openfold-3-benchmarking/runner.yaml at main · aqlaboratory/openfold-3-benchmarking · GitHub

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pl_trainer_args:
  flux_plugin: true
  precision: 32-true

experiment_settings:
  skip_existing: true

model_update:
  presets:
    - predict
    - low_mem
  custom:
    architecture:
      shared:
        num_recycles: 10
      heads:
        pae:
          enabled: true
      msa:
        msa_module_embedder:
          subsample_main_msa: False
          subsample_all_msa: True

output_writer_settings:
  structure_format: cif

data_module_args:
  num_workers: 1

dataset_config_kwargs:
  msa:
    max_seq_counts:
      uniprot_hits: 50000
      mgnify_hits: 5000
      uniref90_hits: 10000
      bfd_hits: 100000000
      cfdb_hits: 10000000
      bfd_uniref_hits: 10000000
      rfam_hits: 10000
      rnacentral_hits: 10000
      nt_hits: 10000
      nucleotide_collection_hits: 10000
    msas_to_pair: ["uniprot_hits"]
    aln_order:
      - uniref90_hits
      - bfd_hits
      - cfdb_hits
      - bfd_uniref_hits
      - mgnify_hits
      - rfam_hits
      - rnacentral_hits
      - nt_hits
      - nucleotide_collection_hits
    subsample_main: False
  template:
    take_top_k: True

template_preprocessor_settings:
  cache_directory: "benchmark_templates"