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<h1>Source code for MMTK.MolecularSurface</h1><div class="highlight"><pre>
<span class="c">#</span>
<span class="c"># Copyright 2000 by Peter McCluskey (pcm@rahul.net).</span>
<span class="c"># You may do anything you want with it, provided this notice is kept intact.</span>
<span class="c">#</span>
<span class="c"># This module is in part a replacement for the MolecularSurface MMTK module</span>
<span class="c"># that uses the NSC code. It has a less restrictive license than the NSC code,</span>
<span class="c"># and is mostly more flexible, but is probably slower and somewhat less</span>
<span class="c"># accurate. It can run (slowly) without any of the C code. It has an</span>
<span class="c"># additional routine surfacePointsAndGradients, which returns area, an</span>
<span class="c"># "up" vector, and surface points for each atom.</span>
<span class="c"># Modifications by Konrad Hinsen <hinsen@cnrs-orleans.fr>:</span>
<span class="c"># - Replaced tabs by spaces</span>
<span class="c"># - Added/adapted docstrings to MMTK conventions</span>
<span class="c"># - Removed assignment of methods to class GroupOfAtoms</span>
<span class="c"># - Use vectors in the return value of surfacePointsAndGradients</span>
<span class="c"># - Replaced "math" module by "Numeric"</span>
<span class="c"># - Renamed module _surface to MMTK_surface</span>
<span class="c"># - Converted docstrings to epydoc</span>
<span class="c"># - Changed first argument name from self to object</span>
<span class="sd">"""</span>
<span class="sd">Molecular surfaces and volumes.</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</span> <span class="kn">import</span> <span class="n">surfm</span>
<span class="kn">from</span> <span class="nn">MMTK.Collections</span> <span class="kn">import</span> <span class="n">Collection</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="n">Vector</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="surfaceAndVolume"><a class="viewcode-back" href="../../modules.html#MMTK.MolecularSurface.surfaceAndVolume">[docs]</a><span class="k">def</span> <span class="nf">surfaceAndVolume</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">probe_radius</span> <span class="o">=</span> <span class="mf">0.</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param object: a chemical object</span>
<span class="sd"> :type object: :class:`~MMTK.Collections.GroupOfAtoms`</span>
<span class="sd"> :param probe_radius: the distance from the vdW-radii of the atoms</span>
<span class="sd"> at which the surface is computed</span>
<span class="sd"> :type probe_radius: float</span>
<span class="sd"> :returns: the molecular surface and volume of object</span>
<span class="sd"> :rtype: tuple</span>
<span class="sd"> """</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">atomList</span><span class="p">()</span>
<span class="n">smap</span> <span class="o">=</span> <span class="n">surfm</span><span class="o">.</span><span class="n">surface_atoms</span><span class="p">(</span><span class="n">atoms</span><span class="p">,</span> <span class="n">probe_radius</span><span class="p">,</span> <span class="n">ret_fmt</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span>
<span class="n">tot_a</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">tot_v</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">:</span>
<span class="n">atom_data</span> <span class="o">=</span> <span class="n">smap</span><span class="p">[</span><span class="n">a</span><span class="p">]</span>
<span class="n">tot_a</span> <span class="o">=</span> <span class="n">tot_a</span> <span class="o">+</span> <span class="n">atom_data</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">tot_v</span> <span class="o">=</span> <span class="n">tot_v</span> <span class="o">+</span> <span class="n">atom_data</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="k">return</span> <span class="p">(</span><span class="n">tot_a</span><span class="p">,</span> <span class="n">tot_v</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="surfaceAtoms"><a class="viewcode-back" href="../../modules.html#MMTK.MolecularSurface.surfaceAtoms">[docs]</a><span class="k">def</span> <span class="nf">surfaceAtoms</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">probe_radius</span> <span class="o">=</span> <span class="mf">0.</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param object: a chemical object</span>
<span class="sd"> :type object: :class:`~MMTK.Collections.GroupOfAtoms`</span>
<span class="sd"> :param probe_radius: the distance from the vdW-radii of the atoms</span>
<span class="sd"> at which the surface is computed</span>
<span class="sd"> :type probe_radius: float</span>
<span class="sd"> :returns: a dictionary that maps the surface atoms to their</span>
<span class="sd"> exposed surface areas</span>
<span class="sd"> :rtype: dict</span>
<span class="sd"> """</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">atomList</span><span class="p">()</span>
