castor-1.1 compatible classes from ant task

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

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index c15455e..e22b94e 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -34,12 +34,16 @@ public class Atom
   public int type;
   Color color = Color.lightGray;
   public String chain;
-  int alignmentMapping = -1;
-
+  public int alignmentMapping = -1;
+  public int atomIndex;
+  public float occupancy=0;
+  public float tfactor=0;
   public boolean isSelected = false;
 
   public Atom(String str)
   {
+    atomIndex = Integer.parseInt(str.substring(6, 11).trim());
+
     name = str.substring(12, 15).trim();
 
     resName = str.substring(17, 20);
@@ -52,7 +56,8 @@ public class Atom
     this.x = (float) (new Float(str.substring(30, 38).trim()).floatValue());
     this.y = (float) (new Float(str.substring(38, 46).trim()).floatValue());
     this.z = (float) (new Float(str.substring(47, 55).trim()).floatValue());
-
+    occupancy = (float) (new Float(str.substring(54,60).trim()).floatValue());
+    tfactor = (float) (new Float(str.substring(60,66).trim()).floatValue());
   }
 
   public Atom(float x, float y, float z)