Faster LENS calculation using FastNS

[tulga-rdn]

<oops, posted the previous pull request through my throwaway account, sorry>

Hello,

I'm an undergraduate researcher at Prof. Taras Pogorelov's lab at UIUC. I am using LENS for my research, and I found a faster way of calculating LENS parameters, so I thought I would share it. I didn't find any issues and the results were identical to your original code, can you please check as well? Thanks!

[andrewtarzia]

Hey @tulga-rdn , we will have a look t this soon, thank you for your interest and support!

[andrewtarzia]

Hey @tulga-rdn, this looks great, and like a simple 1:1 replacement. Thank you!

If you want me to merge this into the main, we will need to fix all the failed checks.

• You can ignore the first ruff check, because that is something we need to change that has nothing to do with the changes you have made.
• For the mypy and ruff-format checks, to reproduce those locally, you can do just check in the terminal at the repositories home if you have just installed. Otherwise you can open the justfile and find out the mypy and ruff-format commands that are used and run those.
• For the pytests, there seems to be an issue with cut-offs that FastNS is stricter about than before? Feel free to modify the conftest.py to handle this issue.

[tulga-rdn]

Oops, it seems to still have errors. Will fix them soon

[SimoneMartino98]

Hey @tulga-rdn, thanks for your interest, I took a look at your last commit and it seems that there is an issue with the argument _prepare_box which, if I understood correctly, is a private argument that read the box dimensions in order to choose the biggest cutoff radius possible. I cannot find the part of code for this argument, can you include that code so we can review it?