Commits · f7451744ff6380a4381793217a0d2a517e69c3a8 · ModelZoo / alphafold2_jax

24 Aug, 2023 1 commit
- remove duplicated code · 2f0d89e7
  zhuwenwen authored Aug 24, 2023
  
  2f0d89e7
10 Apr, 2023 1 commit
- initial alphafold2 · 3972a903
  zhuwenwen authored Apr 10, 2023
  
  3972a903
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

15 Dec, 2022 2 commits

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

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: 495546406
Change-Id: Iaf1bfd2000fee1bffada5138ae16ec192916c076

dd643b1e

11 Dec, 2022 1 commit
- Release code for v2.3.0 · 9b18d6a9
  Augustin Zidek authored Dec 11, 2022
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18 Feb, 2022 1 commit
- Remove prokaryotic pairing from AFOS. · 89a6875f
  Rich Evans authored Feb 18, 2022
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  89a6875f
27 Jan, 2022 1 commit
- Release code for v2.1.2 · 57a2455e
  Augustin Zidek authored Jan 27, 2022
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  57a2455e
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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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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  0be2b30b
10 Sep, 2021 1 commit

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

02 Aug, 2021 1 commit

Fix a few typos. · 41232dc7

Augustin Zidek authored Aug 02, 2021

PiperOrigin-RevId: 388172326
Change-Id: I11d9e498c226cd752947feb51b7d1eb343b4d7ab

41232dc7

29 Jul, 2021 1 commit
- 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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  00c4c91d
27 Jul, 2021 1 commit

Fix import ordering. · 1e216f93

Tom Ward authored Jul 27, 2021

PiperOrigin-RevId: 387085679
Change-Id: I73287fcd0a29e899543b64c596e306195a2f435e

1e216f93

26 Jul, 2021 1 commit
- 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
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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  0bab1bf8
15 Jul, 2021 1 commit
- Initial release of AlphaFold. · 1109480e
  Augustin-Zidek authored Jul 15, 2021
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  1109480e