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  • 1dc1e0ad0b Improve typing and error checks in mask_mean main Augustin Zidek 2026-05-29 05:50:28 -07:00
  • eb5154f441 Fix two typos in docstrings Augustin Zidek 2026-05-28 03:07:50 -07:00
  • b712a3d0a1 Fix descriptions being dropped in some places for protein/RNA chains Augustin Zidek 2026-05-22 04:03:16 -07:00
  • 7d4a236f71 Fix typing issues revealed by Pyrefly in structure_tables Augustin Zidek 2026-05-20 04:22:24 -07:00
  • 5a3d6b6365 Fix typing issues in constants modules revealed by Pyrefly Augustin Zidek 2026-05-18 05:21:28 -07:00
  • 10b18bf702 Fix typing issue in _get_rna_msa revealed by Pyrefly Augustin Zidek 2026-05-14 08:12:53 -07:00
  • 9556a1c9da Fix typing issues found using Pyrefly in folding_input and its test Augustin Zidek 2026-05-13 03:29:07 -07:00
  • 9ea7db2d3b Fix KeyError in string_array.remap_multiple for Python 3.14 Augustin Zidek 2026-05-12 09:47:20 -07:00
  • 8d283f3baf Add basic chem_comp_atoms/chem_comp_bonds data to ChemCompEntry Augustin Zidek 2026-05-12 06:12:52 -07:00
  • 881212473a Fix a typing issue (passing ndarray instead of a list) Augustin Zidek 2026-05-11 05:36:10 -07:00
  • 8850da42a6 Validate that the output_dir is always set and add a missing argument in overload Augustin Zidek 2026-05-11 01:48:25 -07:00
  • eba618977e Fix typing of Nhmmer z values, these are floats Augustin Zidek 2026-05-07 02:52:49 -07:00
  • 62a93afa5d Fix glycan O1 leaving-atom cleanup for standalone glycans Augustin Zidek 2026-05-06 08:23:42 -07:00
  • 97639fff6f Pass correctly all options to Jackhmmer/Nhmmer Augustin Zidek 2026-05-06 06:54:18 -07:00
  • 481beec819 Add fallback version for Docker Augustin Zidek 2026-05-06 04:59:26 -07:00
  • 011b6cf42b Refactor to_mmcif_dict to not use getattr Augustin Zidek 2026-04-24 04:05:49 -07:00
  • 3dfc5a91be Support dynamic version for dev and releases Augustin Zidek 2026-04-23 07:33:19 -07:00
  • de4e7a4f2d Remove unused cleaned_struc from ConvertModelOutput Augustin Zidek 2026-04-22 05:55:33 -07:00
  • 6f882ad224 Use pathlib.Path.home() instead of os.environ.get('HOME') Augustin Zidek 2026-04-22 05:14:19 -07:00
  • e9adcd4dbf Clean up structure cleaning - remove unused code paths Augustin Zidek 2026-04-22 02:32:41 -07:00
  • cfeeedd24d Optimize CIF loop parsing by ~4% - remove modulo in the hot path Augustin Zidek 2026-04-21 01:36:47 -07:00
  • f6a5aecf6e Bump the version to v3.0.2 v3.0.2 Augustin Zidek 2026-04-20 01:53:54 -07:00
  • 24cded8e86 Expose an API to run the model pipeline with a Structure DeepMind 2026-04-10 05:54:00 -07:00
  • 177df6a5c1 Remove obsolete : ... from all python functions parameters annotations. Amer Elsheikh 2026-04-09 14:47:53 -07:00
  • 87bd9e678d Add a missing newline for consistency Augustin Zidek 2026-04-01 04:39:31 -07:00
  • f236bc4e8c Use && instead of ; when building HMMER to stop if there are errors Augustin Zidek 2026-04-01 04:13:36 -07:00
  • 4d20ed540b Import from collections.abc instead of typing Augustin Zidek 2026-03-31 09:31:22 -07:00
  • 58d22e2db5 Fix some Structure type issues uncovered by Pyrefly Augustin Zidek 2026-03-30 06:34:00 -07:00
  • 0f82e0c94c wrap reader into io.BufferedReader. Akvile Zemgulyte 2026-03-25 12:25:09 -07:00
  • 02650a5ded Use --run_*=false instead of --norun_* in docs. Augustin Zidek 2026-03-20 02:19:01 -07:00
  • 608edb684d Update to Tokamax 0.0.11 and JAX 0.9.1 Augustin Zidek 2026-03-10 08:35:55 -07:00
  • 5f7eb57e22 Improve the error when components.cif is not found Augustin Zidek 2026-03-06 09:15:36 -08:00
  • e58932a036 Use the same license format in .h files as in .cc files Augustin Zidek 2026-03-04 06:38:29 -08:00
  • 6daafb546f Remove unused utility functions Augustin Zidek 2026-02-26 09:31:46 -08:00
