X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FDBRefUtils.java;h=4cc888dd3ccc3faa9f58d292c12bbab581f39d01;hb=a16e1965f87dc25c9d6bc6672fbf3a8ad703357e;hp=a757d79679373ed85c98e1bca87417d2157cf3ff;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index a757d79..4cc888d 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -418,11 +418,15 @@ public class DBRefUtils
         // check for chaincode and mapping
         // PFAM style stockhom PDB citation
         com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
-                "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;([0-9]+)-([0-9]+)");
+                "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)");
         if (r.search(acn.trim()))
         {
           String pdbid = r.stringMatched(1);
           String chaincode = r.stringMatched(2);
+          if (chaincode==null)
+          {
+            chaincode = " ";
+          }
           String mapstart = r.stringMatched(3);
           String mapend = r.stringMatched(4);
           if (chaincode.equals(" "))
@@ -433,8 +437,11 @@ public class DBRefUtils
           ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
           PDBEntry pdbr = new PDBEntry();
           pdbr.setId(pdbid);
-          pdbr.getProperty().put("CHAIN",chaincode);
+          pdbr.setProperty(new Hashtable());
+          pdbr.getProperty().put("CHAIN", chaincode);
           seq.addPDBId(pdbr);
+        } else {
+          System.err.println("Malformed PDB DR line:"+acn);
         }
       }
       else