#1113 Atom type error for phosphor

[Patrik Rydberg]

When running addImplicitHydrogens(iAtomContainer) on an iAtomContainer of the sdf-file attached the error is
Exception in thread "main" org.openscience.cdk.exception.CDKException: IAtom is not typed! P
So this type of phoshpor is not recognized by CDK

CDK version used 1.3.7

There are multiple occurences of this atom type in the ZINC database.

[Patrik Rydberg]

sdf file which produces the error

[Patrik Rydberg]

This should be a P.ate phosphorous atom with one attached hydrogen atom.

Suggested change to fix this:
change lines 921-922 in CDKAtomTypeMatcher.java to

            int doubleBonds = countAttachedDoubleBonds(atomContainer, atom);
            if (doubleBonds == 1){
                IAtomType type = getAtomType("P.ate");
                if (isAcceptable(atom, atomContainer, type)) return type;
            }
            else {
                IAtomType type = getAtomType("P.ine");
                if (isAcceptable(atom, atomContainer, type)) return type;
            }

This fix has not been tested on molecules with atoms matching the P.ine atom type.

[Egon Willighagen]

Example structure:

http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=3396560