Lukas Jarosch e2479cb539 Add more efficient script to generate all-seqs FASTA ...

The previous data_dir_to_fasta.py script is very slow and requires fully reparsing mmCIF files. This new script is much faster and uses the sequence information from the alignment data instead. Note that this will not include chains for which alignments could not be generated, but we can't use those during training anyways.

2024-05-05 23:48:19 -07:00

..

alignment_db_scripts

Add duplicate chain file support to alignment DB script

2024-03-19 20:48:26 -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

Add more efficient script to generate all-seqs FASTA

2024-05-05 23:48:19 -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

Add log statement to weight conversion script

2024-02-14 00:48:00 -05:00

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

Adds Soloseq parameter download script.

2023-11-29 18:30:19 -05:00

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_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_roda_duplicates.py

Add script for expanding the alignment dir with duplicates

2024-03-19 21:04:35 -07:00

fasta_to_clusterfile.py

Scripts from Lukas to be used in improved setup process

2024-02-20 12:21:32 -05:00

flatten_roda.sh

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

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

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

Remove env restart from setup script

2023-12-08 16:50:23 -05:00

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

Added UniRef30 to data pipeline

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

vars.sh

Add conda env scripts

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

zero_to_fp32.py

updates zero_to_fp32.py for new deepspeed version and import_weight bugfix

2024-02-08 04:08:35 -05:00