I've been reading your post and looking at the 54 bit fingerprint you mentioned. I was wondering if you could help clear up any confusion on my end; I am not s

I've been reading your post and looking at the 54 bit fingerprint you mentioned. I was wondering if you could help clear up any confusion on my end; I am not sure if I am implementing and applying it correctly. Regarding the 54 bit fingerprint, if I do a substructure match between a target molecule and the query molecule: "O", and I find there are 3 matches, then if the list of the patterns were: "0 2 times O largest 55458" and then later "16 3 times O largest 653" "17 1 times O largest 466" does that mean I should set bit 0, 16, and 17 to 1? If I've understood correctly up to this point, I would have some additional questions, but if I am totally off, my additional questions would not make sense. Edit: I had a mistake in my logic with the second question. Removed it