Commits · 4b726a2ecd81935a6ca9801fe72ce5dd80b1503d · chenzk / AlphaFold2_jax

20 Dec, 2022 1 commit
- Speed up Colab multimer MSA search: fetch each db chunk only once and run all queries against it. · 4b726a2e
  Augustin Zidek authored Dec 20, 2022
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PiperOrigin-RevId: 496636186
Change-Id: I0a428b6269f8e1bcb1a6efb33cad2fc70b0d1f35
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  4b726a2e
19 Dec, 2022 1 commit

[NumPy] Remove references to deprecated NumPy type aliases. · b21167be

Peter Hawkins authored Dec 19, 2022

This change replaces references to a number of deprecated NumPy type aliases (np.bool, np.int, np.float, np.complex, np.object, np.str) with their recommended replacement (bool, int, float, complex, object, str).

NumPy 1.24 drops the deprecated aliases, so we must remove uses before updating NumPy.

PiperOrigin-RevId: 496396651
Change-Id: Ifbf86edb8c7ba3bf1a427c1b5276e8eb33041ab9

b21167be

15 Dec, 2022 3 commits

Restore the max sequence limit to 4000 now that unified memory is fixed. · e80e2524
Andrew Cowie authored Dec 15, 2022
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PiperOrigin-RevId: 495602713
Change-Id: I091644565b3bbb2e95ee434c6cd80d6d54d677dc
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e80e2524

Add query_multiple to Jackhmmer. · ed3ecabf

Augustin Zidek authored Dec 15, 2022

This enables searching with multiple queries against a db chunk without having to re-download it each time.

PiperOrigin-RevId: 495553498
Change-Id: I5e3df1cc31cdcef591a1516797f0372f171e413c

ed3ecabf

[NumPy] Remove references to deprecated NumPy type aliases. · dd643b1e

Peter Hawkins authored Dec 15, 2022

NumPy 1.24 drops the deprecated aliases, so we must remove uses before updating NumPy.

PiperOrigin-RevId: 495546406
Change-Id: Iaf1bfd2000fee1bffada5138ae16ec192916c076

dd643b1e

13 Dec, 2022 1 commit
- Set environment variables before any other code is executed. · a0b0cd9c
  Andrew Cowie authored Dec 13, 2022
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PiperOrigin-RevId: 495028896
Change-Id: I3b1a6ddceca1961bffdaba443e7db47bbfbc4fad
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11 Dec, 2022 2 commits
- Update readme. · 569eb4fe
  Augustin Zidek authored Dec 11, 2022
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  569eb4fe
- Release code for v2.3.0 · 9b18d6a9
  Augustin Zidek authored Dec 11, 2022
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PiperOrigin-RevId: 494507694
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  9b18d6a9
01 Dec, 2022 1 commit
- Bump python in colab to 3.8 · 4494af84
  Hamish Tomlinson authored Dec 01, 2022
  
  4494af84
26 Nov, 2022 1 commit
- Updated Jax to 0.3.25 and Haiku to 0.0.9 · 8537f51d
  Hamish Tomlinson authored Nov 26, 2022
  
  8537f51d
01 Nov, 2022 1 commit
- Update the readme file for the AlphaFold Protein Structure Database (version 4). · b8accc68
  Hamish Tomlinson authored Nov 01, 2022
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PiperOrigin-RevId: 485284393
Change-Id: Ie4c162cfeb18383de335f11060afcf7bd7cad808
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  b8accc68
13 Oct, 2022 1 commit

[JAX] Import scipy submodules directly in code that uses them. · a31061e8

Peter Hawkins authored Oct 13, 2022

JAX will soon import scipy lazily, so code that relies on JAX having already imported submodules of scipy will fail. Change code to import what it uses.

PiperOrigin-RevId: 480841853
Change-Id: I18a744a561d73da3ccd43c26fcd99d10070c058e

a31061e8

12 Oct, 2022 1 commit

Update version in colab · ff4f1c61

Hamish Tomlinson authored Oct 12, 2022

PiperOrigin-RevId: 480643781
Change-Id: Id4bfa90b71cd59b148a3c2a61ddb65c41192712b

ff4f1c61

22 Sep, 2022 1 commit
- Fix missing comma in AlphaFold-Multimer BibTeX entry. · 7b87da53
  Augustin Zidek authored Sep 22, 2022
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PiperOrigin-RevId: 476079314
Change-Id: I926ac12ecdeaf45de0b3f72fede7a5e8bbf4ead3
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  7b87da53
21 Sep, 2022 1 commit

Bump version to 2.2.4 · 5cb2f8c4

Hamish Tomlinson authored Sep 21, 2022

PiperOrigin-RevId: 475836098
Change-Id: Ic01685bcc7c7655cbccdfd379bf9d840a8adfd23

5cb2f8c4

16 Sep, 2022 3 commits
- Fix incorrect length_scale argument · 5352e298
  Hamish Tomlinson authored Sep 16, 2022
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PiperOrigin-RevId: 474834335
Change-Id: I39693e87f05c6306437e276b5539cf93cbfca0dc
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  5352e298
- Reduce size of docker image by cleaning apt, conda and pip caches · 54c73580
  Hamish Tomlinson authored Sep 16, 2022
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PiperOrigin-RevId: 474805792
Change-Id: I103efb2884b056ddb397b424fce8488b04f00348
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  54c73580
- Update Jax and Haiku versions · 5e702ce1
  Hamish Tomlinson authored Sep 16, 2022
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PiperOrigin-RevId: 474776295
Change-Id: I8f5add84f45069f2c48ac905801a611cb298b319
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31 Aug, 2022 1 commit
- Make using GPU in relaxation optional, with default not to use. · 2eb6c0cc
  Hamish Tomlinson authored Aug 31, 2022
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PiperOrigin-RevId: 471264036
Change-Id: Ic2201048f5c9d9d741cb20fdf46f2f27986587f4
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  2eb6c0cc
25 Aug, 2022 2 commits

Bump the version to 2.2.3. · 86a0b8ec

Augustin Zidek authored Aug 25, 2022

PiperOrigin-RevId: 469945208
Change-Id: Ic331b8d781c4fa92ad8bda132a20f89aa2ad72f6

86a0b8ec

Pin Conda version to 4.13.0. · dad1f286

Augustin Zidek authored Aug 25, 2022

PiperOrigin-RevId: 469937063
Change-Id: I24ebf6e1afc9e6f64200ee195ff708be27edb327

dad1f286

12 Aug, 2022 1 commit
- Changed PAE json output to new format that matches the format used in AFDB. · 6f6e8c2e
  DeepMind authored Aug 12, 2022
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PiperOrigin-RevId: 467198544
Change-Id: I504dc91c993b10dbb1cef448ef8eaa1161186acb
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28 Jul, 2022 2 commits
- Internal change · 22fc0eea
  Augustin Zidek authored Jul 28, 2022
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PiperOrigin-RevId: 463799700
Change-Id: I47c79a3d85f85b65677d1ed4f5c5d77dc2d46f83
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- Add a readme file for the AlphaFold Protein Structure Database. · efc5fb88
  Augustin Zidek authored Jul 28, 2022
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PiperOrigin-RevId: 463797947
Change-Id: I0bcba9b4cd71b39b2415d64197bf2fc38757e576
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  efc5fb88
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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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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- 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