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1b10a6058c8a4d4e1e57c6c7fe19efdf8fed0b7f
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23 Commits

Author SHA1 Message Date
Augustin Zidek
1b10a6058c Revert: Bring model config creation in one place by simplifying num_ensemble setting 
PiperOrigin-RevId: 819744016
Change-Id: I15a626c646b45c8c23d6dbd5c8d75314920cbf12
 2025-10-15 07:23:02 -07:00
Augustin Zidek
dbaafbcdea Run Pyformat on the entire AlphaFold 2 codebase. 
PiperOrigin-RevId: 812761281
Change-Id: Iee46a5b923fa6ea512d5ca25fd06f75578e88276
 2025-09-29 06:28:09 -07:00
Harsh Tiku
ecdc85103f Bring model config creation in one place by simplifying num_ensemble setting 
PiperOrigin-RevId: 811346971
Change-Id: Idbd6e84ab372dad81d8f3eb6e1a1af12daf4baeb
 2025-09-25 07:42:58 -07:00
Ryan Pachauri
4b81ad9cfe Add CPU/thread control to MSA tools and update dependencies. 
Addresses the following pull request:
*  https://github.com/google-deepmind/alphafold/pull/358

PiperOrigin-RevId: 810894445
Change-Id: Ib424b3f331c5168f4505edd154b860420e89237e
 2025-09-24 08:30:25 -07:00
Ryan Pachauri
c095a657ad Fix typos. 
Addresses the following pull requests:
* https://github.com/google-deepmind/alphafold/pull/1089
* https://github.com/google-deepmind/alphafold/pull/947
* https://github.com/google-deepmind/alphafold/pull/889

PiperOrigin-RevId: 798028468
Change-Id: I3b6f2874e173f757144533232c661f81b927fd64
 2025-08-21 20:51:32 -07:00
Ryan Pachauri
e57fba02b1 Clarify and fix documentation. 
Addresses the following pull requests:
* https://github.com/google-deepmind/alphafold/pull/1083
* https://github.com/google-deepmind/alphafold/pull/1079
* https://github.com/google-deepmind/alphafold/pull/893

PiperOrigin-RevId: 798021344
Change-Id: I51bbc56998b99d53697b9d95e28cf1d55d562291
 2025-08-21 20:22:24 -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
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
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
Augustin Zidek
9b18d6a966 Release code for v2.3.0 
PiperOrigin-RevId: 494507694
 2022-12-11 11:06:50 +00:00
Tom Ward
157c0eaa62 Remove unused type hint from run_alphafold script. 
PiperOrigin-RevId: 454817469
Change-Id: I677ee0cabbcf64b4682a0f4b218c23daf95ac13e
 2022-06-14 03:41:38 -07:00
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
Augustin Zidek
57a2455e5f Release code for v2.1.2 
PiperOrigin-RevId: 424591903
 2022-01-27 14:41:09 +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
 2021-11-05 02:38:51 -07:00
Augustin-Zidek
0be2b30b98 Add code for AlphaFold-Multimer. 
PiperOrigin-RevId: 407076987
 2021-11-02 14:33:58 +00:00
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
Tom Ward
1e216f93f0 Fix import ordering. 
PiperOrigin-RevId: 387085679
Change-Id: I73287fcd0a29e899543b64c596e306195a2f435e
 2021-07-27 05:31:03 -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
Augustin-Zidek
1109480e6f Initial release of AlphaFold. 
PiperOrigin-RevId: 384954738
 2021-07-15 18:44:37 +01:00