Hi Greg,

I know proteins are sometimes used within periodic boundaries. We aren't
using proteins, but we will be using molecules within crystals. I was
wondering if there is a way in RDKit to calculate RMSD between two periodic
systems (such as two crystals, each containing molecules), and if not, if
there is a way to generate some kind of fingerprint? I know the RMSD and
fingerprinting methods exist for molecules, but I'm not sure if there are
ones for periodic conditions. Note that we may have multiple "molecules"
inside each crystal.

Also, we were running tests with RDKit using Python, but since our program
is written in C++, I think it is easier to integrate it with the C++ API. I
already have an integration set-up that includes the proper headers and
links the proper libraries for our needs. But I had to compile RDKit myself
to do so. I noticed there are repositories for RDKit (like on Ubuntu), but
it looks like they are not up-to-date (some of the functions I need are not
yet present). I was wondering if those will get updated sometime in the

The updated repositories aren't necessary (because I can always have others
compile RDKit themselves if they need to compile our program), but they're
nice to have because they speed up the process.

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