JAL-1919 PDBfile and JmolParser refactor

[jalview.git] / src / MCview / Atom.java

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 4d000af..1e7f973 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -20,6 +20,8 @@
  */
 package MCview;
 
+import jalview.schemes.ResidueProperties;
+
 import java.awt.Color;
 
 public class Atom
@@ -44,6 +46,8 @@ public class Atom
 
   public int type;
 
+  public char ss;
+
   Color color = Color.lightGray;
 
   public String chain;
@@ -73,11 +77,13 @@ public class Atom
     name = str.substring(12, 15).trim();
 
     resName = str.substring(17, 20);
+    // JAL-1828 treat MSE Selenomethionine as MET (etc)
+    resName = ResidueProperties.getCanonicalAminoAcid(resName);
 
     chain = str.substring(21, 22);
 
     resNumber = Integer.parseInt(str.substring(22, 26).trim());
-    resNumIns = str.substring(22, 27).trim();
+    resNumIns = str.substring(22, 27);
     insCode = str.substring(26, 27).charAt(0);
     this.x = (new Float(str.substring(30, 38).trim()).floatValue());
     this.y = (new Float(str.substring(38, 46).trim()).floatValue());