e</a> *lig_file,
<a name="l00487"></a>00487                  <span class="keyword">const</span> std::string &amp;mol_id)
<a name="l00488"></a>00488   {
<a name="l00489"></a>00489     <span class="comment">// write ligands to file</span>
<a name="l00490"></a>00490     <span class="keywordflow">if</span>(<a class="code" href="classSimSite3D_1_1ScoreRigidAlignments.html#14c7215836a55728fa4225078b31cad7">A_write_ligands</a>){
<a name="l00491"></a>00491       tier2_score_mmi align = top_aligns.begin();
<a name="