Commits · 253d1fea810381282a9ecc794037004ee043fda7 · ModelZoo / alphafold2_jax

14 Jun, 2022 4 commits
- Remove unneeded `__init__.py` · 253d1fea
  Tom Ward authored Jun 14, 2022
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PiperOrigin-RevId: 454823637
Change-Id: Ia7a4361b9d2a6bfe5f93542db76fb9ac1797d903
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  253d1fea
- Add matplotlib test dependency so we can run notebook_utils_test. · 725e79ab
  Tom Ward authored Jun 14, 2022
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PiperOrigin-RevId: 454823630
Change-Id: I9903ca5eb2284c8775631e2ffaf452869c7d4d7c
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  725e79ab
- Move `disable_v2_behaviour()` to `setUp` to enable running tests in test suites. · 5f4a9cc3
  Tom Ward authored Jun 14, 2022
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PiperOrigin-RevId: 454823596
Change-Id: I893dc051a5f21d53905acee45a4dcb5c5609daf9
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  5f4a9cc3
- Remove unused type hint from run_alphafold script. · 157c0eaa
  Tom Ward authored Jun 14, 2022
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PiperOrigin-RevId: 454817469
Change-Id: I677ee0cabbcf64b4682a0f4b218c23daf95ac13e
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  157c0eaa
13 Jun, 2022 4 commits
- Bump AlphaFold version to v2.2.2. · b0b7afad
  Augustin Zidek authored Jun 13, 2022
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PiperOrigin-RevId: 454626138
Change-Id: I9a6061ff7411e187ad7c5a94b6eebd8f3663d450
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  b0b7afad
- Replace period with hyphens in place, instead of declaring environment variable. · ab105145
  Tom Ward authored Jun 13, 2022
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PiperOrigin-RevId: 454618760
Change-Id: Ia6501f62ff3769a591497ac3413dc7526b31d1cc
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  ab105145
- Bump AlphaFold version to 2.2.1. · 623cc115
  Augustin Zidek authored Jun 13, 2022
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PiperOrigin-RevId: 454568110
Change-Id: Icd82696dacc250cfc3b7b71fc71d9fcd7669d032
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  623cc115
- Pin protobuf version to 3.20.1. · 0f7ab137
  Augustin Zidek authored Jun 13, 2022
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PiperOrigin-RevId: 454545752
Change-Id: I80656e917ee799fbf808002260634d2b1c38dca0
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  0f7ab137
07 Jun, 2022 1 commit
- Clarify that AlphaFold works only under Linux. · c9a9e870
  Augustin Zidek authored Jun 07, 2022
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PiperOrigin-RevId: 453397654
Change-Id: I7e7d7dfc54a4c76b6a28b47630567677f35ecb30
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  c9a9e870
31 May, 2022 2 commits
- Add support for CUDA patch versions. · 55c948c1
  Tom Ward authored May 31, 2022
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PiperOrigin-RevId: 452008235
Change-Id: Ic6ae00a207d3b0eb809b039b5df9e7bebdaee558
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  55c948c1
- Fix jax.tree_multimap deprecation warning. · d9e5e1d9
  Augustin Zidek authored May 31, 2022
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PiperOrigin-RevId: 451994826
Change-Id: I4573baf61d33010c75de717d3b49f47bc9c6a8ac
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  d9e5e1d9
25 May, 2022 1 commit
- Fix AlphaFold version in setup.py. · 197bd19e
  Augustin Zidek authored May 25, 2022
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PiperOrigin-RevId: 450934613
Change-Id: I2b5f7a740a3d9b87ccd495a65bcf8b4605c72585
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  197bd19e
19 May, 2022 1 commit
- Mention the workaround for the Nvidia public key issue in the README. · c42a96f3
  Augustin Zidek authored May 17, 2022
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PiperOrigin-RevId: 449223429
Change-Id: Iaa59e839fe3822cc319a2ae5600ed36ee4d6777c
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  c42a96f3
21 Mar, 2022 1 commit

Rebecca Chen authored Mar 21, 2022

PiperOrigin-RevId: 436161190
Change-Id: Ia10df42f5f3f638a7a5b7b804c593a1e28a4ef44

ed0886cb

17 Mar, 2022 1 commit
- Do not reuse the temporary output directory in run_alphafold_test. · b85ffe10
  Augustin Zidek authored Mar 17, 2022
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PiperOrigin-RevId: 435373710
Change-Id: I52c46cdfaccf73a456dfad52a2e3a103791653f4
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  b85ffe10
16 Mar, 2022 2 commits
- Fix readme wording. · 0007c352
  Alex Bridgland authored Mar 16, 2022
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PiperOrigin-RevId: 435113747
Change-Id: I8ca82eab2b88c1e5709abc479d5cb876af983c11
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  0007c352
- Add info for getting in touch via email to colab and readme. · 8cdec539
  Alex Bridgland authored Mar 16, 2022
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PiperOrigin-RevId: 435031203
Change-Id: Ib3fdb9931219f3a139b324e751914a00f425fe2c
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  8cdec539
08 Mar, 2022 1 commit
- Add instructions for using multimer v1 model weights. · 918434f5
  Sebastian Bodenstein authored Mar 08, 2022
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PiperOrigin-RevId: 433187350
Change-Id: Ibb524ead7290d7fa0cbf609c5e2df105de5a5fc3
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  918434f5
07 Mar, 2022 2 commits
- Update open source between_residue_clash_loss to take into account multiple chains. · 481b8be2
  Rich Evans authored Mar 07, 2022
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PiperOrigin-RevId: 432934821
Change-Id: If5decaf654823a37c4270151039a12606f526f7a
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  481b8be2
- Update change-log to briefly describe the change in AlphaFold-Multimer models. · 3e046ad9
  Rich Evans authored Mar 07, 2022
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PiperOrigin-RevId: 432931310
Change-Id: I19acd7eb7f3a63922481d9db3bc8d881efbbf550
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  3e046ad9
03 Mar, 2022 1 commit
- Update multimer models to v2. · eba82a65
  Sebastian Bodenstein authored Mar 03, 2022
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PiperOrigin-RevId: 432150462
Change-Id: I508371123adf9dad20f4fe1082c7a6c7cd6815d4
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  eba82a65
02 Mar, 2022 2 commits

