06d28cad2e
Update to Ubuntu 24.04 / CUDA 12.6.3 base image and use Python 3.12
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PiperOrigin-RevId: 765229057
Change-Id: I7b1c8234fd1b067e62e308116d603f0e3d375972
2025-06-04 05:20:40 -07:00
6cc6364a8d
Internal change
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PiperOrigin-RevId: 765224124
Change-Id: I1aad4e6d7cee2e27e3f360c1845b4c4111b4eeec
2025-06-04 05:20:24 -07:00
64723739f5
Update to Ubuntu 24.04 / CUDA 12.6.3 base image and use Python 3.12
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PiperOrigin-RevId: 765219906
Change-Id: I271f442012ee30356ef316eda87abd231319a673
2025-05-30 09:49:16 -07:00
935d47f8d4
Reduce the size of the Docker/Singularity container
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PiperOrigin-RevId: 765209187
Change-Id: I075874b51b243a3e75bc8078ea81920f1984dbc5
2025-05-30 17:12:44 +01:00
5ecdfe883a
Make register_dataclass compatible with JAX < v0.4.36
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PiperOrigin-RevId: 765135084
Change-Id: Ifc89843c9706c38cbe6a9e2ed3c4f918b2c36954
2025-05-30 04:36:47 -07:00
6a34fea9a2
Remove unnecessary dependency on structure test_utils
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PiperOrigin-RevId: 765132514
Change-Id: Ia1acdf55267083741c294864792f25009f5f4542
2025-05-30 04:25:22 -07:00
565f286892
Remove unnecessary chex dependency
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PiperOrigin-RevId: 765086591
Change-Id: I34d7e7b83073d84fe083ee091a3b54e90dcdeba3
2025-05-30 01:44:10 -07:00
17afe151ea
Improve AlphaFold 3 Dockerfile
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* Use `apt-get` instead of `apt`. Should not make much difference since we set the `--quiet` flag though.
* Document better the rationale behind building HMMER from scratch.
* Check SHA-256 hash of the downloaded HMMER tar file.
* Addresses critique from https://www.linkedin.com/pulse/getting-alphafold-3-run-amd-gpus-owain-kenway-egite/ .
PiperOrigin-RevId: 763703614
Change-Id: Ibc231b8c31d1d891f537e2765094c1710a76eaea
2025-05-27 02:54:58 -07:00
e64804c49f
Add a flag to enable skipping unpaired MSA deduplication against paired MSA
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Addresses an issue reported in https://github.com/google-deepmind/alphafold3/issues/404 .
PiperOrigin-RevId: 761917258
Change-Id: I26592af0f40481a40ba611130739a40a62e4a6dc
2025-05-22 05:11:12 -07:00
fbabfe25b0
Name the deletion_matrix feature correctly when produced
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PiperOrigin-RevId: 761487725
Change-Id: I99435be9cb0d1b043c3441b1f498ed31c7783f23
2025-05-21 05:45:06 -07:00
a20a29e021
Internal change.
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PiperOrigin-RevId: 761425868
Change-Id: I1f24f047ad737a6509bc0866e7d86bcb8d725791
2025-05-21 01:58:37 -07:00
62074340cf
Validate bonded atoms against the CCD
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When user specifies a list of bonds in bondedAtomPairs, make sure the atoms that are specified are actually valid atoms within each of the components.
Addresses https://github.com/google-deepmind/alphafold3/issues/406 .
PiperOrigin-RevId: 760603843
Change-Id: Ia1747e47c8ab45557173adff122cf32310c57c34
2025-05-19 06:41:00 -07:00
2d466dc791
Do not limit parallelism of make when building HMMER
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PiperOrigin-RevId: 759516856
Change-Id: I1c926a30edf87f0d3e6feccb42e474ff96c06d6d
2025-05-16 02:07:09 -07:00
0cda346e40
Make template featurisation error messages clearer
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Users hit this already multiple times:
https://github.com/google-deepmind/alphafold3/issues/317
https://github.com/google-deepmind/alphafold3/issues/416
PiperOrigin-RevId: 759101683
Change-Id: I15c21208f5843e02a73579d4a10310ae26aa8494
2025-05-15 05:18:51 -07:00
38a9333b54
Fix flag descriptions for save_embeddings and save_distogram
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PiperOrigin-RevId: 758180480
Change-Id: Iaccb91b1f0be4a6ea6d4b9b77c55d5593a4afd03
2025-05-13 05:52:26 -07:00
267ab05055
Save embeddings as float16 instead of float32 to make them 2x smaller
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PiperOrigin-RevId: 758140305
Change-Id: I70cb7adc53440ce19d20fa89d64bbb36b84b13f7
2025-05-13 03:23:02 -07:00
424201003f
Add an option to save the distogram
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Based on the implementation in https://github.com/google-deepmind/alphafold3/pull/345 by @PasqM.
PiperOrigin-RevId: 758128292
Change-Id: I868d43018833f889d858e5c9a7d687a44cfd3e82
2025-05-13 02:41:03 -07:00
6a0e8b2afe
[alphafold3] avoid use of deprecated jax.util APIs
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jax.util was deprecated in JAX v0.6.0, and will be removed in JAX v0.7.0.
PiperOrigin-RevId: 756703396
Change-Id: I9e0b0267c4a403939aeb413f59d8ff7ef3ee390b
2025-05-09 04:09:41 -07:00
e274d27978
Internal change.
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PiperOrigin-RevId: 748595613
Change-Id: I7e84c89c15c4887b51a66fc708d15c835aa8a0a8
2025-04-17 01:49:55 -07:00
7a4a2f7142
Mention unresolved residues in template documentation
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Fixes https://github.com/google-deepmind/alphafold3/issues/373 .
PiperOrigin-RevId: 747342015
Change-Id: I09586c5d00cda84db18764cdc735b057f2b4d749
2025-04-14 03:40:15 -07:00
5fbae81a9e
Remove unused code
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PiperOrigin-RevId: 744678177
Change-Id: Ib2444fa8ba6c9850f2331d133e038883fc32e681
2025-04-09 14:07:50 +01:00
dfd8b9cb63
Fix test numerics.
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PiperOrigin-RevId: 742607438
Change-Id: I6670124aa30f3000a07efb753ccf75c959881bbe
2025-04-01 02:34:34 -07:00
69b749cb71
Use unsigned int for bias pipelining hack in Triton FlashAttention. A bitwise AND of 0xFFFFFFFF with a negative integer leads to overflow, which got caught by the latest Triton integration.
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PiperOrigin-RevId: 739868199
Change-Id: I732e36901c18e4a07c8907c52412b7475d2ebb64
2025-03-24 03:01:53 -07:00
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
