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lucidrains / alphafold2

To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released
MIT License
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Typo? #95

Closed CiaoHe closed 3 years ago

CiaoHe commented 3 years ago

Hi Phil and Eric @hypnopump

I'm not familiar with the operations on protein structure or whatever :(, but here I wonder is it a mistake when indexing:

https://github.com/lucidrains/alphafold2/blob/521415676df4043ed101a882d0eae7a659c774d0/alphafold2_pytorch/utils.py#L702

Perhaps it should be new_coords[s,:-padding or None, i] since in the inner loop it just constructs the s-th sequence sidechain's coords.

Best,

hypnopump commented 3 years ago

Oh yes! Hidden bug (the function was only used with one sequence so the error ran unnoticed).

In general, the utils need an update (which i do have locally but havent pushed). I'll be updating them in the following days.

CiaoHe commented 3 years ago

Oh yes! Hidden bug (the function was only used with one sequence so the error ran unnoticed).

In general, the utils need an update (which i do have locally but havent pushed). I'll be updating them in the following days.

Thanks a lot eric!

lucidrains commented 3 years ago

@CiaoHe thanks for all the code reviews!