NotImplementedError: Pocket constraints not implemented yet

[zongmingchua]

I installed and verified intallation of boltz-1 in a clean conda env
pip install boltz -U
Requirement already satisfied: boltz in /home/zchua/anaconda3/envs/boltz/lib/python3.12/site-packages (0.3.2)

Also tried clearing cache ~/.boltz/ as well as using a fresh install in a separate conda env but encountered the same error. Boltz-1 otherwise works fine without constraints submitted.

yaml file that was ran:

version: 1  # Optional, defaults to 1
sequences:
#spike protein fragment
  - protein:
      id: 'A'
      sequence: TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPC
#HC Fab of SW186
  - protein:
      id: 'B'
      sequence: QVQLQQSGAELVKPGASVKISCKASGVAFSSYWMNWVKQRPGKGLEWIGQIYPGDGDTNYNGKFKGKATLTADKSSSTAYMQLSSLSSEDSAVYFCARGFIATVEETMDYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCAA
#LC Fab of SW186
  - protein:
      id: 'C'
      sequence: DIQMTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQSHTLPWTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGRVLARASPSPSPSLSREAC

constraints:
  - pocket:
      binder: 'B'
      contacts: [['A', 104], ['A', 105]]

# Run command: 
# boltz predict --out_dir ~/boltz_output ~/12.18.24_8DT3_constrained.yaml --use_msa_server

Error message:

File "/home/zchua/anaconda3/envs/boltz/lib/python3.12/site-packages/boltz/data/parse/schema.py", line 796, in parse_boltz_schema
    raise NotImplementedError(msg)
NotImplementedError: Pocket constraints not implemented yet: B - [['A', 104], ['A', 105]]

I did previously install an older version of boltz-1 - but since a fresh install in a new conda env did not resolve this problem I am a bit stuck right now, thanks for reading :)

[gcorso]

Hi @zongmingchua can you try again with version 0.4.0?