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aws-finetuning-code
openfold/scripts
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Sachin Kadyan 1b5813df76 Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
..
__pycache__
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
alignment_db_scripts
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
slurm_scripts
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
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
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
convert_of_weights_to_jax.py
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
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
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -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_cameo.py
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
download_colabfold_envdb.sh
Add MMseqs2 MSA generation
2021-11-09 02:57:53 -05:00
download_data.sh
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
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
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
download_openfold_params_huggingface.sh
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
download_openfold_params.sh
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
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
execute_on_cluster_expanse.job
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
execute_on_cluster_orig.job
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
execute_on_cluster.job
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
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_esm_embeddings.py
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
generate_mmcif_cache.py
Fix bug in mmCIF cache script
2022-03-14 16:31:02 -04:00
install_hh_suite.sh
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
install_third_party_dependencies.sh
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
precompute_alignments_mmseqs.py
Update precompute_alignments_mmseqs.py
2021-11-29 15:11:41 -06:00
precompute_alignments.py
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
precompute_esm_embeddings.py
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
precompute_template_hits.py
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
prep_mmseqs_dbs.sh
Fix mmseqs script bug
2021-12-10 18:33:23 -05:00
prep_proteinnet_msas.py
Rename prepare_proteinnet_msas.py to prep_proteinnet_msas.py
2021-12-20 00:50:20 -05:00
protein_to_casp15.py
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00
run_unit_tests.sh
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -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
Snapshot of the code used to run the finetuning training on the cluster of 15 AWS p4d instances.
2023-01-09 20:55:03 -05:00