Code

True multimer#190

Code

Merged

DimaMolod merged 134 commits intomainKosinskiLab/AlphaPulldown:mainfrom TrueMultimerKosinskiLab/AlphaPulldown:TrueMultimerCopy head branch name to clipboardNov 15, 2023

+712,455-672

Commits

Commits on Sep 22, 2022

• Update README.md

  

  Jan Kosinski

  committed
  7b99544

  Copy full SHA for 7b99544

• Update README.md

  

  Jan Kosinski

  committed
  cc3a03e

  Copy full SHA for cc3a03e

Commits on Jun 14, 2023

• Added alphafold just to have working version in one place

  

  Dmitry Molodenskiy

  committed
  dfe0887

  Copy full SHA for dfe0887

• True multimer 2.3.2

  DimaMolod

  committed
  baf8538

  Copy full SHA for baf8538

• Merge branch 'TrueMultimer-2.3.2' into 'master'

  Show description for df08a70
  DimaMolod

  committed
  df08a70

  Copy full SHA for df08a70

• New.

  

  Dmitry Molodenskiy

  committed
  b987d28

  Copy full SHA for b987d28

• Merge branch 'master' of git.embl.de:grp-kosinski/AlphaPulldown

  

  Dmitry Molodenskiy

  committed
  9981dfb

  Copy full SHA for 9981dfb

Commits on Jun 16, 2023

• Garbage cleaning

  

  Dmitry Molodenskiy

  committed
  4425307

  Copy full SHA for 4425307

Commits on Jul 3, 2023

• AF,CB and af2plots are removed as directories to be added later as submodules

  

  Dmitry Molodenskiy

  committed
  0da6c21

  Copy full SHA for 0da6c21

• Latest version of AP from github

  

  Dmitry Molodenskiy

  committed
  84a19ae

  Copy full SHA for 84a19ae

• Submodules are removed

  

  Dmitry Molodenskiy

  committed
  5f20d21

  Copy full SHA for 5f20d21

• Added submodules, alphafold is with TM changes

  

  Dmitry Molodenskiy

  committed
  5fea1d6

  Copy full SHA for 5fea1d6

• Update remote URL for AF submodule

  

  Dmitry Molodenskiy

  committed
  0aee614

  Copy full SHA for 0aee614

• Added TM features

  

  Dmitry Molodenskiy

  committed
  fe5844d

  Copy full SHA for fe5844d

• New.

  DimaMolod

  committed
  2cc7edc

  Copy full SHA for 2cc7edc

• Reverted to Geoffrey's version

  

  Dmitry Molodenskiy

  committed
  215c47d

  Copy full SHA for 215c47d

• Merged with github

  

  Dmitry Molodenskiy

  committed
  3223494

  Copy full SHA for 3223494

• Merging with github

  

  Dmitry Molodenskiy

  committed
  eccb0e5

  Copy full SHA for eccb0e5

Commits on Jul 21, 2023

• Sync with github

  DimaMolod

  committed
  3408173

  Copy full SHA for 3408173

Commits on Aug 1, 2023

• Sequential implementation for batch mode

  DimaMolod

  committed
  d3a19ad

  Copy full SHA for d3a19ad

• Added new script for mmt

  DimaMolod

  committed
  2920c1d

  Copy full SHA for 2920c1d

Commits on Aug 2, 2023

• Parallel implementation

  DimaMolod

  committed
  f803221

  Copy full SHA for f803221

• use create_db() also as a standalone script

  DimaMolod

  committed
  b2826e9

  Copy full SHA for b2826e9

Commits on Aug 3, 2023

• Multiple templates for each fasta file

  DimaMolod

  committed
  bde8185

  Copy full SHA for bde8185

Commits on Aug 7, 2023

• Keep templates with identical sequences for TrueMultimer

  DimaMolod

  committed
  68c4a0a

  Copy full SHA for 68c4a0a

Commits on Aug 8, 2023

• Reduce MSA depth for each next model if run with --multimeric_mode=True

  DimaMolod

  committed
  8f49d79

  Copy full SHA for 8f49d79

Commits on Aug 9, 2023

• use np.linspace() for msa depths

  DimaMolod

  committed
  3d497c9

  Copy full SHA for 3d497c9

Commits on Aug 10, 2023

• c_i_f_w_t.py: Reuse functions from c_i_f.py; c_i_f.py: Remove mmt, back to main branch

