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Author SHA1 Message Date
Tom Ward
ab10514597 Replace period with hyphens in place, instead of declaring environment variable. 
PiperOrigin-RevId: 454618760
Change-Id: Ia6501f62ff3769a591497ac3413dc7526b31d1cc
v2.2.2 		2022-06-13 08:49:22 -07:00
Augustin Zidek
623cc1151c Bump AlphaFold version to 2.2.1. 
PiperOrigin-RevId: 454568110
Change-Id: Icd82696dacc250cfc3b7b71fc71d9fcd7669d032
v2.2.1 		2022-06-13 03:54:07 -07:00
Augustin Zidek
0f7ab1377a Pin protobuf version to 3.20.1. 
PiperOrigin-RevId: 454545752
Change-Id: I80656e917ee799fbf808002260634d2b1c38dca0
 2022-06-13 01:19:18 -07:00
Augustin Zidek
c9a9e8707c Clarify that AlphaFold works only under Linux. 
PiperOrigin-RevId: 453397654
Change-Id: I7e7d7dfc54a4c76b6a28b47630567677f35ecb30
 2022-06-07 03:41:14 -07:00
Tom Ward
55c948c1ae Add support for CUDA patch versions. 
PiperOrigin-RevId: 452008235
Change-Id: Ic6ae00a207d3b0eb809b039b5df9e7bebdaee558
 2022-05-31 03:57:27 -07:00
Augustin Zidek
d9e5e1d9c6 Fix jax.tree_multimap deprecation warning. 
PiperOrigin-RevId: 451994826
Change-Id: I4573baf61d33010c75de717d3b49f47bc9c6a8ac
 2022-05-31 02:20:42 -07:00
Augustin Zidek
197bd19ee3 Fix AlphaFold version in setup.py. 
PiperOrigin-RevId: 450934613
Change-Id: I2b5f7a740a3d9b87ccd495a65bcf8b4605c72585
 2022-05-25 08:56:48 -07:00
Augustin Zidek
c42a96f3a5 Mention the workaround for the Nvidia public key issue in the README. 
PiperOrigin-RevId: 449223429
Change-Id: Iaa59e839fe3822cc319a2ae5600ed36ee4d6777c
 2022-05-19 09:57:55 +01:00
Rebecca Chen
ed0886cb98 Silence some pytype errors. 
PiperOrigin-RevId: 436161190
Change-Id: Ia10df42f5f3f638a7a5b7b804c593a1e28a4ef44
 2022-03-21 03:33:46 -07:00
Augustin Zidek
b85ffe1079 Do not reuse the temporary output directory in run_alphafold_test. 
PiperOrigin-RevId: 435373710
Change-Id: I52c46cdfaccf73a456dfad52a2e3a103791653f4
 2022-03-17 09:55:32 -07:00
Alex Bridgland
0007c35227 Fix readme wording. 
PiperOrigin-RevId: 435113747
Change-Id: I8ca82eab2b88c1e5709abc479d5cb876af983c11
 2022-03-16 11:47:07 -07:00
Alex Bridgland
8cdec53989 Add info for getting in touch via email to colab and readme. 
PiperOrigin-RevId: 435031203
Change-Id: Ib3fdb9931219f3a139b324e751914a00f425fe2c
 2022-03-16 06:24:28 -07:00
Sebastian Bodenstein
918434f597 Add instructions for using multimer v1 model weights. 
PiperOrigin-RevId: 433187350
Change-Id: Ibb524ead7290d7fa0cbf609c5e2df105de5a5fc3
v2.2.0 		2022-03-08 05:43:22 -08:00
Rich Evans
481b8be229 Update open source between_residue_clash_loss to take into account multiple chains. 
PiperOrigin-RevId: 432934821
Change-Id: If5decaf654823a37c4270151039a12606f526f7a
 2022-03-07 06:59:58 -08:00
Rich Evans
3e046ad993 Update change-log to briefly describe the change in AlphaFold-Multimer models. 
PiperOrigin-RevId: 432931310
Change-Id: I19acd7eb7f3a63922481d9db3bc8d881efbbf550
 2022-03-07 06:38:35 -08:00
Sebastian Bodenstein
eba82a6521 Update multimer models to v2. 
PiperOrigin-RevId: 432150462
Change-Id: I508371123adf9dad20f4fe1082c7a6c7cd6815d4
 2022-03-03 03:05:55 -08:00
Sebastian Bodenstein
189f7d81f3 Remove unused function casp_model_names. 
PiperOrigin-RevId: 431956393
Change-Id: I1d97992967b8c276dfa978b91bc5066efdd3b62c
 2022-03-02 09:20:16 -08:00
Tom Ward
5f37a5a2ba No longer use runtime=nvidia to expose GPUs to the container. 
Instead use `DeviceRequest`, which is equivalent to running with `--gpu all`.

