Dear CDK team,

I found what might be a bug or a missing part in CDK.  I have an AtomContainer which contains a phosphor atom without bonds. CDK cannot recognize this atomtype. I built a test to show how this occurs. I do not know if it is clear enough since I never generated a test for describing a bug or a change petition.
What can happen now? Is somebody in from the CDK team going to test if this is a bug or not?


public class AtomsPNTest extends TestCase {
public void testP() throws FileNotFoundException, CDKException {
IAtom atomP = new NNAtom(Elements.PHOSPHORUS);
IAtomType atomTypeP = new NNAtomType(Elements.PHOSPHORUS);
AtomTypeManipulator.configure(atomP, atomTypeP);
IAtomContainer ac = atomP.getBuilder().newAtomContainer();
IAtomType type = null;
for (IAtom atom : ac.atoms()) {
type = CDKAtomTypeMatcher.getInstance(ac.getBuilder()).findMatchingAtomType(ac, atom);

Julio E. Peironcely, PhD student
Leiden/Amsterdam Center for Drug Research || Netherlands Metabolomics Centre ||