an class="n">Set</span><span class="p">[</span><span class="nb">int</span><span class="p">]]:</span>
        <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">        Gets residue indices within a particular shapemer across all proteins.</span>
<span class="sd">        &quot;&quot;&quot;</span>
        <span class="n">protein_to_shapemer_residues</span><span class="p">:</span> <span class="n">Dict</span><span class="p">[</span><span class="n">ProteinKey</span><span class="p">,</span> <span class="