I actually want to remove that option :-). I couple of people have sent me some example code that had turned it off. I only really added that for debugging. 

Anyways, the latest IteratingSMILESReader in the snapshot won’t stop and dumps the problem input in a property of an empty container - IteratingSMILESReader.BAD_SMILES_INPUT. 


On 8 Mar 2014, at 19:26, Rajarshi Guha <guhar@mail.nih.gov> wrote:

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

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