_min_num_atoms</a> &gt; 0 &amp;&amp; !lig_file) <span class="keywordflow">return</span> <span class="keyword">false</span>;
<a name="l00292"></a>00292 
<a name="l00293"></a>00293     <span class="comment">// Rename align to something else and get a reference to the align_vi</span>
<a name="l00294"></a>00294     tier1_score_mmci align_map_iter = align_map.begin();
<a name="l00295"></a>00295     <span class="keywordflow">for</span>( ; align_map_iter != align_map.end(); ++align_map_iter){
<a name="l00296"></a>