Remove unused function casp_model_names. · 189f7d81
Sebastian Bodenstein authored Mar 02, 2022
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PiperOrigin-RevId: 431956393
Change-Id: I1d97992967b8c276dfa978b91bc5066efdd3b62c
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189f7d81

No longer use `runtime=nvidia` to expose GPUs to the container. · 5f37a5a2

Tom Ward authored Mar 02, 2022

Instead use `DeviceRequest`, which is equivalent to running with `--gpu all`.

PiperOrigin-RevId: 431933575
Change-Id: Iee9f70ae8f291d16850e4f58349559d9468ef4d8

5f37a5a2

23 Feb, 2022 1 commit

Simplify mounting of files. · 552586eb

Andrew Cowie authored Feb 23, 2022

PiperOrigin-RevId: 430450270
Change-Id: Ie9f30b253d1cabf6b20e596732b9bab4963dc776

552586eb

21 Feb, 2022 1 commit
- Remove unused bias arg in GlobalAttention. · 16bab4d3
  Tim Green authored Feb 21, 2022
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PiperOrigin-RevId: 430053169
Change-Id: Ia7461bc23d6e0c94f5bef8c1ded1c8306193e67e
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  16bab4d3
18 Feb, 2022 2 commits
- Remove prokaryotic pairing from AFOS. · 89a6875f
  Rich Evans authored Feb 18, 2022
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PiperOrigin-RevId: 429521382
Change-Id: Ib9bfce50834bb129af0dbd3508cd0b92856a9bb1
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  89a6875f
- Fix random_seed overflow when seeds per model > 1. · b787ca29
  Rich Evans authored Feb 18, 2022
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PiperOrigin-RevId: 429520386
Change-Id: Ic1ba2b31e25a0511fefe5d0d462fc5a218641a56
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  b787ca29
17 Feb, 2022 1 commit
- Enable multiple seeds per model for AlphaFold-Multimer. · eb49d157
  Rich Evans authored Feb 17, 2022
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PiperOrigin-RevId: 429318717
Change-Id: Ib07df7ecd4bc52feea80a66c585ce51f332ac7a1
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  eb49d157
16 Feb, 2022 1 commit

Improve support for num_recycle=0. · 2cd61ade

Michael Figurnov authored Feb 16, 2022

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

2cd61ade

14 Feb, 2022 1 commit

Add split_rng=False (current default) to sharded_map. · 929b188a

Tom Hennigan authored Feb 13, 2022

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

929b188a

08 Feb, 2022 1 commit

Remove unused code. · b5ed6b76

Augustin Zidek authored Feb 08, 2022

PiperOrigin-RevId: 427128482
Change-Id: I31134f7b0675260c79c799f14626140d74d745d4

b5ed6b76

31 Jan, 2022 1 commit
- Add a note about the AlphaFold output directory. · 9c4ac8a9
  Augustin Zidek authored Jan 31, 2022
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PiperOrigin-RevId: 425323152
Change-Id: Id1aa81316c95617e970ce014f4a331d1ed49ec02
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  9c4ac8a9
28 Jan, 2022 1 commit
- Explain what to do if downloading PDB mmCIF files is too slow. · e93a9eb6
  Augustin Zidek authored Jan 28, 2022
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PiperOrigin-RevId: 424887480
Change-Id: I4ea7a2aba785d037f49cf22c503ebebe3303e468
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  e93a9eb6
27 Jan, 2022 1 commit
- Release code for v2.1.2 · 57a2455e
  Augustin Zidek authored Jan 27, 2022
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PiperOrigin-RevId: 424591903
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  57a2455e
19 Jan, 2022 2 commits
- Update .dockerignore · db039ef4
  Tim Green authored Jan 19, 2022
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Don't ignore the README.md.
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  db039ef4
- Update license of AlphaFold parameters. · 81731171
  Augustin-Zidek authored Jan 19, 2022
  
  81731171
05 Nov, 2021 2 commits

Explain better how to run the AlphaFold-Multimer system. · be37a41d

Augustin Zidek authored Nov 05, 2021

* 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

be37a41d

Fix PAE visualization for single chain predictions. · 91b43223
Rich Evans authored Nov 05, 2021
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PiperOrigin-RevId: 407773747
Change-Id: I8635dd77ecf366f4f5a362993b964adffc3ff186
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91b43223

04 Nov, 2021 1 commit
- Change fasta description used in data pipeline to be chain_<chain number>. · c128d1aa
  Andrew Cowie authored Nov 04, 2021
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PiperOrigin-RevId: 407584472
Change-Id: Icfa755722ddabff71d27f4a3d07f9e88a409c3a6
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  c128d1aa
02 Nov, 2021 1 commit
- Add code for AlphaFold-Multimer. · 0be2b30b
  Augustin-Zidek authored Nov 02, 2021
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PiperOrigin-RevId: 407076987
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  0be2b30b