Chemaxon issues with using MolImporter in existing nodes?

I'm not sure what the issue is here, I'm posting here rather than at Chemaxon because it seems to specifically affect the library within KNIME rather than Marvin itself.


I use the Chemaxon functions to output a series of structures in SMILES format, such as this 


Now this is actually invalid, because of the ambiguity around the five memebred ring, but I can't seem to find a combination of functions that will let me fix this.


The reason I bring it up here is that if you were to import this string into MarvinSketch a valid structure is produced, and indeed Chemaxon renders it, but copying the SMILES from that gives O=C(Nc1ccncc1)c1[nH]cnc1C(=O)OC1CCCCC1, which is perfectly valid.

Is there a snippet of code or something that can be done to clean this up within a node, I've tried the various options of MolImporter to copy the structure into a new Molecule instance, but the invalid form remains.

I would have thought that one of the dearomaize/aromatize combinations would be enough to clear it, but it seems to get 'stuck' in an ambigous state.

Dear James_Wallace,

The reason for the difference is that the Marvin Sketch GUI uses non-default valence check options, which fixes such ambiguous N atoms, and adds an implicit H if needed.
We normally do not do this "fix" automatically (e.g. "molconvert" does not modify the structure): hidden, automatic structure modifications should be avoided in general (of course drawing is different).
For explicit structure checking and modification I would suggest Structure Checker, using the "Valence Error Checker" it can fix such structures.

Best regards,