PiperOrigin-RevId: 431933575
Change-Id: Iee9f70ae8f291d16850e4f58349559d9468ef4d8
 2022-03-02 07:23:23 -08:00
Andrew Cowie
552586eba8 Simplify mounting of files. 
PiperOrigin-RevId: 430450270
Change-Id: Ie9f30b253d1cabf6b20e596732b9bab4963dc776
 2022-02-23 07:44:08 -08:00
Tim Green
16bab4d331 Remove unused bias arg in GlobalAttention. 
PiperOrigin-RevId: 430053169
Change-Id: Ia7461bc23d6e0c94f5bef8c1ded1c8306193e67e
 2022-02-21 09:11:12 -08:00
Rich Evans
89a6875fa4 Remove prokaryotic pairing from AFOS. 
PiperOrigin-RevId: 429521382
Change-Id: Ib9bfce50834bb129af0dbd3508cd0b92856a9bb1
 2022-02-18 03:05:19 -08:00
Rich Evans
b787ca2979 Fix random_seed overflow when seeds per model > 1. 
PiperOrigin-RevId: 429520386
Change-Id: Ic1ba2b31e25a0511fefe5d0d462fc5a218641a56
 2022-02-18 02:58:50 -08:00
Rich Evans
eb49d157be Enable multiple seeds per model for AlphaFold-Multimer. 
PiperOrigin-RevId: 429318717
Change-Id: Ib07df7ecd4bc52feea80a66c585ce51f332ac7a1
 2022-02-17 08:42:39 -08:00
Michael Figurnov
2cd61ade91 Improve support for num_recycle=0. 
Previously, setting num_recycle=0 in a pretrained recycling model skipped creating some Linears and LayerNorms. This meant that the the offsets of these modules were not applied leading to a degraded performance in that case.

PiperOrigin-RevId: 429075328
Change-Id: I9257f859521799f45e2deef3803c249311051225
 2022-02-16 10:02:48 -08:00
Tom Hennigan
929b188a3b Add split_rng=False (current default) to sharded_map. 
Haiku plans to make split_rng a required argument to hk.vmap in an upcoming
release. This change updates AlphaFold to preserve the current behaviour. We
also handle the case where users are using a release of Haiku without the
split_rng option, for these users split_rng=False is implied.

PiperOrigin-RevId: 428429472
Change-Id: I3292396eb330ffabf2f36f5364aa0ae1bc74cf71
 2022-02-13 23:43:43 -08:00
Augustin Zidek
b5ed6b76f4 Remove unused code. 
PiperOrigin-RevId: 427128482
Change-Id: I31134f7b0675260c79c799f14626140d74d745d4
 2022-02-08 01:27:17 -08:00
Augustin Zidek
9c4ac8a921 Add a note about the AlphaFold output directory. 
PiperOrigin-RevId: 425323152
Change-Id: Id1aa81316c95617e970ce014f4a331d1ed49ec02
 2022-01-31 03:18:59 -08:00
Augustin Zidek
e93a9eb64f Explain what to do if downloading PDB mmCIF files is too slow. 
PiperOrigin-RevId: 424887480
Change-Id: I4ea7a2aba785d037f49cf22c503ebebe3303e468
 2022-01-28 09:30:40 -08:00
Augustin Zidek
57a2455e5f Release code for v2.1.2 
PiperOrigin-RevId: 424591903
v2.1.2 		2022-01-27 14:41:09 +00:00
Tim Green
db039ef423 Update .dockerignore 
Don't ignore the README.md.
 2022-01-19 21:39:18 +00:00
Augustin-Zidek
8173117130 Update license of AlphaFold parameters. 2022-01-19 14:58:43 +00:00
Augustin Zidek
be37a41d6f Explain better how to run the AlphaFold-Multimer system. 
* Remove a confusing example that folds multiple complexes at once.
* Add examples on how to create the multimer input FASTA files.
* Add a note about the `model_preset` flag to the API changes.

PiperOrigin-RevId: 407774039
Change-Id: I80277c47febc977ba3956d0615944e62b0d5c3fc
v2.1.1 		2021-11-05 02:38:51 -07:00
Rich Evans
91b4322342 Fix PAE visualization for single chain predictions. 
PiperOrigin-RevId: 407773747
Change-Id: I8635dd77ecf366f4f5a362993b964adffc3ff186
 2021-11-05 02:36:42 -07:00
Andrew Cowie
c128d1aa2c Change fasta description used in data pipeline to be chain_<chain number>. 
PiperOrigin-RevId: 407584472
Change-Id: Icfa755722ddabff71d27f4a3d07f9e88a409c3a6
 2021-11-04 08:21:49 -07:00
Augustin-Zidek
0be2b30b98 Add code for AlphaFold-Multimer. 
PiperOrigin-RevId: 407076987
v2.1.0 		2021-11-02 14:33:58 +00:00
Augustin Zidek
1d43aaff94 Accept any ordering given by ListDir in the assert. 
Addresses https://github.com/deepmind/alphafold/issues/168.

