From b0b27e984d8486610b0c4bffe97f6b4cf3d0a768 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 30 Nov 2005 15:05:12 +0000
Subject: [PATCH] TER flag added

---
 src/MCview/PDBfile.java |   14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index c4fe563..47aa5ac 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -74,6 +74,8 @@ public class PDBfile extends jalview.io.FileParse {
         PDBChain tmpchain;
         String line;
         boolean modelFlag = false;
+        boolean terFlag = false;
+
         for (int i = 0; i < lineArray.size(); i++)
         {
 
@@ -88,17 +90,23 @@ public class PDBfile extends jalview.io.FileParse {
            if(line.indexOf("MODEL")==0)
              modelFlag = true;
 
+           if(line.indexOf("TER")==0)
+             terFlag = true;
+
            if(modelFlag && line.indexOf("ENDMDL")==0)
              break;
 
-           if (line.indexOf("ATOM")==0 || line.indexOf("HETATM")==0 )
+           if (line.indexOf("ATOM")==0
+               || (line.indexOf("HETATM")==0 && !terFlag) )
             {
+              terFlag = false;
+
                     try {
                         Atom tmpatom = new Atom(line);
 
                         //Jalview is only interested in CA bonds????
-                        if(!tmpatom.name.equals("CA"))
-                          continue;
+                     //   if(!tmpatom.name.equals("CA"))
+                     //     continue;
 
                         tmpchain = findChain(tmpatom.chain);
                         if ( tmpchain != null)
-- 
1.7.10.2