v2.3.1 - merge 'beta' into 'main' (#371)
* Added input_features_callback to run() function to allow plotting MSA before structure predictions computation.
* Added lower level plot_pae() and plot_protein_backbone() functions to allow making individual plots instead of multi-pane composite plots.
* Fix typo in new protein backbone plotting code.
* testing v.2.3.0
* adding support for multimer_v3
* updating version number of alphafold-colabfold
* Update batch.py
convert unrelaxed protein features to numpy before saving (to speedup save function)
* add option to enable/disable fuse
* adding option to enable/disable fuse
* download v3 params by default
* adding option for iterating through random_seed(s)
* adding option to iterate through random seeds
* Update poetry.lock
* Delete poetry.lock
* Update batch.py
* Update test.yml
only run test on main branch
* fixing encoding error (when amber relax is used and notebook is run multiple times)
* refactoring code a bit to write the results to jobname directory
* add model_type into filename
* adding model_type to filename
* disable bfloat16 for old (v1, v2) multimer models
* select best view using plddt
* adding option to "save all" outputs of model
* adding option to save_all
* adding max_msa option to notebook
* allow max_msa settings for multimer
* adjust max settings
* updating dm-haiku to fix error in jax
* adding option to disable use_cluster_profile
* Created using Colaboratory
* code cleanup
* code cleanup
* Update models.py
* add option to enable bfloat16
* Fix tensorflow import
* making bfloat16 and fuse the default
* cleanup
* major bugfix for ptm + is_complex (#360)
* Update README.md
* adding option to control num of top models to relax
* control number of models to relax
* Update batch.py
* update pae filename
* remove whitespace from saved images
* addressing memory leak and pae bugfix
all outputs are saved as they are generated to avoid memory leaks. scores reloaded later for plotting.
bugfix: *_predicted_aligned_error_v1.json is now the best ranked output (before it was whichever model was saved first)
* adding leading zeros to rank id and seed id
* adding leading zeros to rank and seed id(s)
* Delete colabfold_alphafold.py
unused file
* monomers can now be predicted with multimer model!
* fix numbering
* Update batch.py
bugfix for custom msa input
run function updated to return model ranks and metrics
* update run function to print metrics and keep track of best model rank
* replacing max_msa
replacing max_msa option with max_seq and max_extra_seq to make easier to control.
* Update batch.py
* Update batch.py
rank_by wasn't computed correctly for multimer ranking
* Update AlphaFold2_batch.ipynb
* Update AlphaFold2_batch.ipynb
* adding TPU support
* remove TPU warning...
* disable BiopythonDeprecationWarning
* Move load_models_and_params to before the job loop (#368)
* Update batch.py
Move load_models_and_params to before the job loop to avoid issues when resuming from an existing directory with already finished jobs.
* Update batch.py
Change to check if it's the first job instead of moving load_models_and_params
* recompile_padding update
padding is now defined as a constant int instead of float
* Update README.md
* Created using Colaboratory
* Update batch.py
* Created using Colaboratory
* adding iptm support to ptm (for complexes)
* removing extra print out
* Update batch.py
* Update batch.py
* add option to save intermediate results
* add option to save_recycles
* Update batch.py
* updating pyproject.toml to use latest alphafold-colabfold v2.3
* Revert "updating pyproject.toml to use latest alphafold-colabfold v2.3"
This reverts commit bcf4ec9ea5
.
* Update alphafold-colabfold to 2.3.1
* attempt to fix test
* Adding link back to old version
* update test data
* Update test_colabfold.py
* fix test (fingers crossed)
* Update test_colabfold.py
* Update README.md
* updating notebooks to use "main" instead of "beta"
---------
Co-authored-by: Tom Goddard <goddard@sonic.net>
Co-authored-by: YoshitakaMo <virgospica93@gmail.com>
Co-authored-by: Milot Mirdita <milot@mirdita.de>
Co-authored-by: Dennis Svedberg <densvedberg@gmail.com>
Co-authored-by: Martin Steinegger <martin.steinegger@mpibpc.mpg.de>
Co-authored-by: Martin Steinegger <themartinsteinegger@gmail.com>
skiptemplatesearch
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