Boltz1 on Modal

ligand.yaml

sequences:
  - protein:
      id: [A, B]
      sequence: MVTPEGNVSLVDESLLVGVTDEDRAVRSAHQFYERLIGLWAPAVMEAAHELGVFAALAEAPADSGELARRLDCDARAMRVLLDALYAYDVIDRIHDTNGFRYLLSAEARECLLPGTLFSLVGKFMHDINVAWPAWRNLAEVVRHGARDTSGAESPNGIAQEDYESLVGGINFWAPPIVTTLSRKLRASGRSGDATASVLDVGCGTGLYSQLLLREFPRWTATGLDVERIATLANAQALRLGVEERFATRAGDFWRGGWGTGYDLVLFANIFHLQTPASAVRLMRHAAACLAPDGLVAVVDQIVDADREPKTPQDRFALLFAASMTNTGGGDAYTFQEYEEWFTAAGLQRIETLDTPMHRILLARRATEPSAVPEGQASENLYFQ
      msa: ./seq1.a3m
  - ligand:
      id: [C, D]
      ccd: SAH
  - ligand:
      id: [E, F]
      smiles: N[C@@H](Cc1ccc(O)cc1)C(=O)O

modal-boltz.py

import modal

image = (
    modal.Image.debian_slim()
    .pip_install("uv")
    .run_commands("uv pip install --system --compile-bytecode boltz")
    .apt_install("wget")
    .run_commands('mkdir /root/.boltz/')
    .run_commands('wget -O /root/.boltz/ccd.pkl "https://www.dropbox.com/scl/fi/h4mjhcbhzzkkj4piu1k6x/ccd.pkl?rlkey=p43trjrs9ots4qk84ygk24seu&st=bymcsoqe&dl=1"')
    .run_commands('wget -O /root/.boltz/boltz1.ckpt "https://www.dropbox.com/scl/fi/8qo9aryyttzp97z74dchn/boltz1.ckpt?rlkey=jvxl2jsn0kajnyfmesbj4lb89&st=dipi1sbw&dl=1"')
)

app = modal.App(name="boltzrun", image=image)

@app.function(
    timeout = 60*5, # 5 mins - increase obviously for bigger or multiple runs. 
    gpu="A100" # got OOMs with anything smaller than A100 on example yaml. 
)
def boltzrun(msadata, ligandyaml):
    # save MSA and input YAML into instance:
    with open('./seq1.a3m', 'w') as f:
        f.write(msadata)
    with open('./ligand.yaml', 'w') as f:
        f.write(ligandyaml)

    import os
    # run boltz:
    os.system('boltz predict ligand.yaml')
    # package outputs:
    os.system("tar czvf temp.tar.gz boltz_results_ligand")
    # load outputs as binary data and return it
    output = open('./temp.tar.gz', 'rb').read()
    return output
    

@app.local_entrypoint()
def main():
    msadata = open('../boltz/examples/msa/seq1.a3m').read()
    ligandyaml = open('./ligand.yaml').read()
    #receive binary data:
    output = boltzrun.remote(msadata, ligandyaml)
    #write
    with open('./result.tar.gz', 'wb') as f:
        f.write(output)

    #now you unpack outside of the script with 'tar xzvf result.tar.gz'