">)]}</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">params</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">evaluatorParameters</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="s">'cosine_dihedral_term'</span><span class="p">]</span>
<span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="n">params</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span>
<span class="n">indices</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">params</span><span class="p">[</span><span class="mi">0</span><span class="p">][:</span><span class="mi">4</span><span class="p">]])</span>
<span class="n">parameters</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">params</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">4</span><span class="p">:]])</span>
<span class="k">return</span> <span class="p">[</span><span class="n">CosineDihedralTerm</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">indices</span><span class="p">,</span> <span class="n">parameters</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)]</span>
</div>
<div class="viewcode-block" id="HarmonicTrapForceField"><a class="viewcode-back" href="../../../modules.html#MMTK.ForceFields.Restraints.HarmonicTrapForceField">[docs]</a><span class="k">class</span> <span class="nc">HarmonicTrapForceField</span><span class="p">(</span><span class="n">ForceField</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Harmonic potential with respect to a fixed point in space</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">obj</span><span class="p">,</span> <span class="n">center</span><span class="p">,</span> <span class="n">force_constant</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param obj: the object on whose center of mass the force field acts</span>
<span class="sd"> :type obj: :class:`~MMTK.Collections.GroupOfAtoms`</span>
<span class="sd"> :param center: the point to which the atom is attached by</span>
<span class="sd"> the harmonic potential</span>
<span class="sd"> :type center: Scientific.Geometry.Vector</span>
<span class="sd"> :param force_constant: the force constant of the harmonic potential</span>
<span class="sd"> :type force_constant: float</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="n">isChemicalObject</span><span class="p">(</span><span class="n">obj</span><span class="p">):</span>
<span class="n">obj</span> <span class="o">=</span> <span class="n">obj</span><span class="o">.</span><span class="n">atomList</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atom_indices</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">getAtomParameterIndices</span><span class="p">(</span><span class="n">obj</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="bp">self</span><span class="o">.</span><span class="n">atom_indices</span><span class="p">,</span> <span class="n">center</span><span class="p">,</span> <span class="n">force_constant</span><span class="p">)</span>
<span class="n">ForceField</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">'harmonic_trap'</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">center</span> <span class="o">=</span> <span class="n">center</span>
<span class="bp">self</span><span class="o">.</span><span class="n">force_constant</span> <span class="o">=</span> <span class="n">force_constant</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">evaluatorParameters</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="k">if</span> <span class="n">universe</span><span class="o">.</span><span class="n">is_periodic</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_indices</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"Center-of-mass restraints not implemented"</span>
<span class="s">" for periodic universes"</span><span class="p">)</span>
<span class="k">for</span> <span class="n">subset</span> <span class="ow">in</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="k">if</span> <span class="n">subset</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">subset</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">subset</span><span class="o">.</span><span class="n">atomIterator</span><span class="p">())</span>
<span class="n">diff</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_indices</span><span class="p">)</span><span class="o">.</span><span class="n">difference</span><span class="p">(</span><span class="n">subset</span><span class="p">)</span>
<span class="k">if</span> <span class="n">diff</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">diff</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_indices</span><span class="p">):</span>
<span class="c"># The subset doesn't contain the restrained atoms.</span>
<span class="k">return</span> <span class="p">{</span><span class="s">'harmonic_trap_cm'</span><span class="p">:</span> <span class="p">[]}</span>
<span class="k">else</span><span class="p">:</span>
<span class="c"># The subset contains some but not all of the</span>
<span class="c"># restrained atoms.</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"Restrained atoms partially "</span>
<span class="s">"in a subset"</span><span class="p">)</span>
<span class="k">return</span> <span class="p">{</span><span class="s">'harmonic_trap_cm'</span><span class="p">:</span>
<span class="p">[(</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_indices</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">center</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">force_constant</span><span class="p">)]}</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">params</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">evaluatorParameters</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="s">'harmonic_trap_cm'</span><span class="p">]</span>
<span class="k">return</span> <span class="p">[</span><span class="n">HarmonicCMTrapTerm</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span>
<span class="n">N</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">p</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span>
<span class="n">universe</span><span class="o">.</span><span class="n">masses</span><span class="p">()</span><span class="o">.</span><span class="n">array</span><span class="p">,</span>
<span class="n">p</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
<span class="n">p</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
<span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">params</span><span class="p">]</span></div>
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