X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=ea969fff4d9c7f0d23ac8df9218c5e3c1b8032d8;hb=0f40a8334651302a74a223ecd3e583451302bb42;hp=0cbeef67c300afedd5ff04a5351ab5c734b24269;hpb=82a6c8e2e25b7534168b68b2c89b9cf195f815a5;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 0cbeef6..ea969ff 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -31,6 +31,7 @@ import jalview.util.MessageManager;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Vector;
@@ -194,21 +195,22 @@ public class JmolParser extends StructureFile implements JmolStatusListener
   private List<Atom> convertSignificantAtoms(ModelSet ms)
   {
     List<Atom> significantAtoms = new ArrayList<Atom>();
+    HashMap<String, org.jmol.modelset.Atom> chainTerMap = new HashMap<String, org.jmol.modelset.Atom>();
+    org.jmol.modelset.Atom prevAtom = null;
     for (org.jmol.modelset.Atom atom : ms.at)
     {
-      // System.out.println("Seq Id : " + atom.getSeqID());
-      // System.out.println("To String : " + atom.toString());
-      if (!StructureImportSettings.isProcessHETATMs() && atom.isHetero())
-      {
-        continue;
-      }
       if (atom.getAtomName().equalsIgnoreCase("CA")
               || atom.getAtomName().equalsIgnoreCase("P"))
       {
+        if (!atomValidated(atom, prevAtom, chainTerMap))
+        {
+          continue;
+        }
         Atom curAtom = new Atom(atom.x, atom.y, atom.z);
         curAtom.atomIndex = atom.getIndex();
         curAtom.chain = atom.getChainIDStr();
-        curAtom.insCode = atom.group.getInsertionCode();
+        curAtom.insCode = atom.group.getInsertionCode() == '\000' ? ' '
+                : atom.group.getInsertionCode();
         curAtom.name = atom.getAtomName();
         curAtom.number = atom.getAtomNumber();
         curAtom.resName = atom.getGroup3(true);
@@ -218,12 +220,65 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode;
         curAtom.tfactor = atom.getBfactor100() / 100f;
         curAtom.type = 0;
-        significantAtoms.add(curAtom);
+        // significantAtoms.add(curAtom);
+        // ignore atoms from subsequent models
+        if (!significantAtoms.contains(curAtom))
+        {
+          significantAtoms.add(curAtom);
+        }
+        prevAtom = atom;
       }
     }
     return significantAtoms;
   }
 
+  private boolean atomValidated(org.jmol.modelset.Atom curAtom,
+          org.jmol.modelset.Atom prevAtom,
+          HashMap<String, org.jmol.modelset.Atom> chainTerMap)
+  {
+    // System.out.println("Atom: " + curAtom.getAtomNumber()
+    // + "   Last atom index " + curAtom.group.lastAtomIndex);
+    if (chainTerMap == null || prevAtom == null)
+    {
+      return true;
+    }
+    String curAtomChId = curAtom.getChainIDStr();
+    String prevAtomChId = prevAtom.getChainIDStr();
+    // new chain encoutered
+    if (!prevAtomChId.equals(curAtomChId))
+    {
+      // On chain switch add previous chain termination to xTerMap if not exists
+      if (!chainTerMap.containsKey(prevAtomChId))
+      {
+        chainTerMap.put(prevAtomChId, prevAtom);
+      }
+      // if current atom belongs to an already terminated chain and the resNum
+      // diff < 5 then mark as valid and update termination Atom
+      if (chainTerMap.containsKey(curAtomChId))
+      {
+        if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
+        {
+          chainTerMap.put(curAtomChId, curAtom);
+          return true;
+        }
+        return false;
+      }
+    }
+    // atom with previously terminated chain encountered
+    else if (chainTerMap.containsKey(curAtomChId))
+    {
+      if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
+      {
+        chainTerMap.put(curAtomChId, curAtom);
+        return true;
+      }
+      return false;
+    }
+    // HETATM with resNum jump > 2
+    return !(curAtom.isHetero() && ((curAtom.getResno() - prevAtom
+            .getResno()) > 2));
+  }
+
   private void createAnnotation(SequenceI sequence, PDBChain chain,
           org.jmol.modelset.Atom[] jmolAtoms)
   {