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Author SHA1 Message Date
Hamish Tomlinson
dbe2a438eb Update requirements: 
- Ubuntu to 20.04
- Cuda to 12.2.2
- Tensorflow to 2.16.1
- Jax to 0.4.26
- Openmm to 8.0.0

PiperOrigin-RevId: 624094170
Change-Id: I49391c3f721e93ac8ccd5a4483cdb6f2ec61cd3b
 2024-04-12 01:57:58 -07:00
Hamish Tomlinson
7e7de59cd2 Remove deprecated PRNGKeyArray. 
PiperOrigin-RevId: 623494831
Change-Id: Ie15c1d517fd7b34662d69d05205151d9c7021da4
 2024-04-10 08:01:46 -07:00
Hamish Tomlinson
5208f1b70e Update jax, haiku and chex versions. 
PiperOrigin-RevId: 623469847
Change-Id: I64a812e00e099f6503b9aa1e0cfde1133ea8a774
 2024-04-10 06:04:14 -07:00
Augustin Zidek
6d95d1982e Fix how we extract mmCIF resolution (fix ordering issue). 
Thanks to @ljarosch for reporting and suggesting a fix in https://github.com/google-deepmind/alphafold/issues/915.

PiperOrigin-RevId: 617817805
Change-Id: I46738b248a054d06fe902626cff161fe521e99f1
 2024-03-21 06:03:34 -07:00
Hamish Tomlinson
032e2f2673 Update conda to 24.1.2. 
PiperOrigin-RevId: 611404763
Change-Id: Icc7d637e1de9fa82da76aa8dccd9b9dce8be6246
 2024-02-29 03:01:46 -08:00
Hamish Tomlinson
632ef575c6 Uninstall keras in notebook to avoid the keras initializer fault. 
PiperOrigin-RevId: 603012242
Change-Id: Icf0120e1baf1278862ea62402a86c9eac5932710
 2024-01-31 04:50:56 -08:00
Matthew Johnson
4f447319e4 Loosen overly tight numerical tolerances to allow for one-time random value 
change from https://github.com/google/jax/discussions/18480

PiperOrigin-RevId: 591243740
Change-Id: I86457bfcaae65771ccb4e39d3e4d929335d71652
 2023-12-15 07:13:05 -08:00
Peter Hawkins
1fa9200c7f [JAX] Replace uses of jax.devices("cpu") with jax.local_devices(backend="cpu"). 
An upcoming change to JAX will include non-local (addressable) CPU devices in jax.devices() when JAX is used multicontroller-style, where there are multiple Python processes.

This change preserves the current behavior by replacing uses of jax.devices("cpu"), which previously only returned local devices, with jax.local_devices("cpu"), which will return local devices both now and in the future.

This change is always be safe (i.e., it should always preserve the previous behavior) but it may sometimes be unnecessary if code is never used in a multicontroller setting.

PiperOrigin-RevId: 582680953
Change-Id: I614739de052185c42932ddb91d1d464751442f65
 2023-11-15 08:11:45 -08:00
Augustin Zidek
f715f016d8 Revert a change that is not compatible with JAX 0.3.25. 
PiperOrigin-RevId: 578486539
Change-Id: Id0e535ebf75916b5179791d093ca714e343ccb69
 2023-11-01 05:32:02 -07:00
Augustin Zidek
f78c589304 Update wwPDB paths from ftp.wwpdb.org to files.wwpdb.org. 
See https://www.wwpdb.org/news/news?year=2022#6303be3b707ecd4f63b3d3d9 for the wwPDB announcement.

PiperOrigin-RevId: 575762003
Change-Id: If25ea2777c33b03f03b27d54046c71753cb33038
 2023-10-23 03:14:49 -07:00
DeepMind
bbc133b060 Add assertion to aid type checking. 
PiperOrigin-RevId: 568220760
Change-Id: Ied9e33692bbd7fb8c02b039f64688cc31f005885
 2023-09-25 08:04:59 -07:00
Jake VanderPlas
a8875a9c0d Replace deprecated PRNGKeyArray isinstance checks 
For details, see https://github.com/google/jax/pull/17297

