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jasonkyuyim / se3_diffusion

Implementation for SE(3) diffusion model with application to protein backbone generation
https://arxiv.org/abs/2302.02277
MIT License
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Small question about chain index shuffling #10

Closed amorehead closed 1 year ago

amorehead commented 1 year ago

Hello. Thank you all for making this awesome project open-source and accessible to us all!

I had a quick question about the following dataloading logic. Is the following line supposed to reference new_chain_idx instead of chain_idx, since new_chain_idx represents the "shuffled" chain indices previously derived above this line?

https://github.com/jasonkyuyim/se3_diffusion/blob/ee15c31b755715855eae9622a9643233bb542d98/data/pdb_data_loader.py#L171

jasonkyuyim commented 1 year ago

Hi, Thanks for the kind words. Yes you're right, it should be new_chain_idx. This luckily doesn't affect our results since we trained on monomers which only had one chain. This feature and randomization is important when training on complexes. I've pushed a fix here https://github.com/jasonkyuyim/se3_diffusion/commit/fb350b69ca4349d7b29b19044ecc8627815dafce