bug in getImplicitHcount()

User 870ab5b546

10-07-2012 14:03:40

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!

ChemAxon e500b51457

12-07-2012 08:29:58

Hi Bob,

This issue will be fixed by the 5.11. release.

Regards,
Erika

User 870ab5b546

12-07-2012 11:51:22

Do you have an estimated time of release for 5.11?

ChemAxon e500b51457

12-07-2012 14:59:46

The estimated time of release 5.11. is September.


Regards, Erika