Code

Copy alphafold from colabfold#1

Code

Merged

ajtritt merged 115 commits intomainlbl-cbg/alphafold-old:mainfrom cbg_updatelbl-cbg/alphafold-old:cbg_updateCopy head branch name to clipboardDec 19, 2023

+1,071-626

Commits

Commits on Nov 10, 2021

• Update residue_constants.py

  konstin

  committed
  a984544

  Copy full SHA for a984544

• Lower log level for unimportant message

  konstin

  committed
  da95c23

  Copy full SHA for da95c23

• Apply config patch

  konstin

  committed
  fe570bf

  Copy full SHA for fe570bf

• Apply model patch

  konstin

  committed
  d92701d

  Copy full SHA for d92701d

• Apply patch

  konstin

  committed
  fd8e5b1

  Copy full SHA for fd8e5b1

• Apply protein patch

  konstin

  committed
  ddf0df3

  Copy full SHA for ddf0df3

• - Remove seen_sequence from make_msa_features to avoid paired sequences to be removed

  Show description for ab7470d
  

  martin-steinegger

  authored and

  konstin

  committed
  ab7470d

  Copy full SHA for ab7470d

• Change name for publishing

  konstin

  committed
  a2cda93

  Copy full SHA for a2cda93

• Comment _merge_homomers_dense_msa to improve monomer prediction

  

  martin-steinegger

  authored and

  konstin

  committed
  e8cd13b

  Copy full SHA for e8cd13b

• Turn on dense MSA again

  

