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39 Commits

Author SHA1 Message Date
Dariusz Lasecki
2ca41b1991 Deprecate the AlphaFold 2 notebook 
PiperOrigin-RevId: 720951827
Change-Id: Ie30be1252f6e6dc4038be6b307395f45e638d5ad
 2025-01-29 06:32:24 -08:00
Augustin Zidek
11a991ea66 Bump Python in Colab to 3.11. 
PiperOrigin-RevId: 718812632
Change-Id: I54b901e7a361a63a2c3f366535dbe2cd3e792b99
 2025-01-23 04:40:44 -08:00
Augustin Zidek
6350ddd63b Update Conda to 24.11.1 to fix Docker build failure and small improvements to the Dockerfile. 
PiperOrigin-RevId: 707479885
Change-Id: Ic3c71229bcf3a935cae86aee64ee7c02220e1085
 2024-12-18 03:26:03 -08:00
Hamish Tomlinson
4d4a1aea99 Update openmm in AlphaFold colab. 
PiperOrigin-RevId: 625019041
Change-Id: If6e5b23edeb1f06bd91b4daf1c449d12ed407895
 2024-04-15 11:08:04 -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
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
DeepMind
6a3af1adb3 Rename get_pae_json function 
PiperOrigin-RevId: 529057928
Change-Id: Idf420cf43eaa6f3e4c6cf10475cba0e06f7165ee
 2023-05-03 05:03:52 -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
 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
Hamish Tomlinson
502d7a1954 Add cell execution order error checking. 
PiperOrigin-RevId: 508360288
Change-Id: I1d976ac08808e4356f89c29428668c1093816056
 2023-02-09 06:46:31 -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
Hamish Tomlinson
d6d2fc0789 Bump version to 2.3.1 
PiperOrigin-RevId: 501297397
Change-Id: Ic1bb166581047e0e8c46845f41f8c55c10f32ef9
 2023-01-11 09:06:18 -08:00
Augustin Zidek
4b726a2ecd Speed up Colab multimer MSA search: fetch each db chunk only once and run all queries against it. 
PiperOrigin-RevId: 496636186
Change-Id: I0a428b6269f8e1bcb1a6efb33cad2fc70b0d1f35
 2022-12-20 05:31:57 -08:00
Andrew Cowie
e80e25243f Restore the max sequence limit to 4000 now that unified memory is fixed. 
PiperOrigin-RevId: 495602713
Change-Id: I091644565b3bbb2e95ee434c6cd80d6d54d677dc
 2022-12-15 08:43:59 -08:00
Andrew Cowie
a0b0cd9cc9 Set environment variables before any other code is executed. 
PiperOrigin-RevId: 495028896
Change-Id: I3b1a6ddceca1961bffdaba443e7db47bbfbc4fad
 2022-12-13 08:27:34 -08:00
Augustin Zidek
9b18d6a966 Release code for v2.3.0 
PiperOrigin-RevId: 494507694
 2022-12-11 11:06:50 +00:00
Hamish Tomlinson
4494af848e Bump python in colab to 3.8 2022-12-01 16:42:53 -06:00
Hamish Tomlinson
ff4f1c6138 Update version in colab 
PiperOrigin-RevId: 480643781
Change-Id: Id4bfa90b71cd59b148a3c2a61ddb65c41192712b
 2022-10-12 09:29:02 -07:00
Hamish Tomlinson
2eb6c0cc58 Make using GPU in relaxation optional, with default not to use. 
PiperOrigin-RevId: 471264036
Change-Id: Ic2201048f5c9d9d741cb20fdf46f2f27986587f4
 2022-08-31 08:39:33 -07:00
Augustin Zidek
dad1f286ae Pin Conda version to 4.13.0. 
PiperOrigin-RevId: 469937063
Change-Id: I24ebf6e1afc9e6f64200ee195ff708be27edb327
 2022-08-25 02:09:15 -07:00
DeepMind
6f6e8c2e50 Changed PAE json output to new format that matches the format used in AFDB. 
PiperOrigin-RevId: 467198544
Change-Id: I504dc91c993b10dbb1cef448ef8eaa1161186acb
 2022-08-12 06:44:37 -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
eba82a6521 Update multimer models to v2. 
PiperOrigin-RevId: 432150462
Change-Id: I508371123adf9dad20f4fe1082c7a6c7cd6815d4
 2022-03-03 03:05:55 -08:00
Rich Evans
89a6875fa4 Remove prokaryotic pairing from AFOS. 
PiperOrigin-RevId: 429521382
Change-Id: Ib9bfce50834bb129af0dbd3508cd0b92856a9bb1
 2022-02-18 03:05:19 -08:00
Augustin Zidek
57a2455e5f Release code for v2.1.2 
PiperOrigin-RevId: 424591903
 2022-01-27 14:41:09 +00:00
Augustin-Zidek
8173117130 Update license of AlphaFold parameters. 2022-01-19 14:58:43 +00:00
Rich Evans
91b4322342 Fix PAE visualization for single chain predictions. 
PiperOrigin-RevId: 407773747
Change-Id: I8635dd77ecf366f4f5a362993b964adffc3ff186
 2021-11-05 02:36:42 -07:00
Augustin-Zidek
0be2b30b98 Add code for AlphaFold-Multimer. 
PiperOrigin-RevId: 407076987
 2021-11-02 14:33:58 +00:00
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
f65e94fc71 Set versions of libraries AlphaFold Colab notebook depends on. 
PiperOrigin-RevId: 390553964
Change-Id: Ia5bc6e12ab3f1a7827b7d914c93f6990a1139780
 2021-08-13 00:39:52 -07:00
Saran Tunyasuvunakool
0bab1bf84d Add a Colab notebook, add reduced BFD, and various other fixes and improvements. 
PiperOrigin-RevId: 386228948
 2021-07-22 15:16:43 +01:00