Merge pull request #280 from cdk/bug/atypevalence

Correct valence calculation in CDKAtomTypeMatcher
cdk · Mar 21, 2017 · 162bce9 · 162bce9
2 parents 57cd683 + 5db4119
commit 162bce9
Showing 1 changed file with 7 additions and 2 deletions.
diff --git a/base/core/src/main/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/base/core/src/main/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
@@ -2511,8 +2511,13 @@ private boolean isAcceptable(IAtom atom, IAtomContainer container, IAtomType typ
         }
 
         // confirm correct valency
-        if (type.getValency() != CDKConstants.UNSET && container.getBondOrderSum(atom) > type.getValency())
-            return false;
+        if (type.getValency() != CDKConstants.UNSET) {
+            double valence = container.getBondOrderSum(atom);
+            if (atom.getImplicitHydrogenCount() != 0)
+                valence += atom.getImplicitHydrogenCount();
+            if (valence > type.getValency())
+                return false;
+        }
 
         // confirm correct formal charge
         if (atom.getFormalCharge() != CDKConstants.UNSET && !atom.getFormalCharge().equals(type.getFormalCharge()))