<span class="n">smap</span> <span class="o">=</span> <span class="n">surfm</span><span class="o">.</span><span class="n">surface_atoms</span><span class="p">(</span><span class="n">atoms</span><span class="p">,</span> <span class="n">probe_radius</span><span class="p">,</span> <span class="n">ret_fmt</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
<span class="n">surface_atoms</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">:</span>
<span class="n">area</span> <span class="o">=</span> <span class="n">smap</span><span class="p">[</span><span class="n">a</span><span class="p">]</span>
<span class="k">if</span> <span class="n">area</span> <span class="o">></span> <span class="mf">0.</span><span class="p">:</span>
<span class="c"># we have a surface atom</span>
<span class="n">surface_atoms</span><span class="p">[</span><span class="n">a</span><span class="p">]</span> <span class="o">=</span> <span class="n">area</span>
<span class="k">return</span> <span class="n">surface_atoms</span>
</div>
<div class="viewcode-block" id="surfacePointsAndGradients"><a class="viewcode-back" href="../../modules.html#MMTK.MolecularSurface.surfacePointsAndGradients">[docs]</a><span class="k">def</span> <span class="nf">surfacePointsAndGradients</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">probe_radius</span> <span class="o">=</span> <span class="mf">0.</span><span class="p">,</span> <span class="n">point_density</span> <span class="o">=</span> <span class="mi">258</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param object: a chemical object</span>
<span class="sd"> :type object: :class:`~MMTK.Collections.GroupOfAtoms`</span>
<span class="sd"> :param probe_radius: the distance from the vdW-radii of the atoms</span>
<span class="sd"> at which the surface is computed</span>
<span class="sd"> :type probe_radius: float</span>
<span class="sd"> :param point_density: the density of points that describe the surface</span>
<span class="sd"> :type point_density: int</span>
<span class="sd"> :returns: a dictionary that maps the surface atoms to a tuple</span>
<span class="sd"> containing three surface-related quantities: the exposed surface</span>
<span class="sd"> area, a list of points in the exposed surface, and a gradient</span>
<span class="sd"> vector pointing outward from the surface.</span>
<span class="sd"> :rtype: dict</span>
<span class="sd"> """</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">atomList</span><span class="p">()</span>
<span class="n">smap</span> <span class="o">=</span> <span class="n">surfm</span><span class="o">.</span><span class="n">surface_atoms</span><span class="p">(</span><span class="n">atoms</span><span class="p">,</span> <span class="n">probe_radius</span><span class="p">,</span> <span class="n">ret_fmt</span> <span class="o">=</span> <span class="mi">4</span><span class="p">,</span>
<span class="n">point_density</span> <span class="o">=</span> <span class="n">point_density</span><span class="p">)</span>
<span class="n">surface_data</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">:</span>
<span class="p">(</span><span class="n">area</span><span class="p">,</span> <span class="n">volume</span><span class="p">,</span> <span class="n">points1</span><span class="p">,</span> <span class="n">grad</span><span class="p">)</span> <span class="o">=</span> <span class="n">smap</span><span class="p">[</span><span class="n">a</span><span class="p">]</span>
<span class="k">if</span> <span class="n">area</span> <span class="o">></span> <span class="mf">0.</span><span class="p">:</span>
<span class="c"># we have a surface atom</span>
<span class="n">surface_data</span><span class="p">[</span><span class="n">a</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">area</span><span class="p">,</span> <span class="nb">map</span><span class="p">(</span><span class="n">Vector</span><span class="p">,</span> <span class="n">points1</span><span class="p">),</span> <span class="n">Vector</span><span class="p">(</span><span class="n">grad</span><span class="p">))</span>
<span class="k">return</span> <span class="n">surface_data</span>
</div>
<span class="k">class</span> <span class="nc">Contact</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">a1</span><span class="p">,</span> <span class="n">a2</span><span class="p">,</span> <span class="n">dist</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">a1</span> <span class="o">=</span> <span class="n">a1</span>
<span class="bp">self</span><span class="o">.</span><span class="n">a2</span> <span class="o">=</span> <span class="n">a2</span>
<span class="k">if</span> <span class="n">dist</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">dist</span> <span class="o">=</span> <span class="p">(</span><span class="n">a1</span><span class="o">.</span><span class="n">position</span><span class="p">()</span> <span class="o">-</span> <span class="n">a2</span><span class="o">.</span><span class="n">position</span><span class="p">())</span><span class="o">.</span><span class="n">length</span><span class="p">()</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">dist</span> <span class="o">=</span> <span class="n">dist</span>
