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Rigid.from_3_points comment

Open Zhu-Siqi opened this issue 1 year ago • 3 comments

Hi, it seems that openfold.utils.rigid_utils.Rigid.from_3_points module is actually different from the algorithm 21 in Alphafold paper. Your code seems to write as v1 = x2 - x1 and v2 = x3 - x2, which is different from the original algorithm. If I misunderstand your code, I suggest that the comments should be changed to make it more clear.

Zhu-Siqi avatar Apr 24 '24 05:04 Zhu-Siqi

I think it's still correct, because when it's called the order is reversed https://github.com/aqlaboratory/openfold/blob/3c1fd31ac47c8da54d088badd9eba61fe0b3fd26/openfold/data/data_transforms.py#L1109-L1114

Thought I agree it's confusing, maybe someone can confirm and we can update the docs?

eamag avatar May 19 '24 09:05 eamag