_aligns-&gt;clear();
<a name="l00453"></a>00453     top_aligns-&gt;insert(top_aligns-&gt;begin(), 
<a name="l00454"></a>00454                        align_pair(top_align-&gt;score, top_align));
<a name="l00455"></a>00455 
<a name="l00456"></a>00456     <span class="comment">// Update ligand fragmentation if we have a ligand</span>
<a name="l00457"></a>00457     <span class="keywordflow">if</span>(lig_file){
<a name="l00458"></a>00458       get_ligand_fragment(*lig_file, A_model-&gt;site_volume_estimate_hand