<span class="k">def</span> <span class="nf">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">index</span><span class="p">):</span>
<span class="k">return</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">a1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">a2</span><span class="p">)[</span><span class="n">index</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">__cmp__</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">b</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">cmp</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">dist</span><span class="p">,</span> <span class="n">b</span><span class="o">.</span><span class="n">dist</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">a1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">a2</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="s">'Contact(</span><span class="si">%s</span><span class="s">, </span><span class="si">%s</span><span class="s">)'</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">a1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">a2</span><span class="p">)</span>
<span class="n">__str__</span> <span class="o">=</span> <span class="n">__repr__</span>
<div class="viewcode-block" id="findContacts"><a class="viewcode-back" href="../../modules.html#MMTK.MolecularSurface.findContacts">[docs]</a><span class="k">def</span> <span class="nf">findContacts</span><span class="p">(</span><span class="n">object1</span><span class="p">,</span> <span class="n">object2</span><span class="p">,</span> <span class="n">contact_factor</span> <span class="o">=</span> <span class="mf">1.0</span><span class="p">,</span> <span class="n">cutoff</span> <span class="o">=</span> <span class="mf">0.0</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Identifies contacts between two molecules. A contact is defined as a pair</span>
<span class="sd"> of atoms whose distance is less than contact_factor*(r1+r2+cutoff),</span>
<span class="sd"> where r1 and r2 are the atomic van-der-Waals radii.</span>
<span class="sd"> :param object1: a chemical object</span>
<span class="sd"> :type object1: :class:`~MMTK.Collections.GroupOfAtoms`</span>
<span class="sd"> :param object2: a chemical object</span>
<span class="sd"> :type object2: :class:`~MMTK.Collections.GroupOfAtoms`</span>
<span class="sd"> :param contact_factor: a scale factor in the contact distance criterion</span>
<span class="sd"> :type contact_factor: float</span>
<span class="sd"> :param cutoff: a constant in the contact distance criterion</span>
<span class="sd"> :type cutoff: float</span>
<span class="sd"> :returns: a list of Contact objects that describe atomic contacts</span>
<span class="sd"> between object1 and object2. </span>
<span class="sd"> :rtype: list</span>
<span class="sd"> """</span>
<span class="n">max_object1</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">object1</span><span class="o">.</span><span class="n">atomList</span><span class="p">())</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="n">object1</span><span class="o">.</span><span class="n">atomList</span><span class="p">()</span> <span class="o">+</span> <span class="n">object2</span><span class="o">.</span><span class="n">atomList</span><span class="p">()</span>
<span class="n">tup</span> <span class="o">=</span> <span class="n">surfm</span><span class="o">.</span><span class="n">get_atom_data</span><span class="p">(</span><span class="n">atoms</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">)</span>
<span class="n">max_rad</span> <span class="o">=</span> <span class="n">tup</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="c"># max vdW_radius</span>
<span class="n">atom_data</span> <span class="o">=</span> <span class="n">tup</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">nbors</span> <span class="o">=</span> <span class="n">surfm</span><span class="o">.</span><span class="n">NeighborList</span><span class="p">(</span><span class="n">atoms</span><span class="p">,</span> <span class="n">contact_factor</span><span class="o">*</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">max_rad</span><span class="o">+</span><span class="n">cutoff</span><span class="p">),</span>
<span class="n">atom_data</span><span class="p">)</span>
<span class="n">clist</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">done</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">index1</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">atoms</span><span class="p">)):</span>
<span class="k">for</span> <span class="p">(</span><span class="n">index2</span><span class="p">,</span> <span class="n">dist2</span><span class="p">)</span> <span class="ow">in</span> <span class="n">nbors</span><span class="p">[</span><span class="n">index1</span><span class="p">]:</span>
<span class="k">if</span> <span class="p">(</span><span class="n">index1</span> <span class="o"><</span> <span class="n">max_object1</span><span class="p">)</span> <span class="o">!=</span> <span class="p">(</span><span class="n">index2</span> <span class="o"><</span> <span class="n">max_object1</span><span class="p">):</span>
