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arneschneuing / DiffSBDD

A Euclidean diffusion model for structure-based drug design.
MIT License
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problem on 'config.yml' #3

Closed prophet-Fang closed 1 year ago

prophet-Fang commented 2 years ago

Hi arneschneuing,

Can you share your 'config.yml'? These parameters in 'train.py' confused me a lot.

Thanks!

arneschneuing commented 2 years ago

Hi @prophet-Fang, have you seen the example configuration file? Is there a particular parameter that you're confused about?

prophet-Fang commented 2 years ago

That really helps a lot, thanks for your time!

prophet-Fang commented 2 years ago

Another question, why does 'pocket_one_hot' have a dimension of 10? (there are 20 kinds of amino acids)

prophet-Fang commented 2 years ago

Another question, why does 'pocket_one_hot' have a dimension of 10? (there are 20 kinds of amino acids)

this result is acquired by running 'process_bindingmoad.py' on the bindingmoad dataset.

arneschneuing commented 2 years ago

If you run the script in full-atom mode, the pocket is represented by atoms and we use 10 different atom types.

arneschneuing commented 1 year ago

Hi, I am closing this issue now but feel free to re-open if you have further questions. Best, Arne