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<div class="section" id="constructing-a-dna-strand-with-a-ligand">
<h1>Constructing a DNA strand with a ligand<a class="headerlink" href="#constructing-a-dna-strand-with-a-ligand" title="Permalink to this headline">ΒΆ</a></h1>
<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
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28</pre></div></td><td class="code"><div class="highlight"><pre><span class="c"># Create a nucleotide chain with a ligand from a PDB file.</span>
<span class="c">#</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="o">*</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.NucleicAcids</span> <span class="kn">import</span> <span class="n">NucleotideChain</span>
<span class="kn">from</span> <span class="nn">MMTK.Visualization</span> <span class="kn">import</span> <span class="n">view</span>
<span class="c"># Load the PDB entry 110d. It contains a single DNA strand with a</span>
<span class="c"># ligand (daunomycin).</span>
<span class="n">configuration</span> <span class="o">=</span> <span class="n">PDBConfiguration</span><span class="p">(</span><span class="s">'110d.pdb'</span><span class="p">)</span>
<span class="c"># Construct the nucleotide chain object. This also constructs positions</span>
<span class="c"># for the missing hydrogens, using geometrical criteria.</span>
<span class="n">chain</span> <span class="o">=</span> <span class="n">configuration</span><span class="o">.</span><span class="n">createNucleotideChains</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
<span class="c"># Construct the ligand. There is no definition of it in the database,</span>
<span class="c"># so it can only be constructed as a collection of atoms. The second</span>
<span class="c"># argument of createMolecules() is set to one in order to allow</span>
<span class="c"># this use of an unknown residue.</span>
<span class="n">ligand</span> <span class="o">=</span> <span class="n">configuration</span><span class="o">.</span><span class="n">createMolecules</span><span class="p">([</span><span class="s">'DM1'</span><span class="p">],</span> <span class="mi">1</span><span class="p">)</span>
<span class="c"># Put everyting in a universe and show it graphically.</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">InfiniteUniverse</span><span class="p">()</span>
<span class="n">universe</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">chain</span><span class="p">)</span>
<span class="n">universe</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">ligand</span><span class="p">)</span>
<span class="n">view</span><span class="p">(</span><span class="n">universe</span><span class="p">)</span>
</pre></div>
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