I have the same problem with the UniversalIsomorphismTester as described
in BugReport: 1060064. The substructure search with my molecules takes
about 6 minutes and returns 10000 RMaps (and the substructure matches
only once). I am using molecules which are saturated with hydrogens
because I must search a generic molecule within a concrete one. If I use
the timeout variable the search process is cancelled by an exception
immediately because the start time was only set if you use the
UIT.getOverlaps() method. Also was the timeout check in the wrong place
within the UIT algorithm.
I have attached a patch to this mail which includes a working timeout
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