8151373a6b
Do not deduplicate unpaired MSA in featurisation
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If we generated the MSA ourselves, it is already deduplicated. If it is user-provided, keep it as is to prevent destroying desired pairing.
Reported in https://github.com/google-deepmind/alphafold3/issues/331 .
PiperOrigin-RevId: 736489145
Change-Id: If0ffe4908e8a4dd93855962b299a7fe84a849119
2025-03-13 06:53:48 -07:00
3f706280fe
Make pseudo_beta_fn work with both np and jnp.
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Fix kindly suggested in https://github.com/google-deepmind/alphafold3/pull/350/files by @popfido.
PiperOrigin-RevId: 736443698
Change-Id: I4c3c20c2291d445976f88f8f44a7f1ac6d6b3cbb
2025-03-13 03:31:33 -07:00
9c0d146f32
Release the GIL when running CifDict::FromString
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PiperOrigin-RevId: 735819832
Change-Id: Ibb4323ef474850bffa2a54ab227d9654091fd07a
2025-03-11 11:06:59 -07:00
b641827717
Make output file names unique for all seeds/samples
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PiperOrigin-RevId: 735310700
Change-Id: I4f42ed52cd38a48d189eb6ba4d563117caff18b0
2025-03-10 03:30:01 -07:00
98e03d944f
Internal change
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PiperOrigin-RevId: 735308466
Change-Id: I9787f324d3357ebb7755987553fc17f988adc232
2025-03-10 03:20:20 -07:00
e9b2f0ce3b
Set ref_max_modified_date when running featurisation
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Addresses https://github.com/google-deepmind/alphafold3/issues/334 .
PiperOrigin-RevId: 735299819
Change-Id: Ib16739fc33ea927b243e4e481582c0a9cdb4128a
2025-03-10 02:43:05 -07:00
2eb2a50b62
Add support for specifying the user-defined CCD using a file
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Prompted by https://github.com/google-deepmind/alphafold3/issues/325 .
PiperOrigin-RevId: 734476458
Change-Id: I0fa681f6e3cb77284b3a3b4b6f429cef14e1638b
2025-03-07 02:29:39 -08:00
eca194325f
Internal change
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PiperOrigin-RevId: 733714336
Change-Id: I82d75c1bfdeed90160c83f81e95a6d9a304c8815
2025-03-05 06:49:18 -08:00
dd1953ad6d
Add a flag to force the output directory to be used even if it already exists and is non-empty
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Suggested in https://github.com/google-deepmind/alphafold3/issues/326 .
PiperOrigin-RevId: 733342793
Change-Id: I7abe85ea4b15f358cc8a4cae3361ed338f9edaac
2025-03-04 08:40:51 -08:00
c848e85140
Check that MSA, template, or user CCD are not paths
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PiperOrigin-RevId: 733325882
Change-Id: I97ff9d17150929ce4b0beff8a0138b1c2ab497f5
2025-03-04 07:45:34 -08:00
792e61e099
Add chirality checking utility.
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PiperOrigin-RevId: 729120255
Change-Id: I4c50b4b1fc7c4b24334804cbd1e0e032784a09c4
2025-02-20 08:22:36 -08:00
daf815510f
Noise level embeddings use fixed fourier weights/bias rather than generate with fixed seed.
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PiperOrigin-RevId: 728200849
Change-Id: I58416b4a351b90138d3c575be498a66a5ba8907e
2025-02-18 07:30:55 -08:00
e015e27daf
Internal change
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PiperOrigin-RevId: 728189441
Change-Id: I0b0c2b4d18ba0b34ee646d14a94aa62eb2fe9a26
2025-02-18 06:49:12 -08:00
2e8c8ec10d
Tidy run_alphafold_test.
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PiperOrigin-RevId: 728178668
Change-Id: I2f787256bc92db972d1f06cfb7f051bb513f39f6
2025-02-18 06:09:33 -08:00
dc7bb0d8b5
Update the version in pyproject.toml and version.py to 3.0.1
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Fixes https://github.com/google-deepmind/alphafold3/issues/303 .
PiperOrigin-RevId: 726923825
Change-Id: I60712e20fafc1f67b9b2d4a5f6260d17acd90d3b
2025-02-14 07:39:48 -08:00
a29153b9e8
run_alphafold_test - use different seed and add masked RMSD checks.
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PiperOrigin-RevId: 725972439
Change-Id: I25ff2d8bb2f816eb3295e99113d7f445f14bc7ad
2025-02-12 02:37:00 -08:00
fe088acf7d
Add translations of legal terms
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PiperOrigin-RevId: 725547540
Change-Id: Iee1354e816d9fd8737caf49358c14f84e77de4cb
2025-02-11 02:36:39 -08:00
bb0e5415ef
Remove excess code from run_alphafold_test, clean up the testing a little.
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PiperOrigin-RevId: 725260840
Change-Id: I5199a62b3b3cac9e898993dc65620c8d135451a9
2025-02-10 10:16:55 -08:00
90c3d05aa4
run_alphafold_test: fix variable name
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PiperOrigin-RevId: 725206516
Change-Id: I87b44ea7aba461d60b5cc27564ad26dd62e784ae
2025-02-10 07:28:18 -08:00
e7510b1117
Crop output embeddings to num_tokens, removing padding tokens
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Reported in https://github.com/google-deepmind/alphafold3/issues/294 .
