engths used in finding bonded atoms. Values</span>
<span class="sd">            from JMol are used as default</span>

<span class="sd">    Returns:</span>
<span class="sd">        (np.ndarray): A numpy array of shape (number of atoms, number of atoms);</span>
<span class="sd">        If any image of atom j is bonded to atom i with periodic boundary</span>
<span class="sd">        conditions, the matrix element [atom i, atom j] is 1.</span>
<span class="sd">    &quot;&quot;&quot;</span>
    <span class="n">n