I'm using version 6.2.0. Please let me know if you have a fix/work-around. Thanks.
Could you send us a short example code which does not work for you? Is NPE thrown by every molecule set or only by a specific?
I'm doing several thousand pairwise comparisons. The vast majority of the comparisons work fine. There may be a better way of doing what I'm trying to do. Please see my method below. The NPE is thrown at the ce.next() method call. Unfortunately, catching the NPE doesn't work.
We have investigated the issue and hopefully we will fix it in the next release.