Commits · 929b188a3b2329387a2a0493dae18427cd0bdb67 · ModelZoo / alphafold2_jax

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
10 Sep, 2021 2 commits

Accept any ordering given by ListDir in the assert. · 1d43aaff

Augustin Zidek authored Sep 10, 2021

Addresses https://github.com/deepmind/alphafold/issues/168.

PiperOrigin-RevId: 395907797
Change-Id: I28c7e951211c9cf6bd5e35d8dfaf57f22e843ed0

1d43aaff

Skip obsolete PDB templates that don't have a replacement. · 50ecd75d

Augustin Zidek authored Sep 10, 2021

Fixes https://github.com/deepmind/alphafold/issues/163.

PiperOrigin-RevId: 395878875
Change-Id: I99a9defa95547582bbfd9fec3ae821386274d77f

50ecd75d

31 Aug, 2021 2 commits

Ensure values passed to jax.numpy functions are arrays rather than lists. · 98caef21

Jake VanderPlas authored Aug 31, 2021

Why? This will soon be a requirement in JAX; see https://github.com/google/jax/issues/7737

PiperOrigin-RevId: 394105499
Change-Id: I6f76e3f47b7906616c1f988be58d29c828414060

98caef21

Update the bibtex citation with the issue number and pages · 495d81ac
Michael Figurnov authored Aug 31, 2021
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PiperOrigin-RevId: 393964942
Change-Id: I9c45191f726b40b66cea1cdd9f2efa2d4082b084
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495d81ac

25 Aug, 2021 1 commit
- Fix TensorFlow versions in AlphaFold Colab notebook. · b1d772d1
  DeepMind authored Aug 25, 2021
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PiperOrigin-RevId: 392861510
Change-Id: I266255479210e5c9b6cbc02977f4024d40c5b94d
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  b1d772d1
13 Aug, 2021 3 commits
- Use tensorflow-cpu in setup.py as well. · 99459eff
  Augustin Zidek authored Aug 13, 2021
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PiperOrigin-RevId: 390608262
Change-Id: I4c49aeb2aea362d578b7de43d16bf2e418fdd96d
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  99459eff
- Use pLDDT in the B-factor column of the output PDBs. · cef198e0
  Augustin Zidek authored Aug 13, 2021
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PiperOrigin-RevId: 390566020
Change-Id: I3fafbe8246d0a5ad018f0398b39bf7dacee00468
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  cef198e0
- Set versions of libraries AlphaFold Colab notebook depends on. · f65e94fc
  Augustin Zidek authored Aug 13, 2021
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PiperOrigin-RevId: 390553964
Change-Id: Ia5bc6e12ab3f1a7827b7d914c93f6990a1139780
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  f65e94fc
12 Aug, 2021 1 commit

Remove a redundant space. · 05db248e

Augustin Zidek authored Aug 12, 2021

PiperOrigin-RevId: 390355132
Change-Id: I920a80db674541af41ee83ef3d5bd5255c782ee9

05db248e

02 Aug, 2021 2 commits

Add a direct link to PDB70 2020-05-13. · 547cbddb
Augustin Zidek authored Aug 02, 2021
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PiperOrigin-RevId: 388195957
Change-Id: Id22b96c964a82e3450a5f457d8facd1e85b1e86a
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547cbddb

Fix a few typos. · 41232dc7

Augustin Zidek authored Aug 02, 2021

PiperOrigin-RevId: 388172326
Change-Id: I11d9e498c226cd752947feb51b7d1eb343b4d7ab

41232dc7

30 Jul, 2021 2 commits
- Add a comment on the TriangleMultiplication notation. · b88f8dac
  DeepMind authored Jul 30, 2021
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PiperOrigin-RevId: 387766802
Change-Id: Ic838537513fe1d5bf41facffffd44046e91c3fa3
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  b88f8dac
- Use Ubuntu 18.04 LTS image. · c9ffb0bc
  Tim Green authored Jul 30, 2021
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PiperOrigin-RevId: 387763552
Change-Id: I2a9753dfca2853de7f5c07c17cc7b2f7d12cf197
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  c9ffb0bc
29 Jul, 2021 3 commits
- Log the total MSA size and number of templates. · 00c4c91d
  Alex Bridgland authored Jul 29, 2021
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PiperOrigin-RevId: 387577557
Change-Id: I37c0a748dd3d8d3d179aae579c5504d7ec92ecaf
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- Switch to Tensorflow CPU-only. GPU not needed for data pipeline. · b3ed8603
  Tim Green authored Jul 29, 2021
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PiperOrigin-RevId: 387576219
Change-Id: Ic735f068df2a3e9f53bed836f172c08f79ac231c
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  b3ed8603
- Change tex -> bibtex for nicer syntax highlighting. · bc5547b6
  Augustin Zidek authored Jul 29, 2021
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PiperOrigin-RevId: 387546070
Change-Id: I24cce3825801dde09be70970cf48141679762a2a
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  bc5547b6
27 Jul, 2021 3 commits
- Fix import ordering. · 1e216f93
  Tom Ward authored Jul 27, 2021
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PiperOrigin-RevId: 387085679
Change-Id: I73287fcd0a29e899543b64c596e306195a2f435e
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  1e216f93
- Collapse hh-suite install steps into single layer. · c9e6fedb
  Tom Ward authored Jul 27, 2021
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PiperOrigin-RevId: 387060806
Change-Id: Ifa71ce119182ed79a379e57946b2b694e134ef14
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  c9e6fedb
- Switch to using cudnn base image. · acf25fc8
  DeepMind authored Jul 27, 2021
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PiperOrigin-RevId: 387058301
Change-Id: If7d2716bfe89228e9fb8f909b72c425bd89f1f7f
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  acf25fc8
26 Jul, 2021 2 commits
- Write out pdb70_hits.hhr alongside other MSA outputs. · 2028cd0a
  DeepMind authored Jul 26, 2021
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PiperOrigin-RevId: 386894639
Change-Id: I1ef2018a48398cf8201ac38fe129b004672ad22f
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  2028cd0a
- Correct mgnify clusters filename. · 20a70577
  DeepMind authored Jul 26, 2021
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PiperOrigin-RevId: 386841647
Change-Id: Ie3ad390fc4b53b839f15c01f3b24bd25c77578b6
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  20a70577
23 Jul, 2021 1 commit

Fix a link in the README · d3a4eefd

DeepMind authored Jul 23, 2021

PiperOrigin-RevId: 386417647
Change-Id: I6f2121f3c02d3ef97467f46c5e651ca1b0f2eab2

d3a4eefd

22 Jul, 2021 1 commit
- Add a Colab notebook, add reduced BFD, and various other fixes and improvements. · 0bab1bf8
  Saran Tunyasuvunakool authored Jul 22, 2021
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PiperOrigin-RevId: 386228948
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  0bab1bf8
16 Jul, 2021 1 commit
- Switch BFD download script to mirror. · d26287ea
  Tim Green authored Jul 16, 2021
  
  d26287ea
15 Jul, 2021 1 commit
- Initial release of AlphaFold. · 1109480e
  Augustin-Zidek authored Jul 15, 2021
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PiperOrigin-RevId: 384954738
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  1109480e