[Cdk-commits] CVS: cdk/src/org/openscience/cdk AtomType.java,1.31,1.32

[Egon W. <eg...@us...>]

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12923/src/org/openscience/cdk

Modified Files:
	AtomType.java 
Log Message:
Added field to hold the formal number of neighbours, for example 4 for a tetrahedral carbon. It turned out that a SMILES parser cannot work without this explicit information, in addition to the maxbondorder and bondordersum fields

Index: AtomType.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/AtomType.java,v
retrieving revision 1.31
retrieving revision 1.32
diff -u -r1.31 -r1.32
--- AtomType.java	2 Jun 2004 13:01:34 -0000	1.31
+++ AtomType.java	20 Jun 2004 15:30:43 -0000	1.32
@@ -77,6 +77,13 @@
     protected int hybridization;
 
     /**
+     * The formal number of neighbours this atom type can have.
+     * This includes explicitely and implicitely connected atoms. The latter
+     * includes implicit hydrogens.
+     */
+    protected int formalNeighbourCount;
+
+    /**
 	 *  Constructor for the AtomType object.
      *
      * @param elementSymbol  Symbol of the atom
@@ -201,6 +208,28 @@
     }
     
     /**
+     *  Sets the formal neighbour count of this atom.
+     *
+     * @param  charge  The neighbour count
+     *
+     * @see    #getFormalNeighbourCount
+     */
+    public void setFormalNeighbourCount(int count) {
+        this.formalNeighbourCount = count;
+    }
+    
+    /**
+     *  Returns the formal neighbour count of this atom.
+     *
+     * @return the formal neighbour count of this atom
+     *
+     * @see    #setFormalNeighbourCount
+     */
+    public int getFormalNeighbourCount() {
+        return this.formalNeighbourCount;
+    }
+    
+    /**
      *  Sets the hybridization of this atom.
      *
      * @param  hybridization  The hybridization
@@ -268,6 +297,7 @@
         sb.append("BOS:" + getBondOrderSum() + ", ");
         sb.append("FC:" + getFormalCharge() + ", ");
         sb.append("H:" + getHybridization() + ", ");
+        sb.append("NC:" + getFormalNeighbourCount() + ", ");
         sb.append(super.toString());
         sb.append(")");
         return sb.toString();