AlphaFold Multimer

import os
import stat
import pickle
from mindsponge import PipeLine
from mindsponge.common.protein import to_pdb_v2, from_prediction_v2

cmd = "wget https://download.mindspore.cn/mindscience/mindsponge/Multimer/examples/6T36.pkl"
os.system(cmd)

pipe = PipeLine(name="Multimer")
pipe.set_device_id(0)
pipe.initialize("predict_256")
pipe.model.from_pretrained()
with open("./6T36.pkl", "rb") as f:
    raw_feature = pickle.load(f)
final_atom_positions, final_atom_mask, confidence, b_factors = pipe.predict(raw_feature)
unrelaxed_protein = from_prediction_v2(final_atom_positions,
                                       final_atom_mask,
                                       raw_feature["aatype"],
                                       raw_feature["residue_index"],
                                       b_factors,
                                       raw_feature["asym_id"],
                                       False)
pdb_file = to_pdb_v2(unrelaxed_protein)
os.makedirs('./result/', exist_ok=True)
os_flags = os.O_RDWR | os.O_CREAT
os_modes = stat.S_IRWXU
pdb_path = './result/unrelaxed_6T36.pdb'
with os.fdopen(os.open(pdb_path, os_flags, os_modes), 'w') as fout:
    fout.write(pdb_file)
print("confidence:", confidence)

@article {AlphaFold-Multimer2021,
  author       = {Evans, Richard and O{\textquoteright}Neill, Michael and Pritzel, Alexander and Antropova, Natasha and Senior, Andrew and Green, Tim and {\v{Z}}{\'\i}dek, Augustin and Bates, Russ and Blackwell, Sam and Yim, Jason and Ronneberger, Olaf and Bodenstein, Sebastian and Zielinski, Michal and Bridgland, Alex and Potapenko, Anna and Cowie, Andrew and Tunyasuvunakool, Kathryn and Jain, Rishub and Clancy, Ellen and Kohli, Pushmeet and Jumper, John and Hassabis, Demis},
  journal      = {bioRxiv},
  title        = {Protein complex prediction with AlphaFold-Multimer},
  year         = {2021},
  elocation-id = {2021.10.04.463034},
  doi          = {10.1101/2021.10.04.463034},
  URL          = {https://www.biorxiv.org/content/early/2021/10/04/2021.10.04.463034},
  eprint       = {https://www.biorxiv.org/content/early/2021/10/04/2021.10.04.463034.full.pdf},
}