Commits · 665ebc301340b34efb85c72503fbbe8315b3a0f4 · ModelZoo / alphafold2_jax

01 Feb, 2023 1 commit

Make `_chem_comp.type` logic case-insensitive. · 665ebc30

Augustin Zidek authored Feb 01, 2023

The specification http://mmcif.rcsb.org/dictionaries/mmcif_pdbx.dic/Items/_chem_comp.type.html says this is case-insensitive and AFDB files use capitalised "PEPTIDE".

PiperOrigin-RevId: 506266651
Change-Id: I2f16d729e41c722c74f94a3b308c7159b289a5c3

665ebc30

27 Jan, 2023 2 commits
- Update readme for relaxation flag. · 18e12d61
  Hamish Tomlinson authored Jan 27, 2023
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  18e12d61
- Improve documentation on how to install aria2c. · 41871c09
  Augustin Zidek authored Jan 27, 2023
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PiperOrigin-RevId: 505082237
Change-Id: I84f2fb3a2952456c6baf4dd2052fff4178b1af4f
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23 Jan, 2023 1 commit

Update tensorflow · fed21ddd

Hamish Tomlinson authored Jan 23, 2023

PiperOrigin-RevId: 503968820
Change-Id: I2ab071d6872bc2f9eaab4a464aed684036b966d2

fed21ddd

17 Jan, 2023 1 commit
- Remove jax dependency from results pkl · 91ac85ac
  Hamish Tomlinson authored Jan 17, 2023
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PiperOrigin-RevId: 502584418
Change-Id: I8ab14363a6342726691213bbeb180c0a8ff7f932
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  91ac85ac
13 Jan, 2023 1 commit
- Add ability to only run relax for the best unrelaxed model. · 684ffa19
  Hamish Tomlinson authored Jan 13, 2023
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PiperOrigin-RevId: 501851892
Change-Id: I7484c2aa7ac30af611d88cfa8d632096c262824a
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  684ffa19
12 Jan, 2023 2 commits
- Use shutil to zip and download colab outputs · 0d9a24b2
  Hamish Tomlinson authored Jan 12, 2023
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PiperOrigin-RevId: 501595938
Change-Id: Ib586090d13279eca1371f0e0b046379b728a3e87
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  0d9a24b2
- Fix typo in a comment in residue constants. · a3941673
  Augustin Zidek authored Jan 12, 2023
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PiperOrigin-RevId: 501515486
Change-Id: I2a86a64ebbf0ab8222689268755ba3b7780878e5
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  a3941673
11 Jan, 2023 2 commits

Bump version to 2.3.1 · d6d2fc07

Hamish Tomlinson authored Jan 11, 2023

PiperOrigin-RevId: 501297397
Change-Id: Ic1bb166581047e0e8c46845f41f8c55c10f32ef9

d6d2fc07

Update of README.md · e3231de1

DeepMind authored Jan 11, 2023

PiperOrigin-RevId: 501279176
Change-Id: I9cf92212322b29691844973ded9e337e81b3a9fd

e3231de1

10 Jan, 2023 1 commit
- Fix GPU relax for longer chains by pinning large memory ops to cpu. · 8f1ebd58
  Ali Cowen-Rivers authored Jan 10, 2023
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PiperOrigin-RevId: 501105389
Change-Id: I6c981d1d3231e008ebae192edb4586479eb5eb34
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  8f1ebd58
23 Dec, 2022 1 commit
- Adding recycle information for timings. · 420fb08f
  Ali Cowen-Rivers authored Dec 23, 2022
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PiperOrigin-RevId: 497360470
Change-Id: I3a9f3ba608ac3ceeaaccfe281a82d43fae1d265e
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  420fb08f
21 Dec, 2022 2 commits
- Adding prediction timings to README. · a9e5451f
  Ali Cowen-Rivers authored Dec 21, 2022
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PiperOrigin-RevId: 496937349
Change-Id: I9e9f447b3ce11d1b5a5c7433aeae7b03a3ed19e9
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- Add `eval_dropout` option for using dropout in trunk at eval time. · f96e254e
  Josh Abramson authored Dec 21, 2022
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PiperOrigin-RevId: 496885301
Change-Id: I42de2dd13784e2b358320349398a3fc88ee0d708
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  f96e254e
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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  a0b0cd9c
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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  5e702ce1
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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  6f6e8c2e
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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  22fc0eea
- 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 1 commit

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