>
<span class="sd">    &quot;&quot;&quot;</span>
    <span class="n">protein_keys</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="n">ProteinKey</span><span class="p">]</span>
    <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">    List of protein names = rows of the output embedding</span>
<span class="sd">    &quot;&quot;&quot;</span>
    <span class="n">shapemer_to_protein_indices</span><span class="p">:</span> <span class="n">Dict</span><span cla