Find molecules from traj

ur-whitelab / hoomd-tf

A plugin that allows the use of Tensorflow in Hoomd-Blue for GPU-accelerated ML+MD

https://hoomd-tf.readthedocs.io

MIT License

30 stars 8 forks source link

Find molecules from traj #269

Closed mehradans92 closed 3 years ago

mehradans92 commented 3 years ago

Added code and test to read molecules from GROAMCS topology
Added code and test for matrix mapping

pep8speaks commented 3 years ago

Hello @mehradans92! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! :beers:

Comment last updated at 2021-02-05 16:53:19 UTC

hgandhi2411 commented 3 years ago

@mehradans92 seems like you are importing MDAnalysis in utils.py. Can you only import it in your functions, since it's an optional dependency? Since we are using mdanalysis for so many functions, it might make sense to make it a depedency?

whitead commented 3 years ago

We would need to modify our compilation instructions (or maybe makefile alone?) to do it. Let's just keep them in functions if possible.