openfold

alignment_db_scripts

Slightly improve comment

2024-05-05 23:49:59 -07:00

slurm_scripts

Add SLURM script acknowledgement

2022-06-21 01:29:42 -04:00

__init__.py

Work on multimer continues

2022-04-28 18:45:54 -04:00

activate_conda_env.sh

Add conda env scripts

2021-09-22 01:29:49 -04:00

alignment_data_to_fasta.py

Improve import formatting

2024-05-05 23:53:31 -07:00

build_deepspeed_config.py

Add missing warmup_num_steps parameter.

2023-03-07 17:29:48 -05:00

colabfold_search.sh

Restore missing shebang

2022-07-14 07:26:57 -04:00

convert_of_weights_to_jax.py

Fix for loading old OF weights into refactored model

2023-11-03 14:26:18 -04:00

convert_v1_to_v2_weights.py

Removes OF copy of zero_to_fp32.py favoring deepspeed.util version

2024-05-02 03:22:55 -04:00

data_dir_to_fasta.py

Fixed bug in triangle multiplicative update and added early stop recycling.

2023-06-02 15:02:45 -04:00

deactivate_conda_env.sh

Add conda env scripts

2021-09-22 01:29:49 -04:00

deepspeed_inference_test.py

Work on multimer continues

2022-04-28 18:45:54 -04:00

download_alphafold_dbs.sh

Multimer v3 updates

2023-04-17 14:25:45 -04:00

download_alphafold_params.sh

Multimer v3 updates

2023-04-17 14:25:45 -04:00

download_bfd.sh

Add +x to download scripts

2022-10-06 01:28:39 -04:00

download_cameo.py

Fix check for max_seqlen.

2023-03-14 16:09:22 -04:00

download_colabfold_envdb.sh

Add +x to download scripts

2022-10-06 01:28:39 -04:00

download_mgnify.sh

Multimer v3 updates

2023-04-17 14:25:45 -04:00

download_mmseqs_dbs.sh

Add +x to download scripts

2022-10-06 01:28:39 -04:00

download_openfold_params_gdrive.sh

Add +x to download scripts

2022-10-06 01:28:39 -04:00

download_openfold_params_huggingface.sh

Switch source of OF parameters to HuggingFace

2022-06-22 15:48:28 -04:00

download_openfold_params.sh

Add region to aws command

2022-07-19 10:36:02 -04:00

download_openfold_soloseq_params.sh

Fix usage example in download_openfold_soloseq_params.sh

2024-03-26 17:35:03 -04:00

download_pdb70.sh

Add +x to download scripts

2022-10-06 01:28:39 -04:00

download_pdb_mmcif.sh

Add +x to download scripts

2022-10-06 01:28:39 -04:00

download_pdb_seqres.sh

Multimer v3 updates

2023-04-17 14:25:45 -04:00

download_roda_pdbs.sh

Improve RODA download process

2022-08-28 17:29:13 -04:00

download_small_bfd.sh

Add +x to download scripts

2022-10-06 01:28:39 -04:00

download_soloseq_embeddings.sh

Add script to download embeddings for training SoloSeq

2024-03-26 17:36:00 -04:00

download_uniclust30.sh

Add +x to download scripts

2022-10-06 01:28:39 -04:00

download_uniprot.sh

Work on multimer continues

2022-04-28 18:45:54 -04:00

download_uniref30.sh

Added UniRef30 to data pipeline

2023-04-18 13:37:36 -04:00

download_uniref90.sh

Add +x to download scripts

2022-10-06 01:28:39 -04:00

expand_alignment_duplicates.py

Give script more descriptive name

2024-05-05 23:49:22 -07:00

fasta_to_clusterfile.py

Set CLI description to more informative module docstring

2024-05-05 23:51:41 -07:00

flatten_roda.sh

updated script

2025-02-23 18:52:59 -05:00

generate_alphafold_feature_dict.py

Bug fixes for multimer inference and monomer training

2023-08-02 15:15:06 -04:00

generate_chain_data_cache.py

Fixed bug in triangle multiplicative update and added early stop recycling.

2023-06-02 15:02:45 -04:00

generate_mmcif_cache.py

Refactoring multimer data pipeline and permutation alignment.

2023-10-16 15:40:40 -04:00

install_hh_suite.sh

Force HHSuite symlink

2022-08-07 16:31:14 -04:00

install_third_party_dependencies.sh

Maintainance to pl_upgrades

2025-04-23 20:13:32 +00:00

precompute_alignments_mmseqs.py

Update precompute_alignments_mmseqs.py

2021-11-29 15:11:41 -06:00

precompute_alignments.py

Added multimer inference to README

2023-10-30 16:15:05 -04:00

precompute_embeddings.py

Separate out input parsing code in EmbeddingGenerator

2023-10-24 12:30:25 -05:00

prep_mmseqs_dbs.sh

Process *.tar and *.tar.gz files.

2022-10-08 16:48:35 -04:00

prep_proteinnet_msas.py

Rename prepare_proteinnet_msas.py to prep_proteinnet_msas.py

2021-12-20 00:50:20 -05:00

run_unit_tests.sh

Add low-memory attention (still needs to be incorporated)

2021-12-17 18:00:06 -05:00

unpack_proteinnet.py

Begin to add ProteinNet support (WIP)

2021-11-09 23:53:14 -05:00

utils.py

in scripts/utils.py account for case where no conda environment is specified.

2024-05-13 16:37:11 +07:00

vars.sh

Add conda env scripts

2021-09-22 01:29:49 -04:00