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dauparas / ProteinMPNN

Code for the ProteinMPNN paper
MIT License
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Getting last layer representations of the encoder and decoder? #14

Closed johnnytam100 closed 1 year ago

johnnytam100 commented 2 years ago

Hi @dauparas ! Would you mind telling us which variables are the last layer representations of the encoder and decoder? I want to output those representations. Thank you!

dauparas commented 2 years ago

Hey!

Sure, the encoder last activations are https://github.com/dauparas/ProteinMPNN/blob/main/protein_mpnn_utils.py#L1048 after this line:

h_V - [batch, protein length, 128] - node embedding h_E - [batch, protein length, 48, 128] - edge embedding

The decoder last activations are: https://github.com/dauparas/ProteinMPNN/blob/main/protein_mpnn_utils.py#L1075 after this line: h_V - [batch, protein length, 128] - node embedding