  martin-steinegger

  authored and

  konstin

  committed
  2ca1db9

  Copy full SHA for 2ca1db9

• Bump to 2.1.1

  konstin

  committed
  14ca53f

  Copy full SHA for 14ca53f

• Rebase fallout

  konstin

  committed
  4c4ba8c

  Copy full SHA for 4c4ba8c

• Update repo url

  konstin

  authored
  2f711c4

  Copy full SHA for 2f711c4

Commits on Nov 25, 2021

• Speed up param loading

  konstin

  committed
  0b49aef

  Copy full SHA for 0b49aef

• Bump to 2.1.2

  konstin

  committed
  b5ae6dc

  Copy full SHA for b5ae6dc

• Publish form github actions

  konstin

  committed
  cb97fbc

  Copy full SHA for cb97fbc

• Stop at score for recycles

  konstin

  committed
  a603b95

  Copy full SHA for a603b95

Commits on Dec 6, 2021

• Make stop_at_score float for google-deepmind#119

  konstin

  committed
  6a1f885

  Copy full SHA for 6a1f885

Commits on Dec 7, 2021

• Show num_recycles for multimer

  konstin

  committed
  48403a4

  Copy full SHA for 48403a4

Commits on Dec 9, 2021

• Bump to 2.1.4

  konstin

  committed
  e2147eb

  Copy full SHA for e2147eb

Commits on Mar 2, 2022

• Set max_subsequence_ratio to 1.0

  martin-steinegger

  authored
  40373b6

  Copy full SHA for 40373b6

Commits on Mar 4, 2022

• Update version to 2.1.6

  martin-steinegger

  authored
  4d3c8d3

  Copy full SHA for 4d3c8d3

Commits on Mar 29, 2022

• Merge branch 'main' of https://github.com/deepmind/alphafold into main

  martin-steinegger

  committed
  c5ca042

  Copy full SHA for c5ca042

• Update setup.py

  martin-steinegger

  authored
  4c3305e

  Copy full SHA for 4c3305e

Commits on Apr 17, 2022

• Remove duplicate, template_sequence len and align_ratio check

  martin-steinegger

  authored
  6675e23

  Copy full SHA for 6675e23

• Update setup.py to 2.1.8

  martin-steinegger

  authored
  871c0e1

  Copy full SHA for 871c0e1

Commits on Jun 13, 2022

• Try to improve compiling

  martin-steinegger

  committed
  442769a

  Copy full SHA for 442769a

• Update setup.py

  martin-steinegger

  authored
  f8fc267

  Copy full SHA for f8fc267

• Update setup.py

  martin-steinegger

  authored
  3ae102a

  Copy full SHA for 3ae102a

Commits on Jun 14, 2022

• Change folding_multimer to compile faster

  martin-steinegger

  committed
  26fd0e1

  Copy full SHA for 26fd0e1

• Merge branch 'main' of https://github.com/steineggerlab/alphafold

  martin-steinegger

  committed
  53c5f4f

  Copy full SHA for 53c5f4f

• Change return type in multimer

  martin-steinegger

  committed
  6aa2c1a

  Copy full SHA for 6aa2c1a

Commits on Jun 15, 2022

• Update modules.py

  sokrypton

  authored
  e9c90a7

  Copy full SHA for e9c90a7

• Update modules.py

  sokrypton

  authored
  caed7d9

  Copy full SHA for caed7d9

• Update modules.py

  sokrypton

  authored
  85458e1

  Copy full SHA for 85458e1

• adding recycling outside of the jax compiled code

  sokrypton

  authored
  3dc7924

  Copy full SHA for 3dc7924

• fixing typo

  sokrypton

  authored
  e0f9e74

  Copy full SHA for e0f9e74

• fixing typos

  sokrypton

  authored
  f0576ed

  Copy full SHA for f0576ed

• fixing typos

  sokrypton

  authored
  99faa88

  Copy full SHA for 99faa88

• typo

  sokrypton

  authored
  3198c24

  Copy full SHA for 3198c24

• Update modules_multimer.py

  sokrypton

  authored
  220e3ca

  Copy full SHA for 220e3ca

• Update modules.py

  sokrypton

  authored
  c677789

  Copy full SHA for c677789

• Update model.py

  sokrypton

  authored
  661205b

  Copy full SHA for 661205b

• adding manual recycling support for multimers

  sokrypton

  authored
  302e502

  Copy full SHA for 302e502

• fixing recycle count

  sokrypton

  authored
  301259c

  Copy full SHA for 301259c

• Update modules_multimer.py

  sokrypton

  authored
  c721f49

  Copy full SHA for c721f49

• rm key subsampling

  sokrypton

  authored
  68a64ac

  Copy full SHA for 68a64ac

• debugging

  sokrypton

  authored
  ac9314b

  Copy full SHA for ac9314b

• debugging

  sokrypton

  authored
  4f0609d

  Copy full SHA for 4f0609d

• Update modules_multimer.py

  sokrypton

  authored
  a4cd359

  Copy full SHA for a4cd359

• Update model.py

  sokrypton

  authored
  66a7fd4

  Copy full SHA for 66a7fd4

• cleaning up the code

  sokrypton

  authored
  8c0e152

  Copy full SHA for 8c0e152

• typo

  sokrypton

  authored
  eee1696

  Copy full SHA for eee1696