  DimaMolod

  committed
  bb963be

  Copy full SHA for bb963be

Commits on Aug 14, 2023

• Remove temp files

  DimaMolod

  committed
  f47546d

  Copy full SHA for f47546d

• Forking.md removed

  DimaMolod

  committed
  7c6bc3d

  Copy full SHA for 7c6bc3d

• Commented out saving multichain mask used for debugging

  DimaMolod

  committed
  c04827a

  Copy full SHA for c04827a

• Changed starting values for num_msa and num_extra_msa for TrueMultimer

  DimaMolod

  committed
  086fa7f

  Copy full SHA for 086fa7f

Commits on Aug 15, 2023

• First version of json metadata file. Added __version__

  DimaMolod

  committed
  2502017

  Copy full SHA for 2502017

• Cosmetic improvements

  DimaMolod

  committed
  607835a

  Copy full SHA for 607835a

Commits on Aug 16, 2023

• New more detailed meta.json

  DimaMolod

  committed
  9fbd12a

  Copy full SHA for 9fbd12a

Commits on Aug 17, 2023

• Save time to meta.json if mmseq2=True

  DimaMolod

  committed
  4d41082

  Copy full SHA for 4d41082

Commits on Aug 21, 2023

• Removed accidently added colabfold script

  DimaMolod

  committed
  e1a7ec6

  Copy full SHA for e1a7ec6

• Update .gitmodules

  dingquanyu

  authored
  252724f

  Copy full SHA for 252724f

Commits on Aug 22, 2023

• Revert file to version from main branch

  DimaMolod

  committed
  0394839

  Copy full SHA for 0394839

• Merge branch 'TrueMultimer' of github.com:KosinskiLab/AlphaPulldown into TrueMultimer

