Boltz-2 affinity prediction fails when using a CCD ligand

[tomgoddard]

The affinity.yaml example runs without errors with my Boltz 2.0.2 installation (Github SHA faa24790861edfc87dd52555d2bd8ad39a39aa85) and produces correct output but if I replace the SMILES string ligand with a CCD ligand EQT in affinity.yaml the structure prediction including the ligand works but the affinity prediction fails with hundreds of warnings

Cropper failed on affinity with error zero-size array to reduction operation minimum which has no identity. Skipping.

followed by hundreds of tracebacks ending with

RecursionError: maximum recursion depth exceeded

The full input and output is in the attached zip file. The output is in file named "output".

affinity_test2.zip

Boltz 2.0.2 was run using

boltz predict affinity.yaml --use_msa_server >& output

Here is the modified affinity.yaml file:

version: 1  # Optional, defaults to 1
sequences:
  - protein:
      id: A
      sequence: MVTPEGNVSLVDESLLVGVTDEDRAVRSAHQFYERLIGLWAPAVMEAAHELGVFAALAEAPADSGELARRLDCDARAMRVLLDALYAYDVIDRIHDTNGFRYLLSAEARECLLPGTLFSLVGKFMHDINVAWPAWRNLAEVVRHGARDTSGAESPNGIAQEDYESLVGGINFWAPPIVTTLSRKLRASGRSGDATASVLDVGCGTGLYSQLLLREFPRWTATGLDVERIATLANAQALRLGVEERFATRAGDFWRGGWGTGYDLVLFANIFHLQTPASAVRLMRHAAACLAPDGLVAVVDQIVDADREPKTPQDRFALLFAASMTNTGGGDAYTFQEYEEWFTAAGLQRIETLDTPMHRILLARRATEPSAVPEGQASENLYFQ
  - ligand:
      id: B
      ccd: EQT
properties:
  - affinity:
      binder: B

[jwohlwend]

Should be fixed in the latest release and on the main branch. Please test and let me know! Make sure to delete your current output folder.

[tomgoddard]

Thanks! I tested 3 affinity predictions with CCD ligands and all are working now.