├── .github └── workflows │ └── workflow.yaml ├── .gitignore ├── LICENSE.md ├── README.md ├── alntools ├── __init__.py ├── alignment.py ├── base.py ├── density │ ├── __init__.py │ ├── iterate.py │ ├── local.py │ └── parallel.py ├── filehandle.py ├── numeric.py ├── parser.py ├── postprocess │ ├── __init__.py │ ├── compare.py │ ├── filter.py │ └── format.py ├── prepare │ ├── __init__.py │ ├── iterate.py │ ├── reduce_duplicates.py │ └── screening.py └── settings.py ├── embedders ├── __init__.py ├── ankh.py ├── base.py ├── checkpoint.py ├── dataset.py ├── esm.py ├── hfautomodel.py ├── prottrans.py └── schema.py ├── embeddings.py ├── examples ├── README.md ├── allvsall.md ├── allvsall.sh ├── bacteria.md ├── data │ ├── figures │ │ ├── cupredoxin.hits_score_ecod.legend.png │ │ └── cupredoxin.hits_score_ecod.png │ ├── input │ │ ├── cupredoxin.fas │ │ ├── immunoglobulin.fas │ │ ├── protein.fas │ │ └── rossmannsdb.fas │ └── output │ │ └── rossmannsdb.fas ├── onevsall.sh ├── scope.md ├── scope.sh ├── scripts │ └── split_fasta.py ├── stepbystep_in_python.md └── use_in_python.md ├── pyproject.toml ├── requirements.txt ├── requirements_dev.txt ├── scripts ├── csv2nice.py ├── dbtofile.py ├── merge.py ├── plmblast.py └── plot.py └── tests ├── _test_numeric.py ├── seq_single.fasta ├── test_data ├── asymetric.fasta ├── asymetric.pt ├── cupredoxin.fas ├── cupredoxin.pt ├── database.csv ├── densitymap_example.pt ├── emb_checkpoint_end.json ├── emb_checkpoint_middle.json ├── emb_checkpoint_mp_0.json ├── emb_checkpoint_start.json ├── embeddings │ ├── 1.emb │ ├── 10000.emb │ ├── 250.emb │ ├── 25000.emb │ ├── 500.emb │ └── 50000.emb ├── multi_query.fas ├── rossmanns.fas ├── rossmannsdb.fas ├── seq.fasta └── seq.p ├── test_density.py ├── test_draw.py ├── test_embeddings.py ├── test_flow.py ├── test_script.py └── test_utils.py /.github/workflows/workflow.yaml: -------------------------------------------------------------------------------- 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