  DimaMolod

  committed
  8e3c1b8

  Copy full SHA for 8e3c1b8

• Revert files to version from main branch

  DimaMolod

  committed
  368f7d9

  Copy full SHA for 368f7d9

• Update run_multimer_jobs.py

  dingquanyu

  authored
  4afc9d0

  Copy full SHA for 4afc9d0

Commits on Aug 25, 2023

• Updated submodule URL

  DimaMolod

  committed
  d92f8e6

  Copy full SHA for d92f8e6

• Update to the latest AlphaFold version

  DimaMolod

  committed
  c30512c

  Copy full SHA for c30512c

• Remove version for openmm and pdbfixer

  DimaMolod

  committed
  c6bdbb1

  Copy full SHA for c6bdbb1

• Save only particular chain to db using biopython

  DimaMolod

  committed
  cf9116b

  Copy full SHA for cf9116b

• fix truncated file, not original

  DimaMolod

  committed
  06dd0ab

  Copy full SHA for 06dd0ab

• metadata output is json

  DimaMolod

  committed
  ed5a85a

  Copy full SHA for ed5a85a

• no truncation of the templates by default

  DimaMolod

  committed
  31bdd8e

  Copy full SHA for 31bdd8e

Commits on Aug 28, 2023

• Remove all lines with UNK residue from the mmcif string for templates

  DimaMolod

  committed
  fba4baa

  Copy full SHA for fba4baa

Commits on Aug 31, 2023

• Replace entity_poly_seq table by full sequence for templates

  DimaMolod

  committed
  a1bcea4

  Copy full SHA for a1bcea4

• Update packages, python 3.1

  DimaMolod

  committed
  26f2e3b

  Copy full SHA for 26f2e3b

Commits on Sep 4, 2023

• Update alphafold to the latest commit from the main branch

  DimaMolod

  committed
  b15bead

  Copy full SHA for b15bead

• Update URL for colabfold

  DimaMolod

  committed
  f2056f8

  Copy full SHA for f2056f8

Commits on Sep 5, 2023

• Update README.md

  dingquanyu

  authored
  7852ba2

  Copy full SHA for 7852ba2

Commits on Sep 6, 2023

• Add a flag to model with different MSA depth. Switched off by default

  DimaMolod

  committed
  c6e74ae

  Copy full SHA for c6e74ae

• Add AF version to meta.json

  DimaMolod

  committed
  627a188

  Copy full SHA for 627a188

Commits on Sep 8, 2023

• Simplified meta.json structure

  DimaMolod

  committed
  5e754e5

  Copy full SHA for 5e754e5

Commits on Sep 11, 2023

• update the urls with https

  DimaMolod

  committed
  19a6ee3

  Copy full SHA for 19a6ee3

• Fixed parsing seqs from cif when chaid id is wrong

  DimaMolod

  committed
  f41ea6a

  Copy full SHA for f41ea6a

• Unification: always pass first chain id, then seq

  DimaMolod

  committed
  9a3a5bd

  Copy full SHA for 9a3a5bd

• Oops

  DimaMolod

  committed
  d28f8b5

  Copy full SHA for d28f8b5

Commits on Sep 13, 2023

• Modify to_mmcif() for TrueMultimer

  DimaMolod

  committed
  e03e565

  Copy full SHA for e03e565

• Reprt num_msa and num_extra_msa in gradient mode

  DimaMolod

  committed
  d8a60ff

  Copy full SHA for d8a60ff

Commits on Sep 14, 2023

• Adapt to_mmcif() for use with TrueMultimer

  DimaMolod

  committed
  fed7fc3

  Copy full SHA for fed7fc3

Commits on Sep 18, 2023

• Point to commit 768f35d

  DimaMolod

  committed
  8d17eb5

  Copy full SHA for 8d17eb5

Commits on Sep 19, 2023

• Different MSA depth for different predictions

  DimaMolod

  committed
  1b12c8b

  Copy full SHA for 1b12c8b

• Use a custom class for handling biopython structure

  DimaMolod

  committed
  a3b9165

  Copy full SHA for a3b9165

• PEP8

  DimaMolod

  committed
  e34b950

  Copy full SHA for e34b950

• fix bug wrong longic with author chain

  DimaMolod

  committed
  0a19074

  Copy full SHA for 0a19074

Commits on Sep 26, 2023

• pytest for create_fake_database.py

  DimaMolod

  committed
  e454652

  Copy full SHA for e454652

• Check number of atoms and that atoms contain only label ids from poly_seq loop

  DimaMolod

  committed
  2169185

  Copy full SHA for 2169185

• Debug printing

  DimaMolod

  committed
  900fc12

  Copy full SHA for 900fc12

Commits on Sep 27, 2023

• Check integrity of _atom_site.label_seq_id in the template mmcifs

  DimaMolod

  committed
  2fc7dfd

  Copy full SHA for 2fc7dfd

• Added test for a bare pdb template

  DimaMolod

  committed
  d4b20d7

  Copy full SHA for d4b20d7

• Remove clashing/low_plddt residues from seqres_to_structure for consistency.

  DimaMolod

  committed
  cd42cba

  Copy full SHA for cd42cba

Commits on Sep 29, 2023

• run_multimer: added model_names and msa_depth flags

  DimaMolod

  committed
  ec4d364

  Copy full SHA for ec4d364

• New.

  DimaMolod

  committed
  d0acd9e

  Copy full SHA for d0acd9e

Commits on Oct 2, 2023

• run_multimer.py: update --gradient_msa_depth description

  Show description for 7a237e3
  DimaMolod

  committed
  7a237e3

  Copy full SHA for 7a237e3

• Update colabfold

  DimaMolod

  committed
  95e4250

  Copy full SHA for 95e4250

• New.

