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Structurebiology-BNL / ESMBind

Deep learning + physical modeling for 3D protein metal ion binding prediction
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seqence length and path fix. #3

Closed alchemistcai closed 2 months ago

alchemistcai commented 2 months ago

In get_esm_embedding.py, result['mask'] raises KeyError.In my test,result only has logits,representations keys.I use esm's official example to calculate sequence length and it works.

In data_process.py,max_repr_esm = np.load("multi_modal_binding/data/normalization_constants/esm_repr_min.npy")` can't locate the file.I change the path to abspath and it works.

    current_dir=os.path.dirname(__file__)
    max_repr_esm_if = np.load(
        os.path.join(current_dir,"normalization_constants/esm_if_repr_max.npy")
    )
alchemistcai commented 2 months ago

Other issues I encontered and my solutions.