• Merge pull request #1 from steineggerlab/beta

  Show description for 6eb24bd
  sokrypton

  authored
  6eb24bd

  Copy full SHA for 6eb24bd

• Cond fix for older jax version

  martin-steinegger

  committed
  c59135e

  Copy full SHA for c59135e

• Add recycle early-stopping to the model

  martin-steinegger

  committed
  6741fa7

  Copy full SHA for 6741fa7

• Update repository to 2.1.10

  martin-steinegger

  committed
  371776f

  Copy full SHA for 371776f

• fixing the missing key in fold_iteration

  sokrypton

  authored
  9efbba8

  Copy full SHA for 9efbba8

Commits on Jun 16, 2022

• Merge branch 'main' of https://github.com/deepmind/alphafold

  martin-steinegger

  committed
  36239c8

  Copy full SHA for 36239c8

• Merge branch 'main' of https://github.com/steineggerlab/alphafold

  martin-steinegger

  committed
  c10b155

  Copy full SHA for c10b155

• Update version to 2.1.11

  martin-steinegger

  committed
  82933e1

  Copy full SHA for 82933e1

Commits on Jun 17, 2022

• bugfix: removing nans from alphafold-multimer+templates

  Show description for bd696aa
  sokrypton

  authored
  bd696aa

  Copy full SHA for bd696aa

• Update to 2.1.12

  martin-steinegger

  authored
  433dbe0

  Copy full SHA for 433dbe0

Commits on Jun 21, 2022

• Update model.py

  sokrypton

  authored
  00ebb93

  Copy full SHA for 00ebb93

• Update model.py

  sokrypton

  authored
  d6bf859

  Copy full SHA for d6bf859

• Add 2.1.13 (fix ensemble)

  martin-steinegger

  committed
  b78a234

  Copy full SHA for b78a234

• Update setup.py

  martin-steinegger

  authored
  829d7f3

  Copy full SHA for 829d7f3

Commits on Nov 20, 2022

• Workaround for breaking change in PDB.PDBIO v1.80 not working correctly with StringIO

  milot-mirdita

  committed
  9719482

  Copy full SHA for 9719482

• Actually fix PDBIO issue

  milot-mirdita

  committed
  68c2feb

  Copy full SHA for 68c2feb

Commits on Dec 24, 2022

• Merge branch 'main' of https://github.com/deepmind/alphafold into deepmind-main

  sokrypton

  committed
  f50fd03

  Copy full SHA for f50fd03

• Merge branch 'deepmind-main' into main

  sokrypton

  committed
  7e373e9

  Copy full SHA for 7e373e9

Commits on Jan 17, 2023

• adding support for fused triangle attention to monomers (google-deepmind#2)

  sokrypton

  authored
  581ddbc

  Copy full SHA for 581ddbc

Commits on Jan 18, 2023

• adding option to "unfuse"

  sokrypton

  committed
  c39f51b

  Copy full SHA for c39f51b

• Update utils.py

  sokrypton

  committed
  dcc29d9

  Copy full SHA for dcc29d9

• Update utils.py

  sokrypton

  committed
  dfeb777

  Copy full SHA for dfeb777

Commits on Jan 19, 2023

• Squashed commit of the following:

  Show description for aec67d0
  sokrypton

  committed
  aec67d0

  Copy full SHA for aec67d0

• set eval_dropout when user specifies is_training

  sokrypton

  committed
  7875336

  Copy full SHA for 7875336

• Update model.py

  sokrypton

  committed
  b66109f

  Copy full SHA for b66109f

Commits on Jan 20, 2023

• adjust config to revert back to old settings for multimer v1/v2

  sokrypton

  committed
  db8d806

  Copy full SHA for db8d806

Commits on Jan 21, 2023

• enable fuse for all models by default

  sokrypton

  committed
  f1f406e

  Copy full SHA for f1f406e

• bugfix: typo in config (v1, v2 multimer settings)

  sokrypton

  committed
  3e865eb

  Copy full SHA for 3e865eb

• add use_cluster_profile and recycle_early_stop_tolerance support

  sokrypton

  committed
  0914bc3

  Copy full SHA for 0914bc3

• adding recycle_early_stop_tolerance support for monomers

  sokrypton

  committed
  ea7f5dd

  Copy full SHA for ea7f5dd

Commits on Jan 22, 2023

• add bfloat16 support for monomers

  sokrypton

  committed
  2aa7093

  Copy full SHA for 2aa7093

• Update model.py

  sokrypton

  committed
  ffccec9

  Copy full SHA for ffccec9

Commits on Jan 28, 2023

• Create stereo_chemical_props.txt

  sokrypton

  committed
  44a144b

  Copy full SHA for 44a144b

• Update setup.py

  sokrypton

  authored
  8b78b68

  Copy full SHA for 8b78b68

Commits on Jan 30, 2023

• fix templates

  sokrypton

  committed
  e322994

  Copy full SHA for e322994

• Create MANIFEST.in

  sokrypton

  authored
  bf7c767

  Copy full SHA for bf7c767

• fix stereo_chemical_props.txt path

  sokrypton

  committed
  8d57312

  Copy full SHA for 8d57312

• Merge branch 'pr/4'