<span class="k">if</span> <span class="n">index1</span> <span class="o"><</span> <span class="n">index2</span><span class="p">:</span>
<span class="n">a1</span> <span class="o">=</span> <span class="n">atoms</span><span class="p">[</span><span class="n">index1</span><span class="p">]</span>
<span class="n">a2</span> <span class="o">=</span> <span class="n">atoms</span><span class="p">[</span><span class="n">index2</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">a1</span> <span class="o">=</span> <span class="n">atoms</span><span class="p">[</span><span class="n">index2</span><span class="p">]</span>
<span class="n">a2</span> <span class="o">=</span> <span class="n">atoms</span><span class="p">[</span><span class="n">index1</span><span class="p">]</span>
<span class="n">dist</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">dist2</span><span class="p">)</span>
<span class="k">if</span> <span class="n">dist</span> <span class="o">>=</span> <span class="n">contact_factor</span><span class="o">*</span><span class="p">(</span><span class="n">a1</span><span class="o">.</span><span class="n">vdW_radius</span> <span class="o">+</span> <span class="n">a2</span><span class="o">.</span><span class="n">vdW_radius</span> <span class="o">+</span> <span class="n">cutoff</span><span class="p">):</span>
<span class="k">continue</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">done</span><span class="o">.</span><span class="n">has_key</span><span class="p">((</span><span class="n">index1</span><span class="p">,</span> <span class="n">index2</span><span class="p">)):</span>
<span class="n">clist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Contact</span><span class="p">(</span><span class="n">a1</span><span class="p">,</span> <span class="n">a2</span><span class="p">,</span> <span class="n">dist</span><span class="p">))</span>
<span class="n">done</span><span class="p">[(</span><span class="n">index1</span><span class="p">,</span> <span class="n">index2</span><span class="p">)]</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">return</span> <span class="n">clist</span>
</div>
<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">'__main__'</span><span class="p">:</span>
<span class="kn">from</span> <span class="nn">MMTK.PDB</span> <span class="kn">import</span> <span class="n">PDBConfiguration</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="n">Units</span>
<span class="kn">import</span> <span class="nn">sys</span>
<span class="n">target_filename</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="n">pdb_conf1</span> <span class="o">=</span> <span class="n">PDBConfiguration</span><span class="p">(</span><span class="n">target_filename</span><span class="p">)</span>
<span class="k">if</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">][:</span><span class="mi">2</span><span class="p">]</span> <span class="o">==</span> <span class="s">'-f'</span><span class="p">:</span>
<span class="n">chains</span> <span class="o">=</span> <span class="n">pdb_conf1</span><span class="o">.</span><span class="n">createNucleotideChains</span><span class="p">()</span>
<span class="n">molecule_names</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">chains</span><span class="p">)</span> <span class="o">>=</span> <span class="mi">2</span><span class="p">:</span>
<span class="n">clist</span> <span class="o">=</span> <span class="n">findContacts</span><span class="p">(</span><span class="n">chains</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">chains</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">molecule_names</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="n">mol</span><span class="p">)</span> <span class="ow">in</span> <span class="n">pdb_conf1</span><span class="o">.</span><span class="n">molecules</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">mol</span><span class="p">:</span>
<span class="n">molecule_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">o</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
<span class="n">targets</span> <span class="o">=</span> <span class="n">pdb_conf1</span><span class="o">.</span><span class="n">createAll</span><span class="p">(</span><span class="n">molecule_names</span> <span class="o">=</span> <span class="n">molecule_names</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">molecule_names</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
<span class="n">clist</span> <span class="o">=</span> <span class="n">findContacts</span><span class="p">(</span><span class="n">targets</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">targets</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="n">targets</span><span class="o">.</span><span class="n">atomList</span><span class="p">()</span>
<span class="n">mid</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">atoms</span><span class="p">)</span><span class="o">/</span><span class="mi">2</span>
