built documentation for cobra pie. now tidy up the installer and roll…

… out beta 1
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+  <h1>Source code for cobra.core.Gene</h1><div class="highlight"><pre>
+<span class="c">#cobra.Gene.py</span>
+<span class="c">#######################</span>
+<span class="c">#BEGIN Class Gene</span>
+<span class="c">#</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">from</span> <span class="nn">.Metabolite</span> <span class="kn">import</span> <span class="n">Metabolite</span>
+<div class="viewcode-block" id="Gene"><a class="viewcode-back" href="../../../cobra.core.html#cobra.core.Gene.Gene">[docs]</a><span class="k">class</span> <span class="nc">Gene</span><span class="p">(</span><span class="n">Metabolite</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;A Gene is a special class of metabolite.</span>
+<span class="sd">    </span>
+
+<span class="sd">    TODO: Make design decisions about TUs and such</span>
+<span class="sd">    &quot;&quot;&quot;</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="nb">id</span><span class="p">,</span> <span class="n">formula</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span>
+                 <span class="n">name</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">compartment</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">strand</span><span class="o">=</span><span class="s">&#39;+&#39;</span><span class="p">,</span>
+                 <span class="n">locus_start</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">locus_end</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">functional</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        id: A string.</span>
+
+<span class="sd">        formula: cobra.Formula or String  of a chemical formula.  Defaults to None</span>
+<span class="sd">        to save time in pickling and such.</span>
+<span class="sd">        </span>
+<span class="sd">        name: String.  A human readable name.</span>
+<span class="sd">        </span>
+<span class="sd">        compartment: None or a dictionary indicating the cellular location</span>
+<span class="sd">        of the metabolite.  Used when in a cobra.Reaction or Model</span>
+<span class="sd">        object</span>
+
+<span class="sd">        strand: &#39;+&#39; or &#39;-&#39; to indicate forward or reverse strand for DNA.</span>
+
+<span class="sd">        locus_start: Int.  The index of the starting base for the gene.</span>
+
+<span class="sd">        locus_end: Int. The index of the last base for the gene.</span>
+
+<span class="sd">        functional: Boolean.  Indicate whether the gene is functional.  If it</span>
+<span class="sd">        is not functional then it cannot be used in an enzyme complex nor</span>
+<span class="sd">        can its products be used.</span>
+<span class="sd">        </span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">Metabolite</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="nb">id</span><span class="p">,</span> <span class="n">formula</span><span class="o">=</span><span class="n">formula</span><span class="p">,</span>
+                            <span class="n">name</span><span class="o">=</span><span class="n">name</span><span class="p">,</span> <span class="n">compartment</span><span class="o">=</span><span class="n">compartment</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">locus_start</span> <span class="o">=</span> <span class="n">locus_start</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">locus_end</span> <span class="o">=</span> <span class="n">locus_end</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">strand</span> <span class="o">=</span> <span class="n">strand</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">functional</span> <span class="o">=</span> <span class="n">functional</span>
+
+<div class="viewcode-block" id="Gene.guided_copy"><a class="viewcode-back" href="../../../cobra.core.html#cobra.core.Gene.Gene.guided_copy">[docs]</a>    <span class="k">def</span> <span class="nf">guided_copy</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">the_model</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Trying to make a faster copy proceedure for cases where large</span>
+<span class="sd">        numbers of metabolites might be copied.  Such as when copying reactions.</span>
+
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">the_copy</span> <span class="o">=</span> <span class="n">Metabolite</span><span class="o">.</span><span class="n">guided_copy</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">the_model</span><span class="p">)</span>
+        <span class="k">return</span><span class="p">(</span><span class="n">the_copy</span><span class="p">)</span>
+</div>
+<div class="viewcode-block" id="Gene.remove_from_model"><a class="viewcode-back" href="../../../cobra.core.html#cobra.core.Gene.Gene.remove_from_model">[docs]</a>    <span class="k">def</span> <span class="nf">remove_from_model</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">the_model</span><span class="p">,</span>
