sd">        standardize (bool): whether to standardize the structure before</span>
<span class="sd">            analysis. Set to False only if you already have the structure in a</span>
<span class="sd">            convention where layers / chains will be along low &lt;hkl&gt; indexes.</span>
<span class="sd">        bonds ({(specie1, specie2): max_bond_dist}: bonds are</span>
<span class="sd">                specified as a dict of tuples: float of specie1, specie2</span>
<span class="sd">                an