  • 1e9ece2cfb Respect LIBCIFPP_DATA_PATH if set, rather than attempt to find it. James Spencer 2026-02-25 05:01:28 -08:00
  • 9e10da6725 Add CifDict.to_dict() method for faster serialisation Augustin Zidek 2026-02-23 09:40:47 -08:00
  • 203e93dfc6 Use const for iter/keys/values/items and release GIL for contains in KeyView Augustin Zidek 2026-02-23 08:58:26 -08:00
  • 4ca8a65692 Document the discrepancy between AlphaFold 3 and AlphaFold Server in Known Issues Augustin Zidek 2026-02-20 07:33:38 -08:00
  • ea1667690e Update Docker build instructions for AlmaLinux/Rocky/RHEL users Augustin Zidek 2026-02-20 03:40:43 -08:00
  • c20f070859 Exit if any of the required programs is not installed Augustin Zidek 2026-02-20 02:24:48 -08:00
  • 703d5c8375 Make sharded Jackhmmer result merging more robust in case of e-value ties Augustin Zidek 2026-02-16 08:29:47 -08:00
  • 2761bf1cfc Use the logging name instead of the one from fold_input Augustin Zidek 2026-02-16 06:13:13 -08:00
  • e2b8ffd6a7 Implement relevant improvements from #615 Augustin Zidek 2026-02-11 03:27:10 -08:00
  • ceb32296c7 Move CONTRIBUTING.md to the root directory Augustin Zidek 2026-02-09 00:40:58 -08:00
  • ebfe70a27a Update Tokamax to 0.0.10 Augustin Zidek 2026-02-04 09:41:06 -08:00
  • c13d928a34 Update RDKit to 2025.9.4 Augustin Zidek 2026-02-04 09:14:59 -08:00
  • cf4bb5bd9e Use UV_LINK_MODE=copy to prevent Docker build issues on some platforms Augustin Zidek 2026-02-04 08:18:24 -08:00
  • 6b50e384d3 Add the glycan modeling paper in the list of community tools Augustin Zidek 2026-01-29 07:02:51 -08:00
  • 22b9ab80d3 Make AlphaFold 3 uv setup compatible with aarch64 Augustin Zidek 2026-01-20 01:55:25 -08:00
  • c7a1ad5c51 Add a documentation on model parameters Augustin Zidek 2026-01-16 04:03:40 -08:00
  • f6032f0f6a Add a flag to compress large output files using zstandard Augustin Zidek 2026-01-15 06:10:57 -08:00
  • 8d0a8db07e Make everything past model_runner mandatory kwarg in process_fold_input Augustin Zidek 2026-01-15 05:15:05 -08:00
  • 3e2bc0ce35 Add JAAG to community tools documentation Augustin Zidek 2026-01-15 03:22:08 -08:00
  • 8d37fc1cb9 Modernize setup, switch to Python 3.12, and migrate to uv Augustin Zidek 2026-01-15 02:13:49 -08:00
  • 2f40800a3a Force the legacy git backend to prevent build errors with new git versions Augustin Zidek 2026-01-14 06:31:36 -08:00
  • d7ab550d1b Update CONTRIBUTING.md with a policy for AI-generated code Augustin Zidek 2026-01-12 09:37:14 -08:00
  • b78e215394 Update tokamax dependency to version 0.0.8 Augustin Zidek 2026-01-09 08:39:04 -08:00
  • a701815575 Upgrade GitHub Actions to the latest version (v6) Augustin Zidek 2026-01-09 03:04:58 -08:00
  • 8eaae04e1d Add CONTRIBUTING.md Augustin Zidek 2026-01-09 03:04:47 -08:00
  • 3a09f049bf remove unused msa and template store code. Josh Abramson 2025-12-02 03:30:47 -08:00
  • 389078218c Migrate AF3 to tokamax.gated_linear_unit and tokamax.dot_product_attention. Ryan Pachauri 2025-11-29 18:54:14 -08:00
  • 2e3703e82a fix support for sharded databases James Spencer 2025-11-25 14:00:57 -08:00
  • e850301268 Internal change Akvile Zemgulyte 2025-11-18 01:33:07 -08:00
  • f3e86f27df Add safe_pickle module for secure loading of pickled data. Foromo Daniel Soromou 2025-11-04 07:55:33 -08:00
  • c0ab1c40f3 Include fully unresolved chains in Structure when going from mmCIF Augustin Zidek 2025-11-03 08:51:25 -08:00
  • 9ecec8d19e Handle CRLF line endings in CIF parsing Augustin Zidek 2025-11-03 03:12:52 -08:00
  • aed6e82cb1 Add an option to make entity IDs unique in structure.concat Augustin Zidek 2025-10-30 07:46:15 -07:00
