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Can ESMC extract embeddings using the structure track?

Open RichenLee opened this issue 10 months ago • 2 comments

Hello,

I am trying to extract embeddings locally using the ESMC model and would like to know whether it is possible to use the structure track for this purpose. I modified the LogitsConfig settings as follows: sequence=True, structure=True, return_embeddings=True However, the output remains unchanged. Additionally, after checking the source code, it seems that embedding extraction might only be supported for the sequence track.

Could you confirm whether it is possible to extract embeddings using the structure track? If so, could you provide guidance on how to achieve this?

Thank you for your help!

RichenLee avatar Mar 11 '25 08:03 RichenLee

i wanna ask the same question! I want to embed my generated proteins structures but i do not have sequences. Is it possible to use the encoder of esm3 to achieve that? thanks :)

123Barry avatar Apr 13 '25 06:04 123Barry

i wanna ask the same question! I want to embed my generated proteins structures but i do not have sequences. Is it possible to use the encoder of esm3 to achieve that? thanks :)

Have you figured out how to do this ? I also want to embed the protein structures.

shijiale0609 avatar Jun 24 '25 04:06 shijiale0609