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.