Fixes and improvements to VN-EGNN restructure #11
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…ocket.sh The script path was somehow linked to BASE="data" which didn't make sense. Now it uses the PROJECT_ROOT
…gs.py call in process_data.sh -b is used for batch_size in this script, hence, the option doesn't make sense here
…res.py "-p" arg was replaced by "-i" which is used by protein_feature.py; "-b" was removed as it's not part of protein_feature.py
Please review this commit carefully. In opinion, from the given README.md, the data should be stored in `vnegnn/data/data/` for experiment=VNEGNN whereas the data for experiment=equipocket should be stored in `vnegnn/data/equipocket`. This commit adapts the paths in the preprocessing scripts as well as the hydro config accordingly.
…ders as defined in the README
Author
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I wanted to add that |
Collaborator
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Hi Tobias, thanks for your pull-request, will try to have a look at it in the next, maybe I set some paths wrong as I prepared the repository for GitHub. |
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Hi, while working through the setup instructions on the VNEGNN repo, I noticed that some steps are a bit unclear / not working on my side. I documented the changes I did locally and provide them to you as a pull request to review them.
The pull request includes
process_data.shandprocess_data_equipocket.sh)Updates to the data scripts
From what I could understand from the README and the provided hydra config, the data should be setup in the way as shown in the data-structure tree I added to the README (see here).
In case this is correct, some paths in the setup scripts and the hydra config were incorrect. In either case, if I follow the original README, download the provided datasets to
data/dataand execute the scripts, it will fail. Also,python src/train.py experiment=vnegnnexpects the data to be indata/equipocket(which I would have imagined forpython src/train.py experiment=equipocketinstead).I updated the paths in the scripts and hydra config accordingly.
Please let me know how it was originally intended so I can reproduce the experiments.