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WillHua127 / EnzymeFlow

EnzymeFlow official.
https://arxiv.org/abs/2410.00327
28 stars 5 forks source link

Dependency issues #1

Open carbondrop-nick opened 4 days ago

carbondrop-nick commented 4 days ago

Super cool, but hard to get going. On top of the stated dependencies I also had to add a lot of modules to my environment to get this working: ipdb einops ml-collections dm-tree ipywidgets jupyter einx torch_geometric tmtools openmm POT rdkit mdtraj pdbfixer

Seems to be missing "sampling" module. The imported configs, inference, and data.loader point to modules that don't exist (unless you meant the ones under Pretrain?)

mdtraj also requires C++ tools to install and pdbfixer can't be installed via pip (conda-forge instead). Would be great to find a better way to distribute this.

WillHua127 commented 4 days ago

i am working on the open-source thing, make everything better!

pgmikhael commented 2 days ago

Hi,

Super exciting work! Will just re-iterate the above. Would also be helpful in general to not import all functions from a script (from file import *) since it makes it harder to follow where things break when/if they do.

WillHua127 commented 2 days ago

Thanks Peter! I am cleaning everything. Plan to release everything in Nov.

WillHua127 commented 1 day ago

things should be fixed, let me know if you can run enzymeflow_demo.ipynb