PiperOrigin-RevId: 565705637
Change-Id: I88c4a3003166580e28111c4e410c8412c23ccb9d
 2023-09-15 09:54:49 -07:00
Augustin Zidek
22f6919174 Add a cast to prevent future Pandas typing issues. 
PiperOrigin-RevId: 563001314
Change-Id: I441729e337e5bf782f70beeb92d8cf0c870bc98a
 2023-09-05 23:17:42 -07:00
Augustin Zidek
c9431c4c12 Remove unused imports. 
PiperOrigin-RevId: 562507313
Change-Id: Ic82f113455c0be50c0af1e9df4498991072e554c
 2023-09-04 03:02:00 -07:00
DeepMind
bbe8a844e0 Fix: return correct renaming mask. 
PiperOrigin-RevId: 558140222
Change-Id: I7fb69e8a7c9ce95a26d0816fb8c1c02cba68f660
 2023-08-18 07:26:42 -07:00
Augustin Zidek
82ef354ca3 Add Conda lib path to LD_LIBRARY_PATH. 
PiperOrigin-RevId: 557487629
Change-Id: I73908cf1cad254bd2bd5ec3189ac7bbae2c5f0b9
 2023-08-16 08:03:22 -07:00
Hamish Tomlinson
7c9114c842 Bump jax to 0.4.14 and haiku to 0.0.10. 
PiperOrigin-RevId: 555464931
Change-Id: I382adafe6e7f35960eeffaa1cceeaeb5e08ce87d
 2023-08-10 06:28:00 -07:00
Jana Cavojska
69afc4df91 Downgrade to pyopenssl 22.0.0 to fix compatibility issue 
PiperOrigin-RevId: 549671013
Change-Id: I8e27f86b7a02b74f8bed9437dd6d17ad8d9cabfc
 2023-07-20 10:30:20 -07:00
Jana Cavojska
6cb85e9684 Update Conda in Colab and fix dependency issues 
PiperOrigin-RevId: 549256996
Change-Id: I1c5fb68a1abe6016a89740cab1e033876c248c56
 2023-07-19 02:55:00 -07:00
Dariusz Lasecki
6c4d833fbd Add saving Protein to mmCIF file and reading Protein from mmCIF file. 
PiperOrigin-RevId: 540873522
Change-Id: I502551e47df701cb39f72b380e9e4e818ea9c04c
 2023-06-16 07:35:46 -07:00
Augustin Zidek
4bd3ff76cc Use HTTPS instead of FTP to download all databases and switch to a faster mirror for UniRef90. 
PiperOrigin-RevId: 536973190
Change-Id: I358b78dbeb401cd066688af69eca7b50858b69d1
 2023-06-01 03:34:10 -07:00
Jake VanderPlas
9bbfdc7c81 alphafold: make compatible with JAX custom PRNG 
This change will not modify the code's behavior, but will make the code compatible with JAX's new custom PRNG, which will soon be the default; see https://github.com/google/jax/issues/9263.

PiperOrigin-RevId: 533069215
Change-Id: Ia98e2dd1e33e1135a628f7dc37c56b50da6c51a5
 2023-05-18 03:06:00 -07:00
Jake VanderPlas
d885c55750 Future-proof alphafold prng test for jax custom PRNG 
PRNG changes described in https://github.com/google/jax/issues/9263. After this change, raw key buffers will no longer be accessible via indexing operations.

PiperOrigin-RevId: 530930051
Change-Id: I02b0759c528c393f7ce1109bae83da13cfd68bfe
 2023-05-10 09:32:25 -07:00
DeepMind
6a3af1adb3 Rename get_pae_json function 
PiperOrigin-RevId: 529057928
Change-Id: Idf420cf43eaa6f3e4c6cf10475cba0e06f7165ee
 2023-05-03 05:03:52 -07:00
Augustin Zidek
c1e92dc524 Bump SciPy version from 1.7.0 to 1.7.3 for compatibility with Python 3.10. 
PiperOrigin-RevId: 528849422
Change-Id: I22068400c1cd764be88e34739cbc9992d023fcda
 2023-05-02 11:58:26 -07:00
Augustin Zidek
955737f12c Upgrade OpenMM from 7.5.1 to 7.7.0 and bump Colab Python version to 3.10. 
We don't need to patch anymore as the fix has been included upstream.

PiperOrigin-RevId: 528742992
Change-Id: I804707216bf00367c8346dffde69aeffcb7dad8f
 2023-05-02 04:33:51 -07:00
DeepMind
2819de4ddd Add pLDDT and PAE files saving to AF runner, update Colab. 
PAE methods are migrated from Colab notebook_utils.py to AFOS and included in run_alphafold.py to save a new file. Colab notebook is updated accordingly. pLDDT data is transformed into JSON as saved as well, as an additional output file.

