├── .github └── workflows │ └── pre-commit.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── assets └── flexdock.png ├── examples └── inference_pdbbind_5.csv ├── flexdock ├── data │ ├── conformers │ │ ├── exceptions.py │ │ ├── modify.py │ │ ├── molecule.py │ │ └── protein.py │ ├── constants.py │ ├── dataset │ │ ├── filter_or_relax.py │ │ └── utils.py │ ├── feature │ │ ├── featurizer.py │ │ ├── helpers.py │ │ ├── molecule.py │ │ └── protein.py │ ├── modules │ │ ├── __init__.py │ │ ├── inference.py │ │ └── training │ │ │ ├── __init__.py │ │ │ ├── docking.py │ │ │ ├── filtering.py │ │ │ ├── pipeline.py │ │ │ └── relaxation.py │ ├── parse │ │ ├── base.py │ │ ├── molecule.py │ │ ├── parser.py │ │ └── protein.py │ ├── pipeline.py │ ├── transforms │ │ ├── docking │ │ │ ├── __init__.py │ │ │ ├── bb_priors.py │ │ │ ├── molecule.py │ │ │ ├── pocket.py │ │ │ └── protein.py │ │ └── relaxation │ │ │ ├── __init__.py │ │ │ ├── components.py │ │ │ ├── molecule.py │ │ │ └── protein.py │ └── write │ │ ├── structure.py │ │ ├── visualize.py │ │ └── writer.py ├── geometry │ ├── manifolds │ │ ├── so3.py │ │ └── torus.py │ └── ops.py ├── metrics │ ├── docking.py │ ├── evaluator.py │ ├── posebusters.py │ └── relaxation.py ├── models │ ├── layers │ │ ├── activation.py │ │ ├── mlp.py │ │ ├── normalization.py │ │ └── tensor_product.py │ ├── loss │ │ ├── docking.py │ │ └── filtering.py │ ├── networks │ │ ├── __init__.py │ │ ├── encoders.py │ │ ├── flow_network.py │ │ └── score_network.py │ ├── optim │ │ ├── ema.py │ │ └── lr_schedulers.py │ ├── pl_modules │ │ ├── __init__.py │ │ ├── docking.py │ │ ├── filtering.py │ │ ├── inference.py │ │ └── relaxation.py │ └── tensor_ops.py ├── sampling │ ├── docking │ │ ├── diffusion.py │ │ ├── sampling.py │ │ └── sampling_fast.py │ └── relaxation │ │ └── sampling.py └── utils │ ├── callbacks.py │ ├── configs.py │ └── parsing.py ├── pyproject.toml ├── scripts ├── evaluate.py ├── generate_pocket_csv.py ├── predict.py ├── preprocess │ ├── convert_pkl_to_individual_caches.py │ ├── esm_embedding_preparation.py │ ├── esm_embeddings_to_pt.py │ ├── extract_sequences_esmfold.py │ ├── preprocess_data.py │ └── run_esmfold.py └── train │ ├── train.py │ └── train_config.py └── setup.py /.github/workflows/pre-commit.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vsomnath/flexdock/HEAD/.github/workflows/pre-commit.yaml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vsomnath/flexdock/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vsomnath/flexdock/HEAD/.pre-commit-config.yaml 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