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7b816f4035
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Add support for protein/DNA/RNA/ligand descriptions
Suggested in https://github.com/google-deepmind/alphafold3/issues/496.
PiperOrigin-RevId: 802081348
Change-Id: I666466fd6a770b6f4a891ed33e6a26651d600c4a
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2025-09-02 04:11:53 -07:00 |
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903a931d36
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Improve documentation on running data pipeline and inference separately
Prompted by https://github.com/google-deepmind/alphafold3/issues/485.
PiperOrigin-RevId: 789700619
Change-Id: I0e876a1130cc537421e8916fcad1230302196b64
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2025-08-01 03:56:58 -07:00 |
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3c4de6bb9b
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Update the output documentation with case sensitivity and force_output_dir
PiperOrigin-RevId: 789369238
Change-Id: I2ccab4e220300646dba2f8882a82ad1e21c1523f
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2025-07-31 09:40:19 -07:00 |
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6cf825575b
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Fix the documentation for RNA MSA
Fixes https://github.com/google-deepmind/alphafold3/issues/448
PiperOrigin-RevId: 774840546
Change-Id: Icd7e34c190052aa6da82d2edffa4050f36e00837
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2025-06-23 10:43:45 -07:00 |
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3f8871d982
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Add empty paired MSA in the full example
Fixes https://github.com/google-deepmind/alphafold3/issues/444
PiperOrigin-RevId: 770122170
Change-Id: Ia82dec2f389cefcdc8c03afe6ec5ac2717b3ac1d
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2025-06-11 06:33:43 -07:00 |
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e64804c49f
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Add a flag to enable skipping unpaired MSA deduplication against paired MSA
Addresses an issue reported in https://github.com/google-deepmind/alphafold3/issues/404.
PiperOrigin-RevId: 761917258
Change-Id: I26592af0f40481a40ba611130739a40a62e4a6dc
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2025-05-22 05:11:12 -07:00 |
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267ab05055
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Save embeddings as float16 instead of float32 to make them 2x smaller
PiperOrigin-RevId: 758140305
Change-Id: I70cb7adc53440ce19d20fa89d64bbb36b84b13f7
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2025-05-13 03:23:02 -07:00 |
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424201003f
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Add an option to save the distogram
Based on the implementation in https://github.com/google-deepmind/alphafold3/pull/345 by @PasqM.
PiperOrigin-RevId: 758128292
Change-Id: I868d43018833f889d858e5c9a7d687a44cfd3e82
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2025-05-13 02:41:03 -07:00 |
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7a4a2f7142
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Mention unresolved residues in template documentation
Fixes https://github.com/google-deepmind/alphafold3/issues/373.
PiperOrigin-RevId: 747342015
Change-Id: I09586c5d00cda84db18764cdc735b057f2b4d749
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2025-04-14 03:40:15 -07:00 |
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b641827717
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Make output file names unique for all seeds/samples
PiperOrigin-RevId: 735310700
Change-Id: I4f42ed52cd38a48d189eb6ba4d563117caff18b0
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2025-03-10 03:30:01 -07:00 |
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2eb2a50b62
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Add support for specifying the user-defined CCD using a file
Prompted by https://github.com/google-deepmind/alphafold3/issues/325.
PiperOrigin-RevId: 734476458
Change-Id: I0fa681f6e3cb77284b3a3b4b6f429cef14e1638b
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2025-03-07 02:29:39 -08:00 |
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792e61e099
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Add chirality checking utility.
PiperOrigin-RevId: 729120255
Change-Id: I4c50b4b1fc7c4b24334804cbd1e0e032784a09c4
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2025-02-20 08:22:36 -08:00 |
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231efc9bb9
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Antibody-antigen docs: mention that we always used the first bioassembly
PiperOrigin-RevId: 717556878
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2025-01-20 17:36:41 +00:00 |
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20ad0a21eb
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Add antibody-antigen metadata from AlphaFold 3 paper
PiperOrigin-RevId: 717534278
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2025-01-20 17:21:34 +00:00 |
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537a9e1d16
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Explain the pair_transition_shard_spec format
PiperOrigin-RevId: 715803444
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2025-01-16 14:27:02 +00:00 |
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721348dc08
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Add documentation for the embeddings output file
PiperOrigin-RevId: 712560296
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2025-01-09 11:52:41 +00:00 |
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1bb31e736b
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Allow _chem_comp_atom.pdbx_leaving_atom_flag to be optional in user CCD
PiperOrigin-RevId: 712539542
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2025-01-06 16:53:10 +00:00 |
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a647a31398
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Fix incorrect bonds in the input documentation
PiperOrigin-RevId: 712526835
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2025-01-06 15:54:43 +00:00 |
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b380a7c085
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Fix a typo in the input documentation for the mmcifPath
PiperOrigin-RevId: 708231647
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2024-12-20 11:11:57 +00:00 |
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802891f85a
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Update custom ligand input documentation
PiperOrigin-RevId: 707914242
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2024-12-19 18:06:14 +00:00 |
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8a285f023d
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Add a conformer_max_iterations flag to allow increasing number of RDKit iterations
PiperOrigin-RevId: 707855849
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2024-12-19 11:45:34 +00:00 |
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2b8e912865
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Document SMILES string escaping in the input JSON
PiperOrigin-RevId: 707488936
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2024-12-18 12:02:36 +00:00 |
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450a38d3f0
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Fix a typo in the input format documentation
PiperOrigin-RevId: 706726897
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2024-12-17 10:34:43 +00:00 |
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781d8d04f9
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Add XLA flag workaround for CUDA Capability 7.x GPUs
PiperOrigin-RevId: 705559274
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2024-12-13 06:35:21 +00:00 |
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2e562355ba
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Expand documentation around running run_alphafold.py
PiperOrigin-RevId: 704634652
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2024-12-10 15:45:44 +00:00 |
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14c741fa8d
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Point users towards the many useful command-line flags for run_alphafold.py.
