├── .gitignore ├── LICENSE ├── MANIFEST ├── README ├── documentation ├── pdb_renumber.txt ├── remove_loop_coords.txt ├── score_scatter_plot.txt ├── score_vs_rmsd.txt ├── sequence_recovery.txt ├── thread_pdb_from_alignment.txt └── top_n_percent.txt ├── rosettautil ├── __init__.py ├── bcl │ ├── __init__.py │ └── file_formats.py ├── graphics │ ├── __init__.py │ └── plotting.py ├── protein │ ├── PSSM.py │ ├── __init__.py │ ├── alignment.py │ ├── naccess.py │ ├── pdbStat.py │ └── util.py ├── rosetta │ ├── __init__.py │ ├── loops.py │ ├── params.py │ ├── rosettaScore.py │ └── weights.py └── util │ ├── __init__.py │ └── fileutil.py ├── scripts ├── amino_acids.py ├── best_models.py ├── clean_pdb.py ├── clustering.py ├── get_fasta_from_pdb.py ├── pdb_renumber.py ├── remove_loop_coords.py ├── score_scatter_plot.py ├── score_vs_rmsd.py ├── sequence_recovery.py ├── small_molecule_rmsd_table.py ├── tabbed_to_bcl.py ├── thread_pdb_from_alignment.py └── top_n_percent.py └── setup.py /.gitignore: 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