├── .github ├── ISSUE_TEMPLATE.md └── workflows │ ├── ci.yaml │ └── release.yaml ├── .gitignore ├── .readthedocs.yaml ├── AUTHORS.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── HISTORY.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── NC_043029.png ├── Pharokka_Phold_Phynteny.png ├── citation.md ├── index.md ├── install.md ├── method.md ├── output.md ├── phold_logo.png ├── phold_workflow.png ├── requirements.txt ├── run.md └── tutorial.md ├── environment.yml ├── img ├── NC_043029.png ├── Pharokka_Phold_Phynteny.png ├── phold_logo.png └── phold_workflow.png ├── mkdocs.yml ├── pyproject.toml ├── run_pharokka_and_phold_and_phynteny.ipynb ├── run_phold.ipynb ├── src └── phold │ ├── __init__.py │ ├── cnn │ ├── cnn_chkpnt │ │ └── model.pt │ └── cnn_chkpnt_finetune │ │ ├── phold_db_model.pth │ │ └── vanilla_model.pth │ ├── databases │ └── db.py │ ├── features │ ├── create_foldseek_db.py │ ├── predict_3Di.py │ ├── query_remote_3Di.py │ └── run_foldseek.py │ ├── io │ ├── handle_genbank.py │ └── sub_db_outputs.py │ ├── plot │ └── plot.py │ ├── results │ └── topfunction.py │ ├── subcommands │ ├── compare.py │ └── predict.py │ └── utils │ ├── CITATION │ ├── VERSION │ ├── constants.py │ ├── external_tools.py │ ├── util.py │ └── validation.py └── tests ├── __init__.py ├── conftest.py ├── test_data ├── KF623293.1_subset_efam.fasta ├── NC_043029.fasta ├── NC_043029.gbk ├── NC_043029_aa.fasta ├── NC_043029_af3_cif │ ├── NC_043029_CDS_0001.cif │ ├── NC_043029_CDS_0002.cif │ ├── NC_043029_CDS_0003.cif │ ├── NC_043029_CDS_0004.cif │ ├── NC_043029_CDS_0005.cif │ ├── NC_043029_CDS_0006.cif │ ├── NC_043029_CDS_0007.cif │ ├── NC_043029_CDS_0008.cif │ ├── NC_043029_CDS_0009.cif │ ├── NC_043029_CDS_0010.cif │ ├── NC_043029_CDS_0011.cif │ ├── NC_043029_CDS_0012.cif │ ├── NC_043029_CDS_0013.cif │ ├── NC_043029_CDS_0014.cif │ └── NC_043029_CDS_0015.cif ├── NC_043029_bakta.gbk ├── NC_043029_intermediate_output_restart_compare │ ├── foldseek_db │ │ ├── phold │ │ ├── phold.dbtype │ │ ├── phold.index │ │ ├── phold_h │ │ ├── phold_h.dbtype │ │ ├── phold_h.index │ │ ├── phold_ss │ │ ├── phold_ss.dbtype │ │ └── phold_ss.index │ ├── foldseek_results.tsv │ ├── logs │ │ ├── foldseek_04db9b85199ac60f2445e481de5b5566fcc70e4cb9e58b4df2e16064dcadb9b9.err │ │ ├── foldseek_04db9b85199ac60f2445e481de5b5566fcc70e4cb9e58b4df2e16064dcadb9b9.out │ │ ├── foldseek_37d5cdc60687a1cedf114d3f53905f4c08c7e1281e9b69adf3467c58e79f5fc5.err │ │ ├── foldseek_37d5cdc60687a1cedf114d3f53905f4c08c7e1281e9b69adf3467c58e79f5fc5.out │ │ ├── foldseek_6199211ca3102ec2075ed1c39aacf99876ca6021ec99488afcf7d89a0c0fdf0b.err │ │ ├── foldseek_6199211ca3102ec2075ed1c39aacf99876ca6021ec99488afcf7d89a0c0fdf0b.out │ │ ├── foldseek_791cfdd6c1ab0b846909336d8e9b769e1a87ac074ca01967bbfdc31b790daeda.err │ │ ├── foldseek_791cfdd6c1ab0b846909336d8e9b769e1a87ac074ca01967bbfdc31b790daeda.out │ │ ├── foldseek_861cc3102ee2c1d6c6cabfc3022a59e197b26b806624012bf211bef0b856dbce.err │ │ └── foldseek_861cc3102ee2c1d6c6cabfc3022a59e197b26b806624012bf211bef0b856dbce.out │ ├── phold_3di.fasta │ ├── phold_aa.fasta │ ├── phold_prostT5_3di_all_probabilities.json │ ├── phold_prostT5_3di_mean_probabilities.csv │ ├── result_db │ │ ├── result_db.0 │ │ ├── result_db.1 │ │ ├── result_db.2 │ │ ├── result_db.3 │ │ ├── result_db.4 │ │ ├── result_db.5 │ │ ├── result_db.6 │ │ ├── result_db.7 │ │ ├── result_db.dbtype │ │ └── result_db.index │ └── temp_db │ │ ├── 12238294553495473419 │ │ └── structuresearch.sh │ │ └── latest ├── NC_043029_intermediate_output_restart_proteins │ ├── foldseek_db │ │ ├── phold │ │ ├── phold.dbtype │ │ ├── phold.index │ │ ├── phold_h │ │ ├── phold_h.dbtype │ │ ├── phold_h.index │ │ ├── phold_ss │ │ ├── phold_ss.dbtype │ │ └── phold_ss.index │ ├── foldseek_results.tsv │ ├── logs │ │ ├── foldseek_2892c7b6f4f204bf2725f365570720f54df3eac42e4819edfc0b3193513bded2.err │ │ ├── foldseek_2892c7b6f4f204bf2725f365570720f54df3eac42e4819edfc0b3193513bded2.out │ │ ├── foldseek_29aa66c9fb52717487175b6873a651d389d3df834bd57b6f40d9f53e83409e86.err │ │ ├── foldseek_29aa66c9fb52717487175b6873a651d389d3df834bd57b6f40d9f53e83409e86.out │ │ ├── foldseek_65209b1f66ee39bee2f98278f251224b1296f83f65a5b5381f3c15d413a1699b.err │ │ ├── foldseek_65209b1f66ee39bee2f98278f251224b1296f83f65a5b5381f3c15d413a1699b.out │ │ ├── foldseek_777cfad43596a9a0ee87c0c5c4cf568d555221eba354ad8e895ccb78fe53992e.err │ │ ├── foldseek_777cfad43596a9a0ee87c0c5c4cf568d555221eba354ad8e895ccb78fe53992e.out │ │ ├── foldseek_90341afc0dc990e8017a0480bd10105491b2f25d5c20f88d4ff102855ea20641.err │ │ └── foldseek_90341afc0dc990e8017a0480bd10105491b2f25d5c20f88d4ff102855ea20641.out │ ├── phold_3di.fasta │ ├── phold_aa.fasta │ ├── result_db │ │ ├── result_db.0 │ │ ├── result_db.1 │ │ ├── result_db.2 │ │ ├── result_db.3 │ │ ├── result_db.4 │ │ ├── result_db.5 │ │ ├── result_db.6 │ │ ├── result_db.7 │ │ ├── result_db.dbtype │ │ └── result_db.index │ └── temp_db │ │ ├── 1077122709128069098 │ │ └── structuresearch.sh │ │ └── latest ├── NC_043029_intermediate_output_restart_run │ ├── foldseek_db │ │ ├── phold │ │ ├── phold.dbtype │ │ ├── phold.index │ │ ├── phold_h │ │ ├── phold_h.dbtype │ │ ├── phold_h.index │ │ ├── phold_ss │ │ ├── phold_ss.dbtype │ │ └── phold_ss.index │ ├── foldseek_results.tsv │ ├── logs │ │ ├── foldseek_04db9b85199ac60f2445e481de5b5566fcc70e4cb9e58b4df2e16064dcadb9b9.err │ │ ├── foldseek_04db9b85199ac60f2445e481de5b5566fcc70e4cb9e58b4df2e16064dcadb9b9.out │ │ ├── foldseek_37d5cdc60687a1cedf114d3f53905f4c08c7e1281e9b69adf3467c58e79f5fc5.err │ │ ├── foldseek_37d5cdc60687a1cedf114d3f53905f4c08c7e1281e9b69adf3467c58e79f5fc5.out │ │ ├── foldseek_6199211ca3102ec2075ed1c39aacf99876ca6021ec99488afcf7d89a0c0fdf0b.err │ │ ├── foldseek_6199211ca3102ec2075ed1c39aacf99876ca6021ec99488afcf7d89a0c0fdf0b.out │ │ ├── foldseek_791cfdd6c1ab0b846909336d8e9b769e1a87ac074ca01967bbfdc31b790daeda.err │ │ ├── foldseek_791cfdd6c1ab0b846909336d8e9b769e1a87ac074ca01967bbfdc31b790daeda.out │ │ ├── foldseek_861cc3102ee2c1d6c6cabfc3022a59e197b26b806624012bf211bef0b856dbce.err │ │ └── foldseek_861cc3102ee2c1d6c6cabfc3022a59e197b26b806624012bf211bef0b856dbce.out │ ├── phold_3di.fasta │ ├── phold_aa.fasta │ ├── phold_prostT5_3di_all_probabilities.json │ ├── phold_prostT5_3di_mean_probabilities.csv │ ├── result_db │ │ ├── result_db.0 │ │ ├── result_db.1 │ │ ├── result_db.2 │ │ ├── result_db.3 │ │ ├── result_db.4 │ │ ├── result_db.5 │ │ ├── result_db.6 │ │ ├── result_db.7 │ │ ├── result_db.dbtype │ │ └── result_db.index │ └── temp_db │ │ ├── 12238294553495473419 │ │ └── structuresearch.sh │ │ └── latest ├── NC_043029_ncbi.gbk ├── NC_043029_pdbs │ ├── NC_043029_CDS_0001.pdb │ ├── NC_043029_CDS_0002.pdb │ ├── NC_043029_CDS_0003.pdb │ ├── NC_043029_CDS_0004.pdb │ ├── NC_043029_CDS_0005.pdb │ ├── NC_043029_CDS_0006.pdb │ ├── NC_043029_CDS_0007.pdb │ ├── NC_043029_CDS_0008.pdb │ ├── NC_043029_CDS_0009.pdb │ ├── NC_043029_CDS_0010.pdb │ ├── NC_043029_CDS_0011.pdb │ ├── NC_043029_CDS_0012.pdb │ ├── NC_043029_CDS_0013.pdb │ ├── NC_043029_CDS_0014.pdb │ ├── NC_043029_CDS_0015.pdb │ └── badly_named.pdb ├── NC_043029_pharokka1.4.1.gbk ├── NC_043029_phold_output.gbk ├── SAOMS1.gbk ├── WP_006719989_subset_test.fasta ├── colon.fasta ├── colon.gbk ├── combined_truncated_acr_defense_vfdb_card.fasta ├── combined_truncated_acr_defense_vfdb_card.gbk ├── dummy_custom_db │ ├── dummy_db │ ├── dummy_db.dbtype │ ├── dummy_db.index │ ├── dummy_db.lookup │ ├── dummy_db.source │ ├── dummy_db_ca │ ├── dummy_db_ca.dbtype │ ├── dummy_db_ca.index │ ├── dummy_db_gpu │ ├── dummy_db_gpu.dbtype │ ├── dummy_db_gpu.index │ ├── dummy_db_gpu.lookup │ ├── dummy_db_gpu.source │ ├── dummy_db_gpu_ca │ ├── dummy_db_gpu_ca.dbtype │ ├── dummy_db_gpu_ca.index │ ├── dummy_db_gpu_h │ ├── dummy_db_gpu_h.dbtype │ ├── dummy_db_gpu_h.index │ ├── dummy_db_gpu_ss │ ├── dummy_db_gpu_ss.dbtype │ ├── dummy_db_gpu_ss.index │ ├── 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