The Suggestion of Output with PAE

[LUDENGZHEN]

It would be great if the output could include the results of PAE. PAE is quite useful in certain applications.

[zhangyuxuann]

@LUDENGZHEN Run inference_demo.sh you can enable more confidence output including pae by

Protenix/configs/configs_inference.py

Line 28 in ef104bf

"need_atom_confidence": False,

export LAYERNORM_TYPE=fast_layernorm
export USE_DEEPSPEED_EVO_ATTTENTION=true

N_sample=5
N_step=200
N_cycle=10
seed=101
use_deepspeed_evo_attention=true
input_json_path="./examples/example.json"
dump_dir="./output"

python3 runner/inference.py \
--seeds ${seed} \
--dump_dir ${dump_dir} \
--input_json_path ${input_json_path} \
--model.N_cycle ${N_cycle} \
--sample_diffusion.N_sample ${N_sample} \
--sample_diffusion.N_step ${N_step} \
--need_atom_confidence true