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StatPhysBio / protein_holography

Code for holographic machine learning of proteins
MIT License
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Bug: hard-wired location of data dir #49

Open lukasz99 opened 1 month ago

lukasz99 commented 1 month ago

Hello, it looks like location of datadir is set (in network_loader.py) as: datadir = '/gscratch/spe/mpun/protein_holography/data' whereas it should be adjusted to wherever the code is installed in.

Otherwise bumping up python version to 3.10 and tensorflow-gpu to 2.8 seems to work on Ubuntu 20.04.6 LTS, whereas the original settings (3.8/2.6) fail. At least in my hands.

michaelpun commented 3 weeks ago

Hi, thanks for your interest and for pointing this out! I have changed to using a relative path in https://github.com/StatPhysBio/protein_holography/commit/ba02d58b021db8a0bbbb7c09dea55496c1a265b4 although I believe there may be more hardcoded paths do exist.

Regarding updating the python version, I think that this is something that I do not currently have the time to test and so I will not take on currently to ensure that the code works as completely as possible for people looking to reproduce the results from the paper. If you are looking for a more up-to-date codebase (and in general anyone interested in this code), you should check out Hermes which features a similar model that has been fine-tuned on stability predictions. for more accurate mutational effect prediction.