Revert "Just count the number of oxygens directly from the containers"

This reverts commit bddda96.
cdk · Jun 24, 2015 · 8b36b5e · 8b36b5e
1 parent 6e21795
commit 8b36b5e
Showing 1 changed file with 19 additions and 13 deletions.
diff --git a/...c/main/java/org/openscience/cdk/qsar/descriptors/substance/OxygenAtomCountDescriptor.java b/...c/main/java/org/openscience/cdk/qsar/descriptors/substance/OxygenAtomCountDescriptor.java
@@ -17,9 +17,9 @@
 package org.openscience.cdk.qsar.descriptors.substance;
 
 import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.interfaces.IAtom;
-import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.interfaces.IIsotope;
+import org.openscience.cdk.interfaces.IMolecularFormula;
 import org.openscience.cdk.interfaces.ISubstance;
 import org.openscience.cdk.qsar.DescriptorSpecification;
 import org.openscience.cdk.qsar.DescriptorValue;
@@ -74,18 +74,24 @@ public void setParameters(Object[] parameters) throws CDKException {
 	public DescriptorValue calculate(ISubstance substance) {
         if (substance == null) return newNaNDescriptor();
 
-	    int count = 0;
-	    for (IAtomContainer container : substance.atomContainers()) {
-			for (IAtom atom : container.atoms()) {
-				if ("O".equals(atom.getSymbol()) || 8 == atom.getAtomicNumber())
-					count++;
-			}
-		}
+	    IMolecularFormula molFormula = SubstanceManipulator.getChemicalComposition(substance);
+	    if (molFormula == null) return newNaNDescriptor();
 
-		return new DescriptorValue(
-		    getSpecification(), getParameterNames(), getParameters(),
-		    new IntegerResult(count), getDescriptorNames()
-		);
+	    int count = 0;
+        for (IIsotope isotope : molFormula.isotopes()) {
+            if ("O".equals(isotope.getSymbol())) {
+                count = molFormula.getIsotopeCount(isotope);
+                return new DescriptorValue(
+                    getSpecification(),
+                    getParameterNames(),
+                    getParameters(),
+                    new IntegerResult(count),
+                    getDescriptorNames()
+                );
+            }
+        }
+
+		return newNaNDescriptor();
 	}
 
 	/**