PiperOrigin-RevId: 525687298
Change-Id: If7f0bcf7d3b39901dae58a67958eaa5687645de2
 2023-04-20 02:22:31 -07:00
Hamish Tomlinson
4d83e3fc08 Bump version to 2.3.2 in setup.py and colab. 
PiperOrigin-RevId: 523341685
Change-Id: Ie332a4db056adb2d42bcd2f4006e4258b8908507
 2023-04-11 02:23:17 -07:00
Hamish Tomlinson
3f31725591 Upgrade pyopenssl in colab. 
PiperOrigin-RevId: 519687065
Change-Id: Ib72232f3f4d09ee8f3a2cc312d7a83d8b892a23e
v2.3.2 		2023-03-27 04:50:49 -07:00
Hamish Tomlinson
e51692c9ae Change softmax to use where and float32. 
PiperOrigin-RevId: 519675443
Change-Id: If87e6d16189ddcc03bb8435308d37f5919353107
 2023-03-27 03:44:27 -07:00
Hamish Tomlinson
e1d2d53af8 Re-enable form cellview. 
PiperOrigin-RevId: 517987165
Change-Id: I6fbb517b9991a9b0bb83bfd612f2c5158067d60f
 2023-03-20 09:16:22 -07:00
Augustin Zidek
2e6a78f08b Bump Python in Colab to 3.9. 
PiperOrigin-RevId: 515639889
Change-Id: If06429d31e0b82986436d747bf05ef95f8ec91fb
 2023-03-10 08:11:13 -08:00
Hamish Tomlinson
651fe8cdb2 Turn off bfloat16 in colab. 
PiperOrigin-RevId: 514446997
Change-Id: I8b1113d39b62f7124d301e40c4b2e4418618bb7c
 2023-03-06 10:13:56 -08:00
Augustin Zidek
6918c085b3 Fix incorrect type annotations. 
PiperOrigin-RevId: 512029306
Change-Id: If2237867d38dd5e0002cd516f68f7eaa67b63443
 2023-02-24 03:35:53 -08:00
Hamish Tomlinson
a54b34c11c Improve readme explanation of ranked_*.pdb. 
PiperOrigin-RevId: 511185129
Change-Id: I035bff2f22d5b863771711f300de335e4fb3e396
 2023-02-21 06:35:33 -08:00
Hamish Tomlinson
502d7a1954 Add cell execution order error checking. 
PiperOrigin-RevId: 508360288
Change-Id: I1d976ac08808e4356f89c29428668c1093816056
 2023-02-09 06:46:31 -08:00
Augustin Zidek
665ebc3013 Make _chem_comp.type logic case-insensitive. 
The specification http://mmcif.rcsb.org/dictionaries/mmcif_pdbx.dic/Items/_chem_comp.type.html says this is case-insensitive and AFDB files use capitalised "PEPTIDE".

PiperOrigin-RevId: 506266651
Change-Id: I2f16d729e41c722c74f94a3b308c7159b289a5c3
 2023-02-01 03:30:56 -08:00
Hamish Tomlinson
18e12d6131 Update readme for relaxation flag. 
PiperOrigin-RevId: 505130241
Change-Id: I09f20581b13b23590e1202de014d96fe9c9063ac
 2023-01-27 08:57:21 -08:00
Augustin Zidek
41871c0989 Improve documentation on how to install aria2c. 
PiperOrigin-RevId: 505082237
Change-Id: I84f2fb3a2952456c6baf4dd2052fff4178b1af4f
 2023-01-27 04:16:34 -08:00
Hamish Tomlinson
fed21ddd04 Update tensorflow 
PiperOrigin-RevId: 503968820
Change-Id: I2ab071d6872bc2f9eaab4a464aed684036b966d2
 2023-01-23 06:29:11 -08:00
Hamish Tomlinson
91ac85ac72 Remove jax dependency from results pkl 
PiperOrigin-RevId: 502584418
Change-Id: I8ab14363a6342726691213bbeb180c0a8ff7f932
 2023-01-17 07:50:31 -08:00
Hamish Tomlinson
684ffa19c6 Add ability to only run relax for the best unrelaxed model. 
PiperOrigin-RevId: 501851892
Change-Id: I7484c2aa7ac30af611d88cfa8d632096c262824a
 2023-01-13 08:17:34 -08:00
Hamish Tomlinson
0d9a24b284 Use shutil to zip and download colab outputs 
PiperOrigin-RevId: 501595938
Change-Id: Ib586090d13279eca1371f0e0b046379b728a3e87
 2023-01-12 10:04:26 -08:00
Augustin Zidek
a3941673e9 Fix typo in a comment in residue constants. 
PiperOrigin-RevId: 501515486
Change-Id: I2a86a64ebbf0ab8222689268755ba3b7780878e5
v2.3.1 		2023-01-12 03:06:31 -08:00
Hamish Tomlinson
d6d2fc0789 Bump version to 2.3.1 
PiperOrigin-RevId: 501297397
Change-Id: Ic1bb166581047e0e8c46845f41f8c55c10f32ef9
 2023-01-11 09:06:18 -08:00
DeepMind
e3231de135 Update of README.md 
PiperOrigin-RevId: 501279176
Change-Id: I9cf92212322b29691844973ded9e337e81b3a9fd
 2023-01-11 07:42:36 -08:00
Ali Cowen-Rivers
8f1ebd5896 Fix GPU relax for longer chains by pinning large memory ops to cpu. 
PiperOrigin-RevId: 501105389
Change-Id: I6c981d1d3231e008ebae192edb4586479eb5eb34
 2023-01-10 15:09:17 -08:00
Ali Cowen-Rivers
420fb08fd5 Adding recycle information for timings. 
PiperOrigin-RevId: 497360470
Change-Id: I3a9f3ba608ac3ceeaaccfe281a82d43fae1d265e
 2022-12-23 05:51:47 -08:00
Ali Cowen-Rivers
a9e5451fcf Adding prediction timings to README. 
PiperOrigin-RevId: 496937349
Change-Id: I9e9f447b3ce11d1b5a5c7433aeae7b03a3ed19e9
 2022-12-21 09:15:20 -08:00
Josh Abramson
f96e254e6d Add eval_dropout option for using dropout in trunk at eval time. 
PiperOrigin-RevId: 496885301
Change-Id: I42de2dd13784e2b358320349398a3fc88ee0d708
 2022-12-21 04:03:26 -08:00