All pull requests

Pull requests

• Add a --write_distogram flag to save the distogram in .npz (AF3 mimic)

  #699·Jahaciel12 opened Jul 28, 2026·

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• docs: clarify affinity output conversion

  #698·Michaelihc opened Jul 28, 2026·

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• Minor update on msa request timeout and recursive search of job definitions in directory.

  #688·neilswainston opened Jun 1, 2026·

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• Fix 4 bugs + add FlashAttention-2 / SDPA GPU acceleration (--flash_attn)

  #682·mooreneural opened May 18, 2026·

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• test: add regression test for CPU autocast device-type behavior

  #671·khanfs opened Apr 13, 2026·

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• fix: validate checkpoint files before loading and surface actionable errors for empty/corrupt weights

  #668·khanfs opened Apr 2, 2026·

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• Added timing to inference

  #666·Pablo-Lemos opened Mar 27, 2026·

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• docs: add Boltz-DAP link for multi-GPU inference

  #661·coqylight opened Mar 18, 2026·

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• Fold-CP: A Context Parallelism Framework for Biomolecular Modeling

  #658·DejunL opened Mar 15, 2026Collaborator·

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• use mol cache when tar archive missing

  #656·tlitfin opened Mar 13, 2026·

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• Add optional capture of transition MLP intermediates

  #651·vash02 opened Mar 2, 2026·

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• Added symmetry.pkl and ccd.rdb writing to the training data prep pipeline

  #614·chmnk opened Nov 11, 2025·

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• Add weighted RMSD validation and shared CIF writer

  #610·AlvandVahedi opened Nov 5, 2025·

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• Specify which device to run on

  #603·delalamo opened Oct 25, 2025·

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• Fixed --write_full_pae and --write_full_pde options. Fixes #585

  #602·tomgoddard opened Oct 24, 2025Contributor·

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• Replace urllib.request.urlretrieve with requests library

  #601·ianandersonlol opened Oct 24, 2025·

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• Add docker support for inference

  #595·juliocesar-io opened Oct 18, 2025·

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• Fix #583 parsing .csv MSA files removes paired sequences.

  #584·tomgoddard opened Sep 26, 2025Contributor·

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• Fix #581 constructing MSA feature array

  #582·tomgoddard opened Sep 26, 2025Contributor·

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• Only consider standard residues in consecutive CA filter

  #576·bcm49 opened Sep 17, 2025·

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• Allow template to have indel compared to the original sequence

  #538·shunsakuraba opened Aug 13, 2025·

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• Add basic support for mps (Apple Silicon) as an accelerator

  #527·colbyford opened Aug 5, 2025·

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• Add PDB loader helper & extend schema to accept pdb_file.

  #517·Bioparticles opened Jul 30, 2025·

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• Generify MinimumLengthFilter name

  #516·amorehead opened Jul 29, 2025·

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• Look up MSA files relative to input fasta/yaml

  #500·Emrys-Merlin opened Jul 22, 2025·

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