  DimaMolod

  committed
  2438c92

  Copy full SHA for 2438c92

Commits on Oct 4, 2023

• just renamed fake to custom :-)

  DimaMolod

  committed
  4095d95

  Copy full SHA for 4095d95

• Copy templates to the custom templates to avoid conflicts with files with the same file names

  DimaMolod

  committed
  979b30a

  Copy full SHA for 979b30a

• check that features are generated for mmt using subprocess

  DimaMolod

  committed
  a22dc69

  Copy full SHA for a22dc69

• check that template seq is not None, atom positions are not all zeros

  DimaMolod

  committed
  a701936

  Copy full SHA for a701936

Commits on Oct 5, 2023

• Check non-zero coordinates for backbone atoms for non-gap residues in template

  DimaMolod

  committed
  df5e165

  Copy full SHA for df5e165

Commits on Oct 6, 2023

• Parse seqres from pdb template using SeqIO

  DimaMolod

  committed
  899d1f3

  Copy full SHA for 899d1f3

• Residues with non-zero atom coords are identical for seqatom and seqres

  DimaMolod

  committed
  772e21e

  Copy full SHA for 772e21e

Commits on Oct 9, 2023

• benchmark models for testing truemultimer

  DimaMolod

  committed
  7eab024

  Copy full SHA for 7eab024

• Only for identical number of atoms for tests

  DimaMolod

  committed
  ab94027

  Copy full SHA for ab94027

• Create uniprot_runner, otherwise test always fails

  DimaMolod

  committed
  2411d57

  Copy full SHA for 2411d57

• Remove unused imports

  DimaMolod

  committed
  5ae2377

  Copy full SHA for 5ae2377

• Added test for truemultimer

  DimaMolod

  committed
  9781549

  Copy full SHA for 9781549

• Run TM tests on 3L4Q

  DimaMolod

  committed
  b99d416

  Copy full SHA for b99d416

Commits on Oct 10, 2023

• test/check_predict_structure.py

  DimaMolod

  committed
  bb258fc

  Copy full SHA for bb258fc

• Check that the best RMSD from 3 models is below 3A

  DimaMolod

  committed
  922c7a2

  Copy full SHA for 922c7a2

• Tests for custom msa depth

  DimaMolod

  committed
  89fd217

  Copy full SHA for 89fd217

• New

  DimaMolod

  committed
  60c5f9a

  Copy full SHA for 60c5f9a

• Bumped to v1.00.0

  DimaMolod

  committed
  dfe6855

  Copy full SHA for dfe6855

• sync names with the main branch

  DimaMolod

  committed
  8441991

  Copy full SHA for 8441991

• Merge remote-tracking branch 'origin/main' into TrueMultimer

  DimaMolod

  committed
  3615451

  Copy full SHA for 3615451

Commits on Oct 16, 2023

• Updated pipeline

  DimaMolod

  committed
  a3a7c61

  Copy full SHA for a3a7c61

• Merge branch 'main' into TrueMultimer

  dingquanyu

  authored
  8d24dff

  Copy full SHA for 8d24dff

• Merge branch 'main' of github.com:KosinskiLab/AlphaPulldown into TrueMultimer

  DimaMolod

  committed
  28d9df4

  Copy full SHA for 28d9df4

• Fix bug in create_model_runners for monomers

  DimaMolod

  committed
  1356255

  Copy full SHA for 1356255

Commits on Oct 17, 2023

• Generate random name for pdb without header and fn>4. More tests

  DimaMolod

  committed
  5b65e3f

  Copy full SHA for 5b65e3f

Commits on Oct 18, 2023

• 1.Correct meta.json and 2.test for pdb with crazy filename

  DimaMolod

  committed
  0f8eea2

  Copy full SHA for 0f8eea2

• Fix assert: code for pdbs is generated randomly each time

  DimaMolod

  committed
  a9801af

  Copy full SHA for a9801af

Commits on Oct 19, 2023

• All tests are run with a single command'