<span class="n">clist</span> <span class="o">=</span> <span class="n">findContacts</span><span class="p">(</span><span class="n">Collection</span><span class="p">(</span><span class="n">atoms</span><span class="p">[:</span><span class="n">mid</span><span class="p">]),</span>
<span class="n">Collection</span><span class="p">(</span><span class="n">atoms</span><span class="p">[</span><span class="n">mid</span><span class="p">:]))</span>
<span class="k">print</span> <span class="nb">len</span><span class="p">(</span><span class="n">clist</span><span class="p">),</span> <span class="s">'contacts'</span>
<span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">clist</span><span class="p">[:</span><span class="mi">8</span><span class="p">]:</span>
<span class="k">print</span> <span class="s">'</span><span class="si">%-64s</span><span class="s"> </span><span class="si">%6.2f</span><span class="s">'</span> <span class="o">%</span> <span class="p">(</span><span class="n">c</span><span class="p">,</span> <span class="n">c</span><span class="o">.</span><span class="n">dist</span><span class="o">/</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">target</span> <span class="o">=</span> <span class="n">pdb_conf1</span><span class="o">.</span><span class="n">createAll</span><span class="p">()</span>
<span class="k">if</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">][:</span><span class="mi">2</span><span class="p">]</span> <span class="o">==</span> <span class="s">'-v'</span><span class="p">:</span>
<span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span> <span class="o">=</span> <span class="n">target</span><span class="o">.</span><span class="n">surfaceAndVolume</span><span class="p">()</span>
<span class="k">print</span> <span class="s">'surface area </span><span class="si">%.2f</span><span class="s"> volume </span><span class="si">%.2f</span><span class="s">'</span> \
<span class="o">%</span> <span class="p">(</span><span class="n">a</span><span class="o">/</span><span class="p">(</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="o">**</span><span class="mi">2</span><span class="p">),</span> <span class="n">v</span><span class="o">/</span><span class="p">(</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="o">**</span><span class="mi">3</span><span class="p">))</span>
<span class="k">elif</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">][:</span><span class="mi">2</span><span class="p">]</span> <span class="o">==</span> <span class="s">'-a'</span><span class="p">:</span>
<span class="n">smap</span> <span class="o">=</span> <span class="n">target</span><span class="o">.</span><span class="n">surfaceAtoms</span><span class="p">(</span><span class="n">probe_radius</span> <span class="o">=</span> <span class="mf">1.4</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">)</span>
<span class="k">print</span> <span class="nb">len</span><span class="p">(</span><span class="n">smap</span><span class="o">.</span><span class="n">keys</span><span class="p">()),</span><span class="s">'of'</span><span class="p">,</span><span class="nb">len</span><span class="p">(</span><span class="n">target</span><span class="o">.</span><span class="n">atomList</span><span class="p">()),</span><span class="s">'atoms on surface'</span>
<span class="k">elif</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">][:</span><span class="mi">2</span><span class="p">]</span> <span class="o">==</span> <span class="s">'-p'</span><span class="p">:</span>
<span class="n">smap</span> <span class="o">=</span> <span class="n">target</span><span class="o">.</span><span class="n">surfacePointsAndGradients</span><span class="p">(</span><span class="n">probe_radius</span> <span class="o">=</span> <span class="mf">1.4</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">)</span>
<span class="k">for</span> <span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">tup</span><span class="p">)</span> <span class="ow">in</span> <span class="n">smap</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="k">print</span> <span class="s">'</span><span class="si">%-40.40s</span><span class="s"> </span><span class="si">%6.2f</span><span class="s"> </span><span class="si">%5d</span><span class="s"> </span><span class="si">%5.1f</span><span class="s"> </span><span class="si">%5.1f</span><span class="s"> </span><span class="si">%5.1f</span><span class="s">'</span> \
<span class="o">%</span> <span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">fullName</span><span class="p">(),</span> <span class="n">tup</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">/</span><span class="p">(</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="o">**</span><span class="mi">2</span><span class="p">),</span> <span class="nb">len</span><span class="p">(</span><span class="n">tup</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span>
<span class="n">tup</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="n">tup</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span> <span class="n">tup</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">2</span><span class="p">])</span>
</pre></div>
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