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etowahadams

updated script

Feb 23, 2025

e8d3558 · Feb 23, 2025

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Name		Name	Last commit message	Last commit date
parent directory ..
alignment_db_scripts		alignment_db_scripts	Slightly improve comment	May 6, 2024
slurm_scripts		slurm_scripts	Add SLURM script acknowledgement	Jun 21, 2022
__init__.py		__init__.py	Work on multimer continues	Apr 28, 2022
activate_conda_env.sh		activate_conda_env.sh	Add conda env scripts	Sep 22, 2021
alignment_data_to_fasta.py		alignment_data_to_fasta.py	Improve import formatting	May 6, 2024
build_deepspeed_config.py		build_deepspeed_config.py	Add missing warmup_num_steps parameter.	Mar 7, 2023
colabfold_search.sh		colabfold_search.sh	Restore missing shebang	Jul 14, 2022
convert_of_weights_to_jax.py		convert_of_weights_to_jax.py	Fix for loading old OF weights into refactored model	Nov 3, 2023
convert_v1_to_v2_weights.py		convert_v1_to_v2_weights.py	Removes OF copy of zero_to_fp32.py favoring deepspeed.util version	May 2, 2024
data_dir_to_fasta.py		data_dir_to_fasta.py	Fixed bug in triangle multiplicative update and added early stop recy…	Jun 2, 2023
deactivate_conda_env.sh		deactivate_conda_env.sh	Add conda env scripts	Sep 22, 2021
deepspeed_inference_test.py		deepspeed_inference_test.py	Work on multimer continues	Apr 28, 2022
download_alphafold_dbs.sh		download_alphafold_dbs.sh	Multimer v3 updates	Apr 17, 2023
download_alphafold_params.sh		download_alphafold_params.sh	Multimer v3 updates	Apr 17, 2023
download_bfd.sh		download_bfd.sh	Add +x to download scripts	Oct 6, 2022
download_cameo.py		download_cameo.py	Fix check for max_seqlen.	Mar 14, 2023
download_colabfold_envdb.sh		download_colabfold_envdb.sh	Add +x to download scripts	Oct 6, 2022
download_mgnify.sh		download_mgnify.sh	Multimer v3 updates	Apr 17, 2023
download_mmseqs_dbs.sh		download_mmseqs_dbs.sh	Add +x to download scripts	Oct 6, 2022
download_openfold_params.sh		download_openfold_params.sh	Add region to aws command	Jul 19, 2022
download_openfold_params_gdrive.sh		download_openfold_params_gdrive.sh	Add +x to download scripts	Oct 6, 2022
download_openfold_params_huggingface.sh		download_openfold_params_huggingface.sh	Switch source of OF parameters to HuggingFace	Jun 22, 2022
download_openfold_soloseq_params.sh		download_openfold_soloseq_params.sh	Fix usage example in download_openfold_soloseq_params.sh	Mar 26, 2024
download_pdb70.sh		download_pdb70.sh	Add +x to download scripts	Oct 6, 2022
download_pdb_mmcif.sh		download_pdb_mmcif.sh	Add +x to download scripts	Oct 6, 2022
download_pdb_seqres.sh		download_pdb_seqres.sh	Multimer v3 updates	Apr 17, 2023
download_roda_pdbs.sh		download_roda_pdbs.sh	Improve RODA download process	Aug 28, 2022
download_small_bfd.sh		download_small_bfd.sh	Add +x to download scripts	Oct 6, 2022
download_soloseq_embeddings.sh		download_soloseq_embeddings.sh	Add script to download embeddings for training SoloSeq	Mar 26, 2024
download_uniclust30.sh		download_uniclust30.sh	Add +x to download scripts	Oct 6, 2022
download_uniprot.sh		download_uniprot.sh	Work on multimer continues	Apr 28, 2022
download_uniref30.sh		download_uniref30.sh	Added UniRef30 to data pipeline	Apr 18, 2023
download_uniref90.sh		download_uniref90.sh	Add +x to download scripts	Oct 6, 2022
expand_alignment_duplicates.py		expand_alignment_duplicates.py	Give script more descriptive name	May 6, 2024
fasta_to_clusterfile.py		fasta_to_clusterfile.py	Set CLI description to more informative module docstring	May 6, 2024
flatten_roda.sh		flatten_roda.sh	updated script	Feb 23, 2025
generate_alphafold_feature_dict.py		generate_alphafold_feature_dict.py	Bug fixes for multimer inference and monomer training	Aug 2, 2023
generate_chain_data_cache.py		generate_chain_data_cache.py	Fixed bug in triangle multiplicative update and added early stop recy…	Jun 2, 2023
generate_mmcif_cache.py		generate_mmcif_cache.py	Refactoring multimer data pipeline and permutation alignment.	Oct 16, 2023
install_hh_suite.sh		install_hh_suite.sh	Force HHSuite symlink	Aug 7, 2022
install_third_party_dependencies.sh		install_third_party_dependencies.sh	Remove env restart from setup script	Dec 8, 2023
precompute_alignments.py		precompute_alignments.py	Added multimer inference to README	Oct 30, 2023
precompute_alignments_mmseqs.py		precompute_alignments_mmseqs.py	Update precompute_alignments_mmseqs.py	Nov 29, 2021
precompute_embeddings.py		precompute_embeddings.py	Separate out input parsing code in EmbeddingGenerator	Oct 24, 2023
prep_mmseqs_dbs.sh		prep_mmseqs_dbs.sh	Process *.tar and *.tar.gz files.	Oct 8, 2022
prep_proteinnet_msas.py		prep_proteinnet_msas.py	Rename prepare_proteinnet_msas.py to prep_proteinnet_msas.py	Dec 20, 2021
run_unit_tests.sh		run_unit_tests.sh	Add low-memory attention (still needs to be incorporated)	Dec 17, 2021
unpack_proteinnet.py		unpack_proteinnet.py	Begin to add ProteinNet support (WIP)	Nov 10, 2021
utils.py		utils.py	in scripts/utils.py account for case where no conda environment is sp…	May 13, 2024
vars.sh		vars.sh	Add conda env scripts	Sep 22, 2021
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