  • 805adc3863 Add option to run Jackhmmer/Nhmmer genetic search in sharded mode (10-30x faster) Augustin Zidek 2025-10-29 07:54:40 -07:00
  • 46fe3f0f60 Add documentation for pre-computing and reusing MSA and templates Augustin Zidek 2025-10-28 10:08:11 -07:00
  • 9c183c8234 Make the ordering of the performance documentation more logical Augustin Zidek 2025-10-27 11:34:53 -07:00
  • ec65897c60 Make unnecessarily public attributes private in tool wrappers Augustin Zidek 2025-10-24 08:26:38 -07:00
  • b77e80447f Increase ranking score upper bound tolerance Augustin Zidek 2025-10-21 09:56:17 -07:00
  • cf404610b5 Explicitly set backend='triton' in pallas_call invocations. Benjamin Chetioui 2025-10-21 02:25:57 -07:00
  • c9121bf646 Improve error message when testing expected scores Augustin Zidek 2025-10-20 01:27:50 -07:00
  • 3c89cc7b89 Improve error message and consistency of ordering Augustin Zidek 2025-10-17 08:05:29 -07:00
  • 142e4bc6e5 Fix residue mapping bug in _maybe_add_missing_scheme_tables Augustin Zidek 2025-10-09 02:29:20 -07:00
  • 03a6c295e5 Return b factors and occupancy from to_res_arrays() DeepMind 2025-10-02 08:31:01 -07:00
  • a8ecdb2d7a Cache the underlying CCD dictionary instead of the whole CCD object. Augustin Zidek 2025-09-08 01:43:38 -07:00
  • 85a03ec086 Use the CPU count available to the process instead of total CPU count Augustin Zidek 2025-09-04 10:20:08 -07:00
  • b467f92160 Improve validation of CIF files. Augustin Zidek 2025-09-03 08:50:25 -07:00
  • 4208665547 Make sure Structure doesn't have a name that is an empty string Augustin Zidek 2025-09-03 08:09:37 -07:00
  • 0ea324ce74 Validate that a non-loop CIF key has only a single value Augustin Zidek 2025-09-03 01:47:50 -07:00
  • 7b816f4035 Add support for protein/DNA/RNA/ligand descriptions Augustin Zidek 2025-09-02 04:11:09 -07:00
  • a2b03dab51 Validate the number of tokens in a CIF loop Augustin Zidek 2025-08-21 08:17:08 -07:00
  • 2e2ffc10ab Improve the gpu_device flag description Augustin Zidek 2025-08-07 03:52:57 -07:00
  • 563896c75c Improve comments in CifDict Augustin Zidek 2025-08-06 04:04:43 -07:00
  • 722437b4ff Fix handling of tokens that contain quotes surrounded by spaces in CifDict::ToString Augustin Zidek 2025-08-06 02:04:51 -07:00
  • f2edd59f87 Undo backwards incompatible Triton API change Augustin Zidek 2025-08-04 01:36:43 -07:00
  • 903a931d36 Improve documentation on running data pipeline and inference separately Augustin Zidek 2025-08-01 03:56:12 -07:00
  • 3c4de6bb9b Update the output documentation with case sensitivity and force_output_dir Augustin Zidek 2025-07-31 09:39:33 -07:00
  • ec4254ac5d Integrate Triton up to [6af1c4b5](6af1c4b507) Tori Baker 2025-07-31 00:13:23 -07:00
  • a14376d249 Make the folding input sanitised name case sensitive Augustin Zidek 2025-07-30 04:45:29 -07:00
  • 042202363b Suppress Jackhmmer stdout and stderr when checking whether seq_limit is supported Augustin Zidek 2025-07-14 09:10:39 -07:00
  • 751a4b8612 Add support for --seq_limit in Jackhmmer - significantly reduces peak RAM use Augustin Zidek 2025-07-14 01:59:30 -07:00
  • a209008f6f Add validation of template JSON keys Augustin Zidek 2025-07-02 01:52:55 -07:00
  • 53d2acc5b7 Make query sequence logging less verbose in MSA tools Augustin Zidek 2025-06-25 05:35:39 -07:00
  • 6cf825575b Fix the documentation for RNA MSA Augustin Zidek 2025-06-23 10:43:04 -07:00
  • 0f865a667c Configure tests to explicitly use jax_threefry_partitionable=False. Josh Abramson 2025-06-11 09:26:11 -07:00
  • 3f8871d982 Add empty paired MSA in the full example Augustin Zidek 2025-06-11 06:31:39 -07:00
  • bc73f5652b Remove redundant aliases mmcif.tokenize and mmcif.split_line Augustin Zidek 2025-06-06 06:51:22 -07:00