Sachin Kadyan 8185c30775 Just-in-time embedding generation for the SoloSeq model

2023-10-24 01:03:20 -05:00

..

alignment_db_scripts

Add alignment DB scripts

2022-06-27 18:23:31 -04:00

slurm_scripts

Add SLURM script acknowledgement

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

activate_conda_env.sh

Add conda env scripts

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

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

Touch up OF/AF conversion script

2022-06-24 02:13:22 -04:00

data_dir_to_fasta.py

Add more ProteinNet functionality

2021-11-10 01:53:46 -05:00

deactivate_conda_env.sh

Add conda env scripts

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

download_alphafold_dbs.sh

Add +x to download scripts

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

download_alphafold_params.sh

Update AlphaFold parameter download link

2022-02-01 12:36:55 -05:00

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

Add +x to download scripts

2022-10-06 01:28:39 -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_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_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_uniref30.sh

Add +x to download scripts

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

download_uniref90.sh

Add +x to download scripts

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

flatten_roda.sh

Fix bug in flattening script

2022-08-09 23:44:30 -04:00

generate_alphafold_feature_dict.py

Add script for generating sample feature dict

2021-12-30 19:51:50 -05:00

generate_chain_data_cache.py

Fixes errors when processing .pdb files

2022-08-02 10:17:52 +02:00

generate_mmcif_cache.py

Fix bug in mmCIF cache script

2022-03-14 16:31:02 -04:00

install_hh_suite.sh

Force HHSuite symlink

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

install_third_party_dependencies.sh

Preserves one copy of tests/test_data/sample_feats.pickle.gz for unit

2023-09-20 13:04:47 -07:00

precompute_alignments_mmseqs.py

Update precompute_alignments_mmseqs.py

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

precompute_alignments.py

Vastly lower peak inference memory usage

2022-06-10 02:19:32 -04:00

precompute_embeddings.py

Just-in-time embedding generation for the SoloSeq model

2023-10-24 01:03:20 -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

Fix get_nvidia_cc to handle cases where cuda.cuGetErrorString gives a None result

2022-08-11 17:18:15 -04:00

vars.sh

Add conda env scripts

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

zero_to_fp32.py

fix incorrect learning rate warm-up after restarting from ckpt

2022-07-29 18:05:07 -05:00