Fixed loading from mmCIF file, secondary structure stays unchanged

CHANGELOG.txt

+Changes in Release <RELEASE NUMBER>
+--------------------------------------------------------------------------------
+  * Removed habit of changing secondary structure of entities when loading
+    from mmCIF files. Before, OST would turn secondary structure 'EEH' into
+    'ECH' to make it look nicer in DNG. Now, 'EEH' stays 'EEH'.
+
 Changes in Release 1.7.1
 --------------------------------------------------------------------------------
 

modules/io/src/mol/mmcif_reader.cc

@@ -1543,17 +1543,7 @@ void MMCifReader::AssignSecStructure(mol::EntityHandle ent)
       continue;
     }
     mol::SecStructure alpha(mol::SecStructure::ALPHA_HELIX);
-    // some PDB files contain helix/strand entries that are adjacent to each 
-    // other. To avoid visual artifacts, we effectively shorten the first of
-    // the two secondary structure segments to insert one residue of coil 
-    // conformation.
-    mol::ResNum start = i->start, end = i->end;
-    if (helix_list_.end() != i+1 && // unit test
-        (*(i+1)).start.GetNum() <= end.GetNum()+1 &&
-        (*(i+1)).end.GetNum() > end.GetNum()) {
-      end = mol::ResNum((*(i+1)).start.GetNum()-2);
-    }
-    chain.AssignSecondaryStructure(alpha, start, end);
+    chain.AssignSecondaryStructure(alpha, i->start, i->end);
   }
 
   for (MMCifHSVector::const_iterator i=strand_list_.begin(),
@@ -1565,14 +1555,7 @@ void MMCifReader::AssignSecStructure(mol::EntityHandle ent)
       continue;
     }
     mol::SecStructure extended(mol::SecStructure::EXTENDED);
-    mol::ResNum start = i->start, end = i->end;
-    // see comment for helix assignment
-    if (strand_list_.end() != i+1 && // unit test
-        (*(i+1)).start.GetNum() <= end.GetNum()+1 &&
-        (*(i+1)).end.GetNum() > end.GetNum()) {
-      end=mol::ResNum((*(i+1)).start.GetNum()-2);
-    }
-    chain.AssignSecondaryStructure(extended, start, end);
+    chain.AssignSecondaryStructure(extended, i->start, i->end);
   }
 }