Gustaf Ahdritz 4e73026983 Fix bug in prep_mmseqs_dbs.sh

2022-06-27 17:32:23 -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

Undo DeepSpeed config change

2022-03-29 20:38:31 -04:00

colabfold_search.sh

Add MMseqs2 MSA generation

2021-11-09 02:57:53 -05:00

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

Fix AlphaFold DB download script

2021-12-19 15:44:13 -05:00

download_alphafold_params.sh

Update AlphaFold parameter download link

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

download_bfd.sh

Added the shell script to download the BFD database for HHBlits queries.

2021-10-08 17:36:34 -04:00

download_colabfold_envdb.sh

Add MMseqs2 MSA generation

2021-11-09 02:57:53 -05:00

download_data.sh

Fix bug in download_data.sh

2022-06-27 17:31:32 -04:00

download_mgnify.sh

Added the shell script to download the Mgnify database for JackHMMer MSA queries.

2021-10-08 17:52:48 -04:00

download_mmseqs_dbs.sh

Add MMseqs2 MSA generation

2021-11-09 02:57:53 -05:00

download_openfold_params_gdrive.sh

Switch source of OF parameters to HuggingFace

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

download_openfold_params_huggingface.sh

Switch source of OF parameters to HuggingFace

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

download_pdb70.sh

Added the shell script to download the PDB70 database.

2021-10-08 18:26:40 -04:00

download_pdb_mmcif.sh

Added the shell script to download the PDB mmCIF database.

2021-10-08 18:27:20 -04:00

download_small_bfd.sh

Added the shell script to download the small BFD database.

2021-10-08 18:27:48 -04:00

download_uniclust30.sh

Added the shell script to download the uniclust30 database.

2021-10-08 18:28:10 -04:00

download_uniref30.sh

Add MMseqs2 MSA generation

2021-11-09 02:57:53 -05:00

download_uniref90.sh

Added the shell script to download the uniref90 database.

2021-10-08 18:28:33 -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

One last adjustment to generate_chain_data_cache.py

2022-02-22 17:46:20 -05:00

generate_mmcif_cache.py

Fix bug in mmCIF cache script

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

install_hh_suite.sh

Fix formatting of install_hh_suite.sh

2022-06-23 23:17:05 -04:00

install_third_party_dependencies.sh

Fix install script

2022-06-23 13:08:00 -04:00

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

prep_mmseqs_dbs.sh

Fix bug in prep_mmseqs_dbs.sh

2022-06-27 17:32:23 -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

Add GPU relaxation

2022-02-03 22:50:34 -05:00

vars.sh

Add conda env scripts

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

zero_to_fp32.py

Fix model checkpointing bug

2021-10-26 16:16:25 -04:00