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| <!DOCTYPE html> | ||
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| <html xmlns="http://www.w3.org/1999/xhtml" lang="en"> | ||
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| <meta charset="utf-8" /> | ||
| <title>gillespy2.solvers.cpp.example_models — GillesPy2 1.4.0 documentation</title> | ||
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| <h1>Source code for gillespy2.solvers.cpp.example_models</h1><div class="highlight"><pre> | ||
| <span></span><span class="kn">from</span> <span class="nn">gillespy2.core</span> <span class="k">import</span> <span class="n">Model</span><span class="p">,</span> <span class="n">Species</span><span class="p">,</span> <span class="n">Reaction</span><span class="p">,</span> <span class="n">Parameter</span> | ||
| <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span> | ||
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| <div class="viewcode-block" id="Example"><a class="viewcode-back" href="../../../../classes/gillespy2.solvers.cpp.html#gillespy2.solvers.cpp.example_models.Example">[docs]</a><span class="k">class</span> <span class="nc">Example</span><span class="p">(</span><span class="n">Model</span><span class="p">):</span> | ||
| <span class="sd">"""</span> | ||
| <span class="sd"> This is a simple example for mass-action degradation of species S.</span> | ||
| <span class="sd"> """</span> | ||
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| <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">parameter_values</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> | ||
| <span class="c1"># Initialize the model.</span> | ||
| <span class="n">Model</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">"Example"</span><span class="p">)</span> | ||
| <span class="c1"># Species</span> | ||
| <span class="n">S</span> <span class="o">=</span> <span class="n">Species</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">'Sp'</span><span class="p">,</span> <span class="n">initial_value</span><span class="o">=</span><span class="mi">100</span><span class="p">)</span> | ||
| <span class="bp">self</span><span class="o">.</span><span class="n">add_species</span><span class="p">([</span><span class="n">S</span><span class="p">])</span> | ||
| <span class="c1"># Parameters</span> | ||
| <span class="n">k1</span> <span class="o">=</span> <span class="n">Parameter</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">'k1'</span><span class="p">,</span> <span class="n">expression</span><span class="o">=</span><span class="mf">3.0</span><span class="p">)</span> | ||
| <span class="bp">self</span><span class="o">.</span><span class="n">add_parameter</span><span class="p">([</span><span class="n">k1</span><span class="p">])</span> | ||
| <span class="c1"># Reactions</span> | ||
| <span class="n">rxn1</span> <span class="o">=</span> <span class="n">Reaction</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">'S degradation'</span><span class="p">,</span> <span class="n">reactants</span><span class="o">=</span><span class="p">{</span><span class="n">S</span><span class="p">:</span> <span class="mi">1</span><span class="p">},</span> <span class="n">products</span><span class="o">=</span><span class="p">{},</span> <span class="n">rate</span><span class="o">=</span><span class="n">k1</span><span class="p">)</span> | ||
| <span class="bp">self</span><span class="o">.</span><span class="n">add_reaction</span><span class="p">([</span><span class="n">rxn1</span><span class="p">])</span> | ||
| <span class="bp">self</span><span class="o">.</span><span class="n">timespan</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">20</span><span class="p">,</span> <span class="mi">101</span><span class="p">))</span></div> | ||
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| <span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span><span class="s1">'Trichloroethylene'</span><span class="p">,</span> <span class="s1">'LacOperon'</span><span class="p">,</span> <span class="s1">'Schlogl'</span><span class="p">,</span> <span class="s1">'MichaelisMenten'</span><span class="p">,</span> | ||
| <span class="s1">'ToggleSwitch'</span><span class="p">,</span> <span class="s1">'Example'</span><span class="p">,</span> <span class="s1">'Tyson2StateOscillator'</span><span class="p">,</span> <span class="s1">'Oregonator'</span><span class="p">]</span> | ||
| </pre></div> | ||
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