  DimaMolod

  committed
  d48e0cc

  Copy full SHA for d48e0cc

• Added requirements for pdb filenames

  DimaMolod

  committed
  79055cb

  Copy full SHA for 79055cb

Commits on Oct 20, 2023

• Major update of dependencies and structure

  DimaMolod

  committed
  966633c

  Copy full SHA for 966633c

Commits on Oct 23, 2023

• New. For developing

  DimaMolod

  committed
  49d7dd1

  Copy full SHA for 49d7dd1

Commits on Oct 24, 2023

• temp disable falling tests

  DimaMolod

  committed
  cf36ac8

  Copy full SHA for cf36ac8

• New. environment.yml for development, meta.yaml for installation

  DimaMolod

  committed
  d340c4e

  Copy full SHA for d340c4e

• Fix wrong path to pickles in test 6

  DimaMolod

  committed
  78b2eee

  Copy full SHA for 78b2eee

• Push to pypi-test on release

  DimaMolod

  committed
  dba0f4c

  Copy full SHA for dba0f4c

• New. Print doctstrings upon execution

  DimaMolod

  committed
  457aa43

  Copy full SHA for 457aa43

Commits on Oct 25, 2023

• All sub modules must be added explicitly to setup.cfg

  DimaMolod

  committed
  83faf52

  Copy full SHA for 83faf52

Commits on Oct 27, 2023

• update template searching process when running mmseq2 mode and using TrueMultimer at the same time

  dingquanyu

  committed
  6c3edbe

  Copy full SHA for 6c3edbe

Commits on Nov 5, 2023

• Added the failing gappy PDB custom template + minor fix in test_features_with_templates.py tearDown

  jkosinski

  committed
  cc48155

  Copy full SHA for cc48155

• Symlink individual files instead of the entire directory

  jkosinski

  committed
  4de40e2

  Copy full SHA for 4de40e2

Commits on Nov 7, 2023

• Merge pull request #197 from KosinskiLab/gappy_pdb

  Show description for accd168
  DimaMolod

  authored
  accd168

  Copy full SHA for accd168

Commits on Nov 8, 2023

• Changes to meta.json

  DimaMolod

  committed
  69bf6fa

  Copy full SHA for 69bf6fa

Commits on Nov 13, 2023

• revert to load_module for parsing af flags

  DimaMolod

  committed
  c6c9bef

  Copy full SHA for c6c9bef

• Fix for gappy test pdb

  DimaMolod

  committed
  404fd65

  Copy full SHA for 404fd65

• Clean dynamically created files for test_features_with_templates and move to tmp

  DimaMolod

  committed
  35c6240

  Copy full SHA for 35c6240

Commits on Nov 14, 2023

• Use protein descritpions instead of fasta files in description.csv

  DimaMolod

  committed
  1ac7012

  Copy full SHA for 1ac7012

Commits on Nov 15, 2023

• Use protein description instead of path to fasta. Updated instructions for developers

  DimaMolod

  committed
  98bc1ce

  Copy full SHA for 98bc1ce

• Fixed double removal of > in fasta description

  DimaMolod

  committed
  741aa0e

  Copy full SHA for 741aa0e

• Add example slurm script for features generation

  DimaMolod

  committed
  759964e

  Copy full SHA for 759964e

• Added missing '\' to slurm scripts

  DimaMolod

  committed
  54dd2bd

  Copy full SHA for 54dd2bd

• MmcifChainFiltered takes now pathlib, not string

  DimaMolod

  committed
  aa8beb9

  Copy full SHA for aa8beb9

• Checkout from main

  DimaMolod

  committed
  768fc68

  Copy full SHA for 768fc68

• Merge branch 'main' into TrueMultimer

  DimaMolod

  authored
  0ed62cd

  Copy full SHA for 0ed62cd