+                          <span class="n">make_dependent_reactions_nonfunctional</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Removes the association</span>
+
+<span class="sd">        the_model: cobra.Model object.  remove the reaction from this model.</span>
+
+<span class="sd">        make_dependent_reactions_nonfunctional: Boolean.  If True then replace</span>
+<span class="sd">        the gene with &#39;False&#39; in the gene association, else replace the gene</span>
+<span class="sd">        with &#39;True&#39;</span>
+
+<span class="sd">        TODO:  Better handling of the gene association</span>
+<span class="sd">        </span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">if</span> <span class="n">make_dependent_reactions_nonfunctional</span><span class="p">:</span>
+            <span class="n">gene_state</span> <span class="o">=</span> <span class="s">&#39;False&#39;</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">gene_state</span> <span class="o">=</span> <span class="s">&#39;True&#39;</span>
+        <span class="n">the_gene_re</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="s">&#39;(^|(?&lt;=( |\()))</span><span class="si">%s</span><span class="s">(?=( |\)|$))&#39;</span><span class="o">%</span><span class="n">re</span><span class="o">.</span><span class="n">escape</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">id</span><span class="p">))</span>
+        <span class="k">if</span> <span class="n">the_model</span> <span class="o">!=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_model</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">&#39;</span><span class="si">%s</span><span class="s"> not in </span><span class="si">%s</span><span class="s"> ergo it cannot be removed. (</span><span class="si">%s</span><span class="s">)&#39;</span><span class="o">%</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
+                                                                  <span class="n">the_model</span><span class="p">,</span>
+                                                                  <span class="bp">self</span><span class="o">.</span><span class="n">_model</span><span class="p">))</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_model</span><span class="o">.</span><span class="n">genes</span><span class="o">.</span><span class="n">remove</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">_model</span> <span class="o">=</span> <span class="bp">None</span>
+
+        <span class="k">for</span> <span class="n">the_reaction</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_reaction</span><span class="p">:</span>
+            <span class="n">the_reaction</span><span class="o">.</span><span class="n">gene_reaction_rule</span> <span class="o">=</span> <span class="n">the_gene_re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="n">gene_state</span><span class="p">,</span>
+                                                              <span class="n">the_reaction</span><span class="o">.</span><span class="n">gene_reaction_rule</span><span class="p">)</span>
+            <span class="n">the_reaction</span><span class="o">.</span><span class="n">_genes</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+            <span class="c">#Now deactivate the reaction if its gene association evaluates to False</span>
+            <span class="n">the_gene_reaction_relation</span> <span class="o">=</span> <span class="n">the_reaction</span><span class="o">.</span><span class="n">gene_reaction_rule</span>
+            <span class="k">for</span> <span class="n">other_gene</span> <span class="ow">in</span> <span class="n">the_reaction</span><span class="o">.</span><span class="n">_genes</span><span class="p">:</span>
+                <span class="n">other_gene_re</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="s">&#39;(^|(?&lt;=( |\()))</span><span class="si">%s</span><span class="s">(?=( |\)|$))&#39;</span><span class="o">%</span><span class="n">re</span><span class="o">.</span><span class="n">escape</span><span class="p">(</span><span class="n">other_gene</span><span class="o">.</span><span class="n">id</span><span class="p">))</span>
+                <span class="n">the_gene_reaction_relation</span> <span class="o">=</span> <span class="n">other_gene_re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s">&#39;True&#39;</span><span class="p">,</span> <span class="n">the_gene_reaction_relation</span><span class="p">)</span>
+            <span class="c">#</span>
+            <span class="k">if</span> <span class="ow">not</span> <span class="nb">eval</span><span class="p">(</span><span class="n">the_gene_reaction_relation</span><span class="p">):</span>
+                <span class="n">the_reaction</span><span class="o">.</span><span class="n">lower_bound</span> <span class="o">=</span> <span class="mi">0</span>
+                <span class="n">the_reaction</span><span class="o">.</span><span class="n">upper_bound</span> <span class="o">=</span> <span class="mi">0</span>
+
+<span class="c">#</span>
+<span class="c">#END Class Gene</span>
+<span class="c">########################</span></div></div>
+</pre></div>
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