├── .gitignore ├── Network.svg ├── README.md ├── Umol.ipynb ├── data └── test_case │ └── 7NB4 │ ├── 7NB4.a3m │ ├── 7NB4.fasta │ ├── 7NB4.pdb1 │ ├── 7NB4_pocket_indices.npy │ ├── 7nb4.pdb1 │ ├── ligand_inp_features.pkl │ └── msa_features.pkl ├── environment.yml ├── install_dependencies.sh ├── predict.sh └── src ├── check_msa_colab.py ├── make_ligand_feats.py ├── make_ligand_feats_colab.py ├── make_msa_seq_feats.py ├── make_msa_seq_feats_colab.py ├── make_targetpost_npy.py ├── net ├── common │ ├── __init__.py │ ├── confidence.py │ ├── protein.py │ └── residue_constants.py ├── data │ └── parsers.py └── model │ ├── __init__.py │ ├── all_atom.py │ ├── common_modules.py │ ├── config.py │ ├── data.py │ ├── features.py │ ├── folding.py │ ├── layer_stack.py │ ├── lddt.py │ ├── map_ligand_test.py │ ├── mapping.py │ ├── model.py │ ├── modules.py │ ├── prng.py │ ├── quat_affine.py │ ├── r3.py │ ├── tf │ ├── __init__.py │ ├── data_transforms.py │ ├── input_pipeline.py │ ├── protein_features.py │ ├── protein_features_test.py │ ├── proteins_dataset.py │ ├── shape_helpers.py │ ├── shape_helpers_test.py │ ├── shape_placeholders.py │ └── utils.py │ └── utils.py ├── parse_pocket.py ├── predict.py ├── predict_colab.py └── relax ├── add_plddt_to_relaxed.py ├── align_ligand_conformer.py ├── align_ligand_conformer_colab.py └── openmm_relax.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/patrickbryant1/Umol/HEAD/.gitignore -------------------------------------------------------------------------------- /Network.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/patrickbryant1/Umol/HEAD/Network.svg -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/patrickbryant1/Umol/HEAD/README.md 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