[Cdk-commits] SF.net SVN: cdk: [8396] trunk/cdk/src/org/openscience/cdk/geometry/ BondTools.java

[<raj...@us...>]

Revision: 8396
          http://svn.sourceforge.net/cdk/?rev=8396&view=rev
Author:   rajarshi
Date:     2007-06-23 20:17:39 -0700 (Sat, 23 Jun 2007)

Log Message:
-----------
Updated to take into account that the default value of hydrogen count ight be a null value, in which case we take it to be 0

Modified Paths:
--------------
    trunk/cdk/src/org/openscience/cdk/geometry/BondTools.java

Modified: trunk/cdk/src/org/openscience/cdk/geometry/BondTools.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/geometry/BondTools.java	2007-06-24 02:59:25 UTC (rev 8395)
+++ trunk/cdk/src/org/openscience/cdk/geometry/BondTools.java	2007-06-24 03:17:39 UTC (rev 8396)
@@ -204,8 +204,18 @@
     if (container.getBondNumber(atom, parent) == -1 || doubleBondConfiguration.length <= container.getBondNumber(atom, parent) || !doubleBondConfiguration[container.getBondNumber(atom, parent)]) {
       return false;
     }
-    int lengthAtom = container.getConnectedAtomsList(atom).size() + atom.getHydrogenCount();
-    int lengthParent = container.getConnectedAtomsList(parent).size() + parent.getHydrogenCount();
+
+      int hcount;
+      if (atom.getHydrogenCount() == CDKConstants.UNSET) hcount = 0;
+      else hcount = atom.getHydrogenCount();
+
+    int lengthAtom = container.getConnectedAtomsList(atom).size() + hcount;
+
+       if (parent.getHydrogenCount() == CDKConstants.UNSET) hcount = 0;
+      else hcount = parent.getHydrogenCount();
+
+    int lengthParent = container.getConnectedAtomsList(parent).size() + hcount;
+      
     if (container.getBond(atom, parent) != null) {
       if (container.getBond(atom, parent).getOrder() == CDKConstants.BONDORDER_DOUBLE && (lengthAtom == 3 || (lengthAtom == 2 && atom.getSymbol().equals("N"))) && (lengthParent == 3 || (lengthParent == 2 && parent.getSymbol().equals("N")))) {
         java.util.List atoms = container.getConnectedAtomsList(atom);
@@ -243,7 +253,12 @@
    * @return                          false=is not start of configuration, true=is
    */
   private static boolean isStartOfDoubleBond(IAtomContainer container, org.openscience.cdk.interfaces.IAtom a, org.openscience.cdk.interfaces.IAtom parent, boolean[] doubleBondConfiguration) {
-    int lengthAtom = container.getConnectedAtomsList(a).size() + a.getHydrogenCount();
+      int hcount;
+      if (a.getHydrogenCount() == CDKConstants.UNSET) hcount = 0;
+      else hcount = a.getHydrogenCount();
+
+    int lengthAtom = container.getConnectedAtomsList(a).size() + hcount;
+      
     if (lengthAtom != 3 && (lengthAtom != 2 && a.getSymbol() != ("N"))) {
       return (false);
     }


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