lass="c1"># get reactions except the protected ones</span>
        <span class="n">to_remove</span> <span class="o">=</span> <span class="n">all_reactions</span> <span class="o">-</span> <span class="n">protected</span>
        <span class="k">for</span> <span class="n">rid</span> <span class="ow">in</span> <span class="n">to_remove</span><span class="p">:</span>
            <span class="c1"># knock-out reactions not in the model</span>
            <span class="n">context_specific_model</span><span class="o