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jonathanking / sidechainnet

An all-atom protein structure dataset for machine learning.
BSD 3-Clause "New" or "Revised" License
330 stars 38 forks source link

Issue with not importing sidechainnet #63

Closed Shishir8957 closed 7 months ago

Shishir8957 commented 9 months ago

image

jonathanking commented 9 months ago

Hi,

As mentioned in the README, OpenMM is now a required package for SidechainNet.

If you do the following, it should work:


conda install -c conda-forge openmm
pip install sidechainnet

Please let me know if you have any further questions!

Best, Jonathan

Shishir8957 commented 9 months ago

hi jonathanking, I have encountered a persistent error in OpenMM despite multiple attempts. I've diligently followed the methods recommended by both ChatGPT and other sources, yet the issue persists. This is a critical problem for our final year major project, and we need assistance as we're currently unsure how to resolve it. Any help would be greatly appreciated.

image image

jonathanking commented 9 months ago

Ah, yeah that is unexpected! This is an issue installing OpenMM via conda. I am looking around for a solution, but haven't had luck yet. Reaching out to the OpenMM developers may be a good way forward if we cannot figure it out here.

jonathanking commented 9 months ago

The issue seems to be that OpenMM says it needs cudatoolkit=12.2, but this doesn't exist on the conda-forge or nvidia channels. If we downgrade the cuda toolkit version, it seems to work.

Try the following (remove ! if not running in colab):

!conda install -c conda-forge openmm cudatoolkit==11.8

Shishir8957 commented 9 months ago

Thank you jonathankin, the above problem is been solved but. We are using sidchainnet of 0.6.0 In new version error on d['train'].key() we got error of keyword error at train And we got dimensions error We are trying to run this code https://colab.research.google.com/drive/1J5pUnPuANM6cPXaR2eVNLI6c5wfZgr3X#scrollTo=oUs2Wh5vcEaU inbound8437265090111556072

jonathanking commented 9 months ago

Ah, that's correct. The new version of SidechainNet has changed the underlying format of the data. I would highly recommend using the latest version of SidechainNet. Hopefully I can assist with any further problems you find.

Shishir8957 commented 9 months ago

Hi Jonathan King,

I hope this message finds you well. We've encountered several errors while running our Colab notebook, even after attempting a new method. Specifically, we are facing issues with the attributes of our dataset.

If it's not too much trouble, could you please take a look and run the Colab notebook? Your expertise in troubleshooting these types of issues would be immensely valuable to us. Any updates or insights you can provide will be greatly appreciated.

Thank you so much for your assistance.

https://colab.research.google.com/drive/1J5pUnPuANM6cPXaR2eVNLI6c5wfZgr3X#scrollTo=oUs2Wh5vcEaU