how to use .a3m file as input

[lzhangUT]

Hi, Can i use fastfold to run just inference? for example, I dont need jackmmer to run the msa search, I already have my msa search result (.a3m file) ready. I also have GPU available for the model inference, how should i implement with fastfold? what arguments should be there? Thanks

[Shenggan]

I think you can see the code part of use_precomputed_alignments, https://github.com/hpcaitech/FastFold/blob/ad7f0cb5d00975e698b690ecc3c44eddc446c7e1/inference.py#L155-L171

The inference scripts will save the alignment results in local_alignment_dir, so you can put your msa search result in right place and use argument use_precomputed_alignments.