lass="p">)</span>
<span class="k">def</span> <span class="nf">make_count_matrix</span><span class="p">(</span><span class="n">residues_list</span><span class="p">,</span> <span class="n">alphabet_size</span><span class="p">:</span> <span class="nb">int</span><span class="p">):</span>
    <span class="n">out</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="nb">len</span><span class="p">(</span><span class="n">re