 class="sd">        tolerance (float): length in angstroms used in finding bonded atoms.</span>
<span class="sd">            Two atoms are considered bonded if (radius of atom 1) + (radius of</span>
<span class="sd">            atom 2) + (tolerance) &lt; (distance between atoms 1 and 2). Default</span>
<span class="sd">            value = 0.45, the value used by JMol and Cheon et al.</span>
<span class="sd">        ldict (dict): dictionary of bond lengths used in finding bonded atoms.</span>
<span class="sd