bug in getImplicitHcount()

Marvin 5.4.1.1 displays [O-][N++]=O correctly when implicit H atoms on heteroatoms are turned on (no H atoms on N), but after the string is imported into a Molecule by JChem 5.9.0, MolAtom.getImplicitHcount() returns 2 for the N.

Also interesting: The imported molecule is converted by MolExporter.exportToFormat(mol, "mrv") into:

<?xml version="1.0"?><cml version="ChemAxon file format v5.9.0, generated by v5.9.0">

<MDocument><MChemicalStruct><molecule molID="m1"><atomArray atomID="a1 a2 a3" elementType="N O O" formalCharge="2 0 -1" x2="18.76423579261527 17.528444328763342 18.54793332678599" y2="-2.4947746044951256 -0.8972829407054199 -4.649328319359502"></atomArray><bondArray><bond atomRefs2="a1 a2" order="2"></bond><bond atomRefs2="a1 a3" order="1"></bond></bondArray></molecule></MChemicalStruct></MDocument>

</cml>

But MolExporter.exportToFormat(mol, "smiles") converts it into [O-][NH2++]=O.  This is especially bizarre, because the N in [O-][NH2++]=O is pentavalent.

I just checked Marvin 5.10, and it puts two implicit H atoms on the N(2+) in [O-][N++]=O and C[N++], giving pentavalent N atoms in both. Ack!

Hi Bob,

This issue will be fixed by the 5.11. release.

Regards,
Erika

Do you have an estimated time of release for 5.11?

The estimated time of release 5.11. is September.

Regards, Erika