PiperOrigin-RevId: 725180868
Change-Id: If5616162d655494d73fdfa9b8ecc0bbed092b403
2025-02-10 05:52:32 -08:00
a3cf058e92
Check uniqueness and residue numbers when validating bonds
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PiperOrigin-RevId: 723912607
Change-Id: I668632a9737e69243618a00a2fefc5c542203c3d
2025-02-06 06:30:12 -08:00
e825aea738
Include more details in log/print lines
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PiperOrigin-RevId: 723494655
Change-Id: I03c463e3f1fd2c04477818f2102adeabb99c2fc5
2025-02-05 06:59:38 -08:00
7f6edd04a4
Fix templates to work with empty a3m
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Second fix needed for https://github.com/google-deepmind/alphafold3/issues/244
PiperOrigin-RevId: 721790067
Change-Id: Ib3eebf30f270b45d08cc94057a4feca5b4753d63
2025-01-31 08:55:20 -08:00
4d0e7a6e06
Fix a crash when Hmmsearch finds no hits
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Fixes https://github.com/google-deepmind/alphafold3/issues/244 .
PiperOrigin-RevId: 721761887
Change-Id: I386fcda7b11f8a9904eda81b1c82a6c3d506aebb
2025-01-31 07:08:47 -08:00
bb334af5ee
Internal change
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PiperOrigin-RevId: 721759769
Change-Id: Ife74e1d501514a43402406f9494d2f716669ca4e
2025-01-31 07:00:01 -08:00
bb174e6ba9
Fix user CCD validation to check all provided records
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PiperOrigin-RevId: 721292410
Change-Id: Ie843e314a9ef8ab309558b792dcda278ee33eed7
2025-01-30 01:17:29 -08:00
140fe3c649
Internal change
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PiperOrigin-RevId: 720558092
Change-Id: I448fabf929489910a667ffd66fa17bd09c912276
2025-01-28 06:53:22 -08:00
66cda58f70
Add support for useStructureTemplate and maxTemplateDate in the AlphaFold Server JSON format
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PiperOrigin-RevId: 720196790
Change-Id: I5ff911d7fda3473b1ad9008d7673f8821cd615f7
2025-01-27 09:22:25 -08:00
7acc88f926
Make AlphaFold logging more consistent, logical, and brief
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PiperOrigin-RevId: 720097581
Change-Id: Ic6d489d742aaf4d3bbdb7fcfa39910f4ee682e35
2025-01-27 03:11:06 -08:00
a5c1185367
Fix token chain IDs to be the same as the input chain IDs and add a test
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PiperOrigin-RevId: 719296728
Change-Id: I2f8ec7091276b4a2f8bec0b69995d4c3cb16e69d
2025-01-24 15:45:04 +00:00
4f1d653edd
Internal change
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PiperOrigin-RevId: 719289023
Change-Id: Idb530bd493174fa910ec51529e058b60fa305723
2025-01-24 15:44:49 +00:00
2420622656
Clean up logging and reduce duplicate outputs
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PiperOrigin-RevId: 718910656
Change-Id: I6b2bb962e6ba33f1c4b0f3a2f6c358d701867a44
2025-01-24 15:44:32 +00:00
4cd0a5b893
Disable tqdm when running in non-TTY environment
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PiperOrigin-RevId: 718830513
Change-Id: I6f41a46e2342a815f4868f57f343887616dbcce2
2025-01-24 15:44:15 +00:00
231efc9bb9
Antibody-antigen docs: mention that we always used the first bioassembly
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PiperOrigin-RevId: 717556878
2025-01-20 17:36:41 +00:00
20ad0a21eb
Add antibody-antigen metadata from AlphaFold 3 paper
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PiperOrigin-RevId: 717534278
2025-01-20 17:21:34 +00:00
121716e144
Provide per-residue pLDDT in the output mmCIF
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PiperOrigin-RevId: 717490268
2025-01-20 17:16:23 +00:00
5c0379ccd8
Do not test ref_pos which depends on a specific RDKit version
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PiperOrigin-RevId: 716300884
2025-01-16 19:04:20 +00:00
155f844c5a
Fix a typo: featursation -> featurisation
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PiperOrigin-RevId: 716236614
2025-01-16 18:06:23 +00:00
f40741228a
Raise when GPU capability is 7 and flash_attention_implementation is not XLA
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PiperOrigin-RevId: 716213043
2025-01-16 14:37:42 +00:00
bb9a51b0a4
Add num_recycles and num_seeds flags
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PiperOrigin-RevId: 716202654
2025-01-16 14:29:40 +00:00
537a9e1d16
Explain the pair_transition_shard_spec format
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PiperOrigin-RevId: 715803444
2025-01-16 14:27:02 +00:00
f33a2ebad2
jax.numpy.clip: update use of deprecated arguments
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PiperOrigin-RevId: 714894410
2025-01-16 14:24:05 +00:00
ea040346e1
Use true chain type for paired_msa creation
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PiperOrigin-RevId: 713617070
2025-01-09 12:59:41 +00:00
3d06f4bfad
Fix RASA calculation to work with arbitrary chain IDs
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PiperOrigin-RevId: 713612793
2025-01-09 11:59:59 +00:00
17b02c977b
Make it possible to set which GPU to use on a multi-GPU system
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PiperOrigin-RevId: 713260432
2025-01-09 11:56:13 +00:00
765844c82f
Test embedding shapes
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PiperOrigin-RevId: 712930622
2025-01-09 11:55:13 +00:00
721348dc08
Add documentation for the embeddings output file
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PiperOrigin-RevId: 712560296
2025-01-09 11:52:41 +00:00
1bb31e736b
Allow _chem_comp_atom.pdbx_leaving_atom_flag to be optional in user CCD
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PiperOrigin-RevId: 712539542
2025-01-06 16:53:10 +00:00
a647a31398
Fix incorrect bonds in the input documentation
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PiperOrigin-RevId: 712526835
2025-01-06 15:54:43 +00:00
a9c88317d3
Remove allow_pickle=True which does not exist in Numpy < 2.2.0
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PiperOrigin-RevId: 712523919
2025-01-06 15:38:17 +00:00
