From fe5f751c21190cad65c44f0ec892e99f8efcbb62 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 11 Jun 2010 09:40:43 +0000
Subject: [PATCH] patch for JAL-556

---
 src/MCview/PDBChain.java |   29 +++++++++++++++++++++++------
 1 file changed, 23 insertions(+), 6 deletions(-)

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 2eaf8a3..bd1f640 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -46,7 +46,7 @@ public class PDBChain
   public int offset;
 
   public Sequence sequence;
-
+  public boolean isNa=false;
   public boolean isVisible = true;
 
   public int pdbstart = 0;
@@ -163,17 +163,29 @@ public class PDBChain
 
   public void makeCaBondList()
   {
+    boolean na=false;
+    int numNa=0;
     for (int i = 0; i < (residues.size() - 1); i++)
     {
       Residue tmpres = (Residue) residues.elementAt(i);
       Residue tmpres2 = (Residue) residues.elementAt(i + 1);
       Atom at1 = tmpres.findAtom("CA");
       Atom at2 = tmpres2.findAtom("CA");
-
-      if ((at1 != null) && (at2 != null))
+      na=false;
+      if ((at1 == null) && (at2 == null))
+      {
+        na=true;
+        at1 = tmpres.findAtom("P");
+        at1 = tmpres2.findAtom("P");
+      }
+      if ((at1 == null) && (at2 == null))
       {
         if (at1.chain.equals(at2.chain))
         {
+          if (na)
+          {
+            numNa++;
+          }
           makeBond(at1, at2);
         }
       }
@@ -182,6 +194,10 @@ public class PDBChain
         System.out.println("not found " + i);
       }
     }
+    if (numNa>0 && ((numNa/residues.size())>0.99))
+    {
+      isNa=true;
+    }
   }
 
   public void makeBond(Atom at1, Atom at2)
@@ -257,7 +273,8 @@ public class PDBChain
       // Keep totting up the sequence
       if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
       {
-        if (ResidueProperties.nucleotideIndex[tmpat.resName.charAt(0)] == -1)
+        String nucname=tmpat.resName.trim();
+        if (ResidueProperties.nucleotideIndex[nucname.charAt(0)] == -1)
         {
           seq.append("X");
           // System.err.println("PDBReader:Null aa3Hash for " +
@@ -267,7 +284,7 @@ public class PDBChain
         {
           // nucleotide flag
           nucleotide = true;
-          seq.append(tmpat.resName.charAt(0));
+          seq.append(nucname.charAt(0));
         }
       }
       else
@@ -286,7 +303,7 @@ public class PDBChain
     {
       id = " ";
     }
-
+    isNa=nucleotide;
     sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
     // resNumber-offset
     // ~=
-- 
1.7.10.2