Hydrogens need to be added because we build the molecule from scratch.

johnmay · johnmay · commit c793b0165cd0 · 2019-01-28T14:58:18.000Z
diff --git a/descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptorTest.java b/descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptorTest.java
@@ -27,6 +27,7 @@
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.qsar.DescriptorValue;
 import org.openscience.cdk.qsar.result.DoubleArrayResult;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
 import org.openscience.cdk.tools.CDKHydrogenAdder;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 
@@ -60,12 +61,12 @@ public void testChloroButane() throws Exception {
         mol.addAtom(c2);
         mol.addAtom(c3);
         mol.addAtom(cl);
-
         mol.addBond(new Bond(c1, c2));
         mol.addBond(new Bond(c2, c3));
         mol.addBond(new Bond(c3, cl));
-
         AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
+        CDKHydrogenAdder.getInstance(SilentChemObjectBuilder.getInstance())
+                        .addImplicitHydrogens(mol);
 
         DescriptorValue v = descriptor.calculate(mol);
         Assert.assertEquals(0.5192, ((DoubleArrayResult) v.getValue()).get(0), 0.0001);
