├── .dockerignore ├── Dockerfile ├── LICENCE ├── README.md ├── datasets └── custom │ ├── 1a05B │ ├── 1a05B.pdb │ └── pockets │ │ ├── pocket0_atm.pdb │ │ ├── pocket0_vert.pqr │ │ ├── pocket1_atm.pdb │ │ ├── pocket1_vert.pqr │ │ ├── pocket2_atm.pdb │ │ ├── pocket2_vert.pqr │ │ ├── pocket3_atm.pdb │ │ ├── pocket3_vert.pqr │ │ ├── pocket4_atm.pdb │ │ ├── pocket4_vert.pqr │ │ ├── pocket5_atm.pdb │ │ ├── pocket5_vert.pqr │ │ ├── pocket6_atm.pdb │ │ └── pocket6_vert.pqr │ ├── 1a9t │ ├── 1a9t.pdb │ ├── 1a9t_clean.pdb │ ├── 1a9t_lig_1.pdb │ └── 1a9t_site_1.pdb │ └── pairs.csv ├── datasets_downloader.sh ├── deeplytough ├── datasets │ ├── __init__.py │ ├── custom.py │ ├── prospeccts.py │ ├── toughm1.py │ └── vertex.py ├── engine │ ├── datasets.py │ ├── models.py │ └── predictor.py ├── matchers │ ├── __init__.py │ ├── deeply_tough.py │ ├── pocket_matcher.py │ └── tough_officials.py ├── misc │ ├── cc_ligands.py │ ├── ligand_extract.py │ └── utils.py └── scripts │ ├── custom_evaluation.py │ ├── prospeccts_benchmark.py │ ├── toughm1_benchmark.py │ ├── train.py │ └── vertex_benchmark.py ├── networks ├── deeplytough_prospeccts.pth.tar ├── deeplytough_toughm1_test.pth.tar └── deeplytough_vertex.pth.tar ├── overview.png ├── requirements.txt └── results ├── Prospeccts-DeeplyTough-deeplytough_prospeccts-P1.2.csv ├── Prospeccts-DeeplyTough-deeplytough_prospeccts-P1.csv ├── Prospeccts-DeeplyTough-deeplytough_prospeccts-P2.csv ├── Prospeccts-DeeplyTough-deeplytough_prospeccts-P3.csv ├── Prospeccts-DeeplyTough-deeplytough_prospeccts-P4.csv ├── Prospeccts-DeeplyTough-deeplytough_prospeccts-P5.2.csv ├── Prospeccts-DeeplyTough-deeplytough_prospeccts-P5.csv ├── Prospeccts-DeeplyTough-deeplytough_prospeccts-P6.2.csv ├── Prospeccts-DeeplyTough-deeplytough_prospeccts-P6.csv ├── Prospeccts-DeeplyTough-deeplytough_prospeccts-P7.csv ├── ToughM1-DeeplyTough-deeplytough_toughm1_test.csv └── Vertex-DeeplyTough-deeplytough_vertex.csv /.dockerignore: 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