From: jprocter <Jim Procter>
Date: Fri, 18 Nov 2005 13:30:08 +0000 (+0000)
Subject: added 3 letter IUB codes for ambiguous residues/bases
X-Git-Tag: Release_2_07~60
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=952ede10e4daf14f554d5867e5eb74591aafddb3;p=jalview.git

added 3 letter IUB codes for ambiguous residues/bases
---

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index fbaab81..4906eb7 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -156,9 +156,10 @@ public class ResidueProperties
     aa3Hash.put("TRP", new Integer(17));
     aa3Hash.put("TYR", new Integer(18));
     aa3Hash.put("VAL", new Integer(19));
-    aa3Hash.put("B", new Integer(20));
-    aa3Hash.put("Z", new Integer(21));
-    aa3Hash.put("X", new Integer(22));
+    // IUB Nomenclature for ambiguous peptides
+    aa3Hash.put("ASX", new Integer(20)); // "B";
+    aa3Hash.put("GLX", new Integer(21)); // X
+    aa3Hash.put("XAA", new Integer(22));// X unknown
     aa3Hash.put("-", new Integer(23));
     aa3Hash.put("*", new Integer(23));
     aa3Hash.put(".", new Integer(23));