From 7074cf51318a3bef44a0845ee27c3ec740d664c2 Mon Sep 17 00:00:00 2001
From: mark_rynbeek <markr@ebi.ac.uk>
Date: Wed, 28 Oct 2009 14:27:49 +0000
Subject: [PATCH] CDKHydrogenAdder should not attempt addImplicitHydrogen for
 pseudo atoms in an atom container

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
---
 .../cdk/tools/CDKHydrogenAdder.java            | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/src/main/org/openscience/cdk/tools/CDKHydrogenAdder.java b/src/main/org/openscience/cdk/tools/CDKHydrogenAdder.java
index e21ab1de195..4a8b319a014 100644
--- a/src/main/org/openscience/cdk/tools/CDKHydrogenAdder.java
+++ b/src/main/org/openscience/cdk/tools/CDKHydrogenAdder.java
@@ -1,6 +1,5 @@
-/* $Revision$ $Author$ $Date$
- *  
- * Copyright (C) 2007  Egon Willighagen
+/* Copyright (C) 2007  Egon Willighagen
+ *               2009  Mark Rijnbeek <markr@ebi.ac.uk>
  *
  * Contact: cdk-devel@lists.sourceforge.net
  *
@@ -24,6 +23,9 @@
  */
 package org.openscience.cdk.tools;
 
+import java.util.Hashtable;
+import java.util.Map;
+
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.annotations.TestClass;
 import org.openscience.cdk.annotations.TestMethod;
@@ -33,9 +35,7 @@
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IAtomType;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
-
-import java.util.Hashtable;
-import java.util.Map;
+import org.openscience.cdk.interfaces.IPseudoAtom;
 
 /**
  * Adds implicit hydrogens based on atom type definitions. The class assumes
@@ -107,9 +107,11 @@ public static CDKHydrogenAdder getInstance(IChemObjectBuilder builder) {
     @TestMethod("testMethane,testFormaldehyde,testHCN")
     public void addImplicitHydrogens(IAtomContainer container) throws CDKException {
         for (IAtom atom : container.atoms()) {
-            addImplicitHydrogens(container, atom);
+            if ( !(atom instanceof IPseudoAtom) ){
+                addImplicitHydrogens(container, atom);
+            }
         }        
-	}
+    }
 	
 	/**
 	 * Sets the implicit hydrogen count for the indicated IAtom in the given IAtomContainer.