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alignment_db_scripts
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Slightly improve comment
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2024-05-05 23:49:59 -07:00 |
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slurm_scripts
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Add SLURM script acknowledgement
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2022-06-21 01:29:42 -04:00 |
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__init__.py
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Work on multimer continues
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2022-04-28 18:45:54 -04:00 |
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activate_conda_env.sh
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Add conda env scripts
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2021-09-22 01:29:49 -04:00 |
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alignment_data_to_fasta.py
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Improve import formatting
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2024-05-05 23:53:31 -07:00 |
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build_deepspeed_config.py
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Add missing warmup_num_steps parameter.
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2023-03-07 17:29:48 -05:00 |
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colabfold_search.sh
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Restore missing shebang
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2022-07-14 07:26:57 -04:00 |
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convert_of_weights_to_jax.py
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Fix for loading old OF weights into refactored model
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2023-11-03 14:26:18 -04:00 |
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convert_v1_to_v2_weights.py
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Removes OF copy of zero_to_fp32.py favoring deepspeed.util version
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2024-05-02 03:22:55 -04:00 |
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data_dir_to_fasta.py
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Fixed bug in triangle multiplicative update and added early stop recycling.
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2023-06-02 15:02:45 -04:00 |
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deactivate_conda_env.sh
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Add conda env scripts
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2021-09-22 01:29:49 -04:00 |
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deepspeed_inference_test.py
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Work on multimer continues
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2022-04-28 18:45:54 -04:00 |
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download_alphafold_dbs.sh
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Multimer v3 updates
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2023-04-17 14:25:45 -04:00 |
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download_alphafold_params.sh
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Multimer v3 updates
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2023-04-17 14:25:45 -04:00 |
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download_bfd.sh
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Add +x to download scripts
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2022-10-06 01:28:39 -04:00 |
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download_cameo.py
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Fix check for max_seqlen.
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2023-03-14 16:09:22 -04:00 |
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download_colabfold_envdb.sh
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Add +x to download scripts
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2022-10-06 01:28:39 -04:00 |
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download_mgnify.sh
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Multimer v3 updates
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2023-04-17 14:25:45 -04:00 |
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download_mmseqs_dbs.sh
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Add +x to download scripts
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2022-10-06 01:28:39 -04:00 |
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download_openfold_params.sh
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Add region to aws command
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2022-07-19 10:36:02 -04:00 |
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download_openfold_params_gdrive.sh
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Add +x to download scripts
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2022-10-06 01:28:39 -04:00 |
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download_openfold_params_huggingface.sh
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Switch source of OF parameters to HuggingFace
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2022-06-22 15:48:28 -04:00 |
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download_openfold_soloseq_params.sh
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Fix usage example in `download_openfold_soloseq_params.sh`
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2024-03-26 17:35:03 -04:00 |
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download_pdb70.sh
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Add +x to download scripts
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2022-10-06 01:28:39 -04:00 |
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download_pdb_mmcif.sh
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Add +x to download scripts
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2022-10-06 01:28:39 -04:00 |
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download_pdb_seqres.sh
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Multimer v3 updates
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2023-04-17 14:25:45 -04:00 |
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download_roda_pdbs.sh
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Improve RODA download process
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2022-08-28 17:29:13 -04:00 |
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download_small_bfd.sh
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Add +x to download scripts
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2022-10-06 01:28:39 -04:00 |
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download_soloseq_embeddings.sh
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Add script to download embeddings for training SoloSeq
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2024-03-26 17:36:00 -04:00 |
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download_uniclust30.sh
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Add +x to download scripts
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2022-10-06 01:28:39 -04:00 |
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download_uniprot.sh
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Work on multimer continues
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2022-04-28 18:45:54 -04:00 |
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download_uniref30.sh
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Added UniRef30 to data pipeline
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2023-04-18 13:37:36 -04:00 |
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download_uniref90.sh
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Add +x to download scripts
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2022-10-06 01:28:39 -04:00 |
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expand_alignment_duplicates.py
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Give script more descriptive name
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2024-05-05 23:49:22 -07:00 |
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fasta_to_clusterfile.py
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Set CLI description to more informative module docstring
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2024-05-05 23:51:41 -07:00 |
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flatten_roda.sh
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Fixed bug in triangle multiplicative update and added early stop recycling.
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2023-06-02 15:02:45 -04:00 |
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generate_alphafold_feature_dict.py
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Bug fixes for multimer inference and monomer training
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2023-08-02 15:15:06 -04:00 |
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generate_chain_data_cache.py
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Fixed bug in triangle multiplicative update and added early stop recycling.
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2023-06-02 15:02:45 -04:00 |
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generate_mmcif_cache.py
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Refactoring multimer data pipeline and permutation alignment.
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2023-10-16 15:40:40 -04:00 |
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install_hh_suite.sh
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Force HHSuite symlink
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2022-08-07 16:31:14 -04:00 |
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install_third_party_dependencies.sh
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Remove env restart from setup script
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2023-12-08 16:50:23 -05:00 |
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precompute_alignments.py
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Added multimer inference to README
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2023-10-30 16:15:05 -04:00 |
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precompute_alignments_mmseqs.py
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Update precompute_alignments_mmseqs.py
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2021-11-29 15:11:41 -06:00 |
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precompute_embeddings.py
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Separate out input parsing code in `EmbeddingGenerator`
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2023-10-24 12:30:25 -05:00 |
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prep_mmseqs_dbs.sh
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Process *.tar and *.tar.gz files.
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2022-10-08 16:48:35 -04:00 |
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prep_proteinnet_msas.py
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Rename prepare_proteinnet_msas.py to prep_proteinnet_msas.py
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2021-12-20 00:50:20 -05:00 |
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run_unit_tests.sh
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Add low-memory attention (still needs to be incorporated)
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2021-12-17 18:00:06 -05:00 |
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unpack_proteinnet.py
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Begin to add ProteinNet support (WIP)
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2021-11-09 23:53:14 -05:00 |
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utils.py
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in scripts/utils.py account for case where no conda environment is specified.
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2024-05-13 16:37:11 +07:00 |
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vars.sh
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Add conda env scripts
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2021-09-22 01:29:49 -04:00 |
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