├── .gitignore ├── LICENSE ├── 3rd_party │ ├── LICENSE_FLASH_ATTENTION │ ├── LICENSE_GA │ ├── LICENSE_MDLM │ ├── LICENSE_MOOD │ ├── LICENSE_PMO │ └── LICENSE_SAFE ├── license_code.txt ├── license_weights.txt └── third-party.txt ├── MODEL_CARD.md ├── README.md ├── VERSION ├── assets └── concept.png ├── configs └── base.yaml ├── data ├── fragments.csv └── len.pk ├── env ├── fix_safe_imports.sh ├── requirements.txt ├── requirements.yaml └── setup.sh ├── pyproject.toml ├── scripts ├── __init__.py ├── exps │ ├── __init__.py │ ├── denovo │ │ ├── hparams.yaml │ │ ├── hparams_v2.yaml │ │ └── run.py │ ├── frag │ │ ├── hparams.yaml │ │ ├── hparams_v2.yaml │ │ └── run.py │ ├── lead │ │ ├── __init__.py │ │ ├── docking │ │ │ ├── 5ht1b.pdbqt │ │ │ ├── __init__.py │ │ │ ├── actives.csv │ │ │ ├── braf.pdbqt │ │ │ ├── docking.py │ │ │ ├── fa7.pdbqt │ │ │ ├── jak2.pdbqt │ │ │ ├── parp1.pdbqt │ │ │ └── qvina02 │ │ ├── eval.py │ │ └── run.py │ └── pmo │ │ ├── __init__.py │ │ ├── eval.py │ │ ├── get_vocab.py │ │ ├── main │ │ ├── __init__.py │ │ ├── genmol │ │ │ ├── __init__.py │ │ │ ├── hparams.yaml │ │ │ └── run.py │ │ └── optimizer.py │ │ ├── run.py │ │ └── vocab │ │ ├── albuterol_similarity.csv │ │ ├── amlodipine_mpo.csv │ │ ├── celecoxib_rediscovery.csv │ │ ├── deco_hop.csv │ │ ├── drd2.csv │ │ ├── fexofenadine_mpo.csv │ │ ├── gsk3b.csv │ │ ├── isomers_c7h8n2o2.csv │ │ ├── isomers_c9h10n2o2pf2cl.csv │ │ ├── jnk3.csv │ │ ├── median1.csv │ │ ├── median2.csv │ │ ├── mestranol_similarity.csv │ │ ├── osimertinib_mpo.csv │ │ ├── perindopril_mpo.csv │ │ ├── qed.csv │ │ ├── ranolazine_mpo.csv │ │ ├── scaffold_hop.csv │ │ ├── sitagliptin_mpo.csv │ │ ├── thiothixene_rediscovery.csv │ │ ├── troglitazone_rediscovery.csv │ │ ├── valsartan_smarts.csv │ │ └── zaleplon_mpo.csv ├── preprocess