search

hpcaitech / FastFold

Optimizing AlphaFold Training and Inference on GPU Clusters
Apache License 2.0
557 stars 86 forks source link

Is the use of template a must for running FastFold? #111

Open kwanUm opened 1 year ago

kwanUm commented 1 year ago

Hi, I'd like to run FastFold for a long sequence with no templates. Is this setting supported by FastFold?

I'm building an MSA only from Uniref90 DB for starters.

Shenggan commented 1 year ago

Similar to AlphaFold/OpenFold, you can set flag c.model.template.enabled = False in fastfold/config.py to disable template.

And you can refer to

https://github.com/hpcaitech/FastFold/blob/8a59989555569a0edfc68f4de6d48d81dbe8a2b6/fastfold/model/hub/alphafold.py#L255-L256

to see the part that this flag affects.