From 79a12145585663fd828ca50f6c6fc56262f91d1f Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 12 Apr 2018 14:11:42 +0200
Subject: [PATCH] Fixed loading from PDB file, secondary structure stays
 unchanged

---
 CHANGELOG.txt                    |  4 ++--
 modules/io/src/mol/pdb_reader.cc | 19 ++-----------------
 2 files changed, 4 insertions(+), 19 deletions(-)

diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index 4eb6a634d..249616245 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -1,8 +1,8 @@
 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'.
+    from mmCIF PDB 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
 --------------------------------------------------------------------------------
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index a203234ec..ffa04e6ec 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -520,16 +520,7 @@ void PDBReader::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 && (*(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 (HSList::const_iterator i=strand_list_.begin(), e=strand_list_.end();
@@ -540,13 +531,7 @@ void PDBReader::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 && (*(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);
   }
 }
 
-- 
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