Commits · 624a44966619218f546852863f0f9220fc9c2849 · ModelZoo / alphafold2_jax

20 Jun, 2022 1 commit
- Fix Dockerfile breakage due to google/jax#11142. · 624a4496
  Tim Green authored Jun 20, 2022
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PiperOrigin-RevId: 456029742
Change-Id: I908c5fe07d14168d65fccc3e42cb5c994200b0e2
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  624a4496
14 Jun, 2022 5 commits

Migrate from `collections.Iterable` to `collections.abc.Iterable`. · 7b2a4c5a

Tom Ward authored Jun 14, 2022

Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.10 it will stop working.

PiperOrigin-RevId: 454823734
Change-Id: Ic1d22c0badd76c41693967f785f8861746657731

7b2a4c5a

Remove unneeded `__init__.py` · 253d1fea

Tom Ward authored Jun 14, 2022

PiperOrigin-RevId: 454823637
Change-Id: Ia7a4361b9d2a6bfe5f93542db76fb9ac1797d903

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

Silence some pytype errors. · ed0886cb

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
```
PiperOrigin-RevId: 407773747
Change-Id: I8635dd77ecf366f4f5a362993b964adffc3ff186
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91b43223