PiperOrigin-RevId: 704442670
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2024-12-10 15:45:12 +00:00 |
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0a46c7a398
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Add "Incorrect handling of two-letter atoms in SMILES ligands" into known issues
PiperOrigin-RevId: 703531029
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2024-12-06 17:55:55 +00:00 |
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63132c4e46
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Ensure user CCD contains all necessary fields and improve docs
PiperOrigin-RevId: 703469364
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2024-12-06 14:54:20 +00:00 |
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6bba345002
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Allow specifying MSA and templates as external files and bump input format version
PiperOrigin-RevId: 702263653
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2024-12-03 13:11:05 +00:00 |
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86116e9efb
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Note that Docker containers requires CUDA 12.6 on the host machine
PiperOrigin-RevId: 702253330
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2024-12-03 13:09:13 +00:00 |
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f24cf5de56
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Fix incorrect statement about paired/unpaired MSA in the input documentation
PiperOrigin-RevId: 701276770
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2024-11-29 14:45:49 +00:00 |
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e56abb7a55
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Update advice for different devices
PiperOrigin-RevId: 700993687
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2024-11-28 16:44:11 +00:00 |
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cdbcf41b71
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Allow running template search when MSA provided
PiperOrigin-RevId: 699993191
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2024-11-25 16:41:11 +00:00 |
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fd4873f661
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Clean up installation instructions
PiperOrigin-RevId: 699941708
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2024-11-25 13:16:06 +00:00 |
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1942639ba8
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Make it possible to run template-free, but still search for MSA
PiperOrigin-RevId: 699920007
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2024-11-25 12:09:27 +00:00 |
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eec6d72af6
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Fix bad capitalisation of userCCD in input documentation
PiperOrigin-RevId: 698783729
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2024-11-21 16:10:59 +00:00 |
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65328c9cfb
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Fix Singularity run commands
PiperOrigin-RevId: 698024666
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2024-11-19 16:21:50 +00:00 |
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b108eedc04
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Add a table of H100 inference timings to docs/performance.md
PiperOrigin-RevId: 697644061
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2024-11-18 16:53:42 +00:00 |
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4b2b567103
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Documentation updates - older GPUs and JAX installation
PiperOrigin-RevId: 697634146
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2024-11-18 16:21:14 +00:00 |
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01b87c245c
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Replace the db download script with a faster one and add GCP post-processing scripts
PiperOrigin-RevId: 697631760
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2024-11-18 16:12:16 +00:00 |
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2ffe43f574
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Fix pallas GLU kernel on large inputs and update documentation for compilation buckets.
PiperOrigin-RevId: 696513320
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2024-11-14 15:20:38 +00:00 |
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44e1fd572a
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Update fetch_databases to use os.access to test permissions
PiperOrigin-RevId: 696093699
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2024-11-13 13:29:43 +00:00 |
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e07682c064
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Update singularity instructions (thanks davidecarlson!)
PiperOrigin-RevId: 695790186
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2024-11-12 18:39:19 +00:00 |
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0341fb7f24
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Documentation fixes and silence irrelevant warning
PiperOrigin-RevId: 695740242
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2024-11-12 16:24:34 +00:00 |
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77f84ea6a7
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Small documentation fixes
PiperOrigin-RevId: 695328242
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2024-11-11 15:26:46 +00:00 |
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4f52a3bb62
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Initial release of AlphaFold 3
PiperOrigin-RevId: 695257954
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2024-11-11 10:42:47 +00:00 |
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