PiperOrigin-RevId: 395907797
Change-Id: I28c7e951211c9cf6bd5e35d8dfaf57f22e843ed0
v2.0.1 		2021-09-10 05:34:22 -07:00
Augustin Zidek
50ecd75dac Skip obsolete PDB templates that don't have a replacement. 
Fixes https://github.com/deepmind/alphafold/issues/163.

PiperOrigin-RevId: 395878875
Change-Id: I99a9defa95547582bbfd9fec3ae821386274d77f
 2021-09-10 01:45:04 -07:00
Jake VanderPlas
98caef21ef Ensure values passed to jax.numpy functions are arrays rather than lists. 
Why? This will soon be a requirement in JAX; see https://github.com/google/jax/issues/7737

PiperOrigin-RevId: 394105499
Change-Id: I6f76e3f47b7906616c1f988be58d29c828414060
 2021-08-31 16:03:05 -07:00
Michael Figurnov
495d81ac1f Update the bibtex citation with the issue number and pages 
PiperOrigin-RevId: 393964942
Change-Id: I9c45191f726b40b66cea1cdd9f2efa2d4082b084
 2021-08-31 04:24:38 -07:00
DeepMind
b1d772d127 Fix TensorFlow versions in AlphaFold Colab notebook. 
PiperOrigin-RevId: 392861510
Change-Id: I266255479210e5c9b6cbc02977f4024d40c5b94d
 2021-08-25 03:51:49 -07:00
Augustin Zidek
99459effce Use tensorflow-cpu in setup.py as well. 
PiperOrigin-RevId: 390608262
Change-Id: I4c49aeb2aea362d578b7de43d16bf2e418fdd96d
 2021-08-13 07:29:34 -07:00
Augustin Zidek
cef198e0b6 Use pLDDT in the B-factor column of the output PDBs. 
PiperOrigin-RevId: 390566020
Change-Id: I3fafbe8246d0a5ad018f0398b39bf7dacee00468
 2021-08-13 02:13:24 -07:00
Augustin Zidek
f65e94fc71 Set versions of libraries AlphaFold Colab notebook depends on. 
PiperOrigin-RevId: 390553964
Change-Id: Ia5bc6e12ab3f1a7827b7d914c93f6990a1139780
 2021-08-13 00:39:52 -07:00
Augustin Zidek
05db248e91 Remove a redundant space. 
PiperOrigin-RevId: 390355132
Change-Id: I920a80db674541af41ee83ef3d5bd5255c782ee9
 2021-08-12 06:27:04 -07:00
Augustin Zidek
547cbddbf1 Add a direct link to PDB70 2020-05-13. 
PiperOrigin-RevId: 388195957
Change-Id: Id22b96c964a82e3450a5f457d8facd1e85b1e86a
 2021-08-02 05:22:45 -07:00
Augustin Zidek
41232dc756 Fix a few typos. 
PiperOrigin-RevId: 388172326
Change-Id: I11d9e498c226cd752947feb51b7d1eb343b4d7ab
 2021-08-02 02:04:31 -07:00
DeepMind
b88f8dacef Add a comment on the TriangleMultiplication notation. 
PiperOrigin-RevId: 387766802
Change-Id: Ic838537513fe1d5bf41facffffd44046e91c3fa3
 2021-07-30 02:47:12 -07:00
Tim Green
c9ffb0bc18 Use Ubuntu 18.04 LTS image. 
PiperOrigin-RevId: 387763552
Change-Id: I2a9753dfca2853de7f5c07c17cc7b2f7d12cf197
 2021-07-30 02:20:00 -07:00
Alex Bridgland
00c4c91dcc Log the total MSA size and number of templates. 
PiperOrigin-RevId: 387577557
Change-Id: I37c0a748dd3d8d3d179aae579c5504d7ec92ecaf
 2021-07-29 07:16:10 -07:00
Tim Green
b3ed8603e8 Switch to Tensorflow CPU-only. GPU not needed for data pipeline. 
PiperOrigin-RevId: 387576219
Change-Id: Ic735f068df2a3e9f53bed836f172c08f79ac231c
 2021-07-29 07:07:05 -07:00