├── .gitignore ├── LICENSE.txt ├── README.md ├── analysis └── Results.ipynb ├── clipzyme ├── __init__.py ├── callbacks │ ├── __init__.py │ └── basic.py ├── datasets │ ├── __init__.py │ ├── abstract.py │ ├── enzyme_screening.py │ ├── enzymemap.py │ └── reaction.py ├── learning │ ├── losses │ │ ├── __init__.py │ │ ├── basic.py │ │ └── contrastive.py │ ├── metrics │ │ ├── __init__.py │ │ ├── basic.py │ │ └── representation.py │ ├── optimizers │ │ ├── __init__.py │ │ └── basic.py │ ├── schedulers │ │ ├── __init__.py │ │ ├── basic.py │ │ └── warmup.py │ └── utils.py ├── lightning │ ├── __init__.py │ ├── base.py │ └── clipzyme.py ├── loggers │ ├── __init__.py │ ├── tensorboard.py │ └── wandb.py ├── models │ ├── __init__.py │ ├── abstract.py │ ├── chemprop.py │ ├── classifier.py │ ├── egnn.py │ ├── fair_esm.py │ ├── gat.py │ ├── protmol.py │ ├── seq2seq.py │ └── wln.py └── utils │ ├── __init__.py │ ├── amino_acids.py │ ├── callbacks.py │ ├── classes.py │ ├── colabfold_msa.py │ ├── loading.py │ ├── messages.py │ ├── parsing.py │ ├── protein_utils.py │ ├── proteins.py │ ├── pyg.py │ ├── reactions.py │ ├── registry.py │ ├── sampler.py │ ├── screening.py │ ├── smiles.py │ └── wln_processing.py ├── configs ├── eval │ ├── clip_cgr_egnn.json │ ├── clip_egnn.json │ ├── clip_egnn_train_esm.json │ ├── clip_esm.json │ ├── clip_esm_frozen.json │ ├── clip_msa.json │ ├── clip_msa_esm.json │ ├── clip_rxn_str.json │ └── clip_wldn.json ├── screening.json └── train │ ├── clip_cgr.json │ ├── clip_cgr_rxn_string.json │ ├── clip_egnn.json │ ├── clip_esm.json │ ├── clip_esm_frozen.json │ ├── clip_msa.json │ └── clip_wldn.json ├── environment.yml ├── files ├── AF-P69905-F1-model_v4.cif └── new_data.csv ├── pyproject.toml ├── scripts ├── data │ ├── colabfold_search.py │ ├── enzymemap_maker.py │ ├── generate_msa.py │ └── pull_brenda_biomolecules.py ├── dispatcher.py ├── main.py └── screen.py └── tests └── __init__.py /.gitignore: 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