While the SmilesParse has the ability to ignore kekulisation, this doesn't seem to be available in the IteratingSMILESReader. Is that the case? or is there a way to pass this option to it?

Currently when iterating over a large SMILES file, if it hits an entry such as c1cccn1 it (correctly) stops iterating. What I'd like to do is to catch an exception and continue on to the next entry

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Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science