Thank you Greg. I am working in C++. I can poke around with this if I knew which members of the AdditionalOutput struct are used by which fingerprint generators. I just wanted to make sure there wasn't an explanation somewhere I missed.
I can see that with the AtomPairs fingerprints I can do the following //mol is an *ROMol and fpg is a *FingerprintGenerator RDKit::AdditionalOutput ao; std::vector<std::vector<std::uint64_t>> atomtobits(mol->getNumAtoms()); ao.atomToBits = &atb; auto res = fpg->getSparseCountFingerprint(*mo, nullptr, nullptr, -1, &ao); after which atomtobits contains a list of bits for each atom. From the comments I think the bitInfo member should be used by the RDKitFingerprintGenerator, but I don't see where it is used in the code. Is that the part that wasn't finished? Is it possible to get information about the atoms/environments that set particular bits in the Morgan or RDKit fingerprints using the new API? Jason Biggs On Fri, Mar 13, 2020 at 10:20 AM Greg Landrum <greg.land...@gmail.com> wrote: > Hi Jason, > > At the moment there's nothing available here except what's in the C++ > tests. This part of the code didn't end up being completely finished before > the GSoC project ended and it's never bubbled up on my priority list to > finish it. > > I haven't spent much time with this code, but I can probably put together > an example. > Are you working from C++? > > -greg > > > On Thu, Mar 12, 2020 at 10:42 PM Jason Biggs <jasondbi...@gmail.com> > wrote: > >> I am taking a look at the FingerprintGenerator class and I really like >> this unified interface for these four types of fingerprints. I have very >> limited experience with the fingerprint code before the generator API was >> introduced. >> >> What I'm not sure about is how to get information about the >> atoms/environments that set the bits. I believe I need to use the >> AdditionalOutput struct, >> https://www.rdkit.org/docs/cppapi/structRDKit_1_1AdditionalOutput.html, >> but I'm not exactly sure how to do so. I normally would look at the c++ >> test files to see how it is used, and from that I see the atomToBits member >> is used in the atom pairs fingerprints, but I'm not sure about the other >> members of this struct. For example there is a bitInfo member, is this >> where I would find information for the RDKit and Morgan fingerprints? >> >> Are there any examples somewhere that I could follow to find out more >> information? >> >> Thank you >> >> Jason >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
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