  sokrypton

  committed
  978543a

  Copy full SHA for 978543a

Commits on Feb 1, 2023

• speedup

  Show description for 83b076e
  sokrypton

  committed
  83b076e

  Copy full SHA for 83b076e

• speedup

  Show description for 4f00a9b
  sokrypton

  authored
  4f00a9b

  Copy full SHA for 4f00a9b

Commits on Feb 2, 2023

• adding mask to ptm/iptm calculation

  Show description for 96a3a2b
  sokrypton

  committed
  96a3a2b

  Copy full SHA for 96a3a2b

• adding iptm support for ptm models

  sokrypton

  committed
  bebd0e2

  Copy full SHA for bebd0e2

Commits on Feb 3, 2023

• Update modules.py

  sokrypton

  committed
  36c5925

  Copy full SHA for 36c5925

• Merge pull request google-deepmind#3 from sokrypton/main

  Show description for 15eb3e0
  martin-steinegger

  authored
  15eb3e0

  Copy full SHA for 15eb3e0

Commits on Feb 7, 2023

• moving key splitting to model.py

  sokrypton

  committed
  80092dc

  Copy full SHA for 80092dc

• keep raw outputs

  sokrypton

  committed
  5b00c00

  Copy full SHA for 5b00c00

• Update model.py

  sokrypton

  committed
  627a7e9

  Copy full SHA for 627a7e9

Commits on Feb 10, 2023

• Update modules.py

  sokrypton

  authored
  8730453

  Copy full SHA for 8730453

• allow for no batch inputs

  sokrypton

  committed
  cf096a6

  Copy full SHA for cf096a6

Commits on Feb 11, 2023

• v2.3.2

  sokrypton

  authored
  ba75383

  Copy full SHA for ba75383

Commits on Feb 14, 2023

• v2.3.3 - fixing memory leaks

  Show description for 8f50ccb
  sokrypton

  authored
  8f50ccb

  Copy full SHA for 8f50ccb

Commits on Feb 18, 2023

• v2.3.4 - fix memory leaks (attempt 2) (google-deepmind#6)

  Show description for 41807ea
  sokrypton

  authored
  41807ea

  Copy full SHA for 41807ea

Commits on Feb 20, 2023

• Update modules.py

  sokrypton

  committed
  bec81ee

  Copy full SHA for bec81ee

Commits on Feb 21, 2023

• add option to provide custom offset

  sokrypton

  committed
  405dd85

  Copy full SHA for 405dd85

• Update config.py

  sokrypton

  committed
  b39d7dd

  Copy full SHA for b39d7dd

• Update config.py

  sokrypton

  committed
  3d3fdde

  Copy full SHA for 3d3fdde

Commits on Apr 29, 2023

• Update OpenMM imports to work with new OpenMM API

  milot-mirdita

  committed
  7386194

  Copy full SHA for 7386194

Commits on May 10, 2023

• Merge pull request #1 from steineggerlab/main

  Show description for ba597e0
  sokrypton

  authored
  ba597e0

  Copy full SHA for ba597e0

Commits on May 24, 2023

• patch for jax > 0.3.25

  sokrypton

  authored
  1f04253

  Copy full SHA for 1f04253

Commits on Jun 2, 2023

• fix single representation

  Show description for 024dcb2
  sokrypton

  committed
  024dcb2

  Copy full SHA for 024dcb2

Commits on Jul 24, 2023

• Update modules_multimer.py

  sokrypton

  authored
  7c09316

  Copy full SHA for 7c09316

Commits on Dec 19, 2023

• Update to sokrypton version of alphafold

  ajtritt

  committed
  ee6bbad

  Copy full SHA for ee6bbad