Actually I misread what you originally quoted. I'm not sure why (if it is)
the listeners that're causing a problem. I still can't figure out whether
it's a genuine Thread collision, or if it's an iterator having an
addition/removal somewhere. The stack trace seems to point to the
listeners
Ok, I'll give in my modified version of the original CDK method I obtained
(forgot how). Be warned though - there're a lot of hacks in this because
basically - AMBIT SMARTS had issues regarding implicit hydrogens, and when
you are dealing with SMARTS atom types I did the minimum necessary to get
On 6 August 2015 at 17:36, Edmund Duesbury lip1...@sheffield.ac.uk wrote:
it's an iterator having an addition/removal somewhere
Not a thread collision. Do you have your calculateImplicitHydrogens method.
Also note implicit H on a query atom is currently superfluous unless you
use it your self.
Though the code you've quoted is the part that's causing the bug.
Can you provide the full stack place please.
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