atom3d.datasets.ppi.neighbors not in atom3d codebase

[hnisonoff]

I am unable to do import atom3d.datasets.ppi.neighbors as nb as described in the atom3d.py file. I tried installing the atom3d version specified in setup.py as well as the most recent but neither appear to have a ppi submodule of datasets. Thanks!

[ecust-hc]

Hello, I also have this problem. Have you solved it？

[junhaobearxiong]

Same issue here.

[stgzr]

Maybe you can import atom3d from source code of atom3d via branch v0.2.1, instead of using pip install atom3d==0.2.1.
The missing file is located as the link.
It seems better to use v0.2.2 for running run_atom3d.py.

[tuanle618]

Hi @hnisonoff , @ecust-hc , @junhaobearxiong, I am currently also trying to run the benchmark on my own model and came across the same issue.
I found out that the neighbors module is placed in the example directory of Atom3D. So in case you want to use the most recent Atom3D version, have a look here: https://github.com/drorlab/atom3d/blob/master/examples/ppi/dataset/neighbors.py

To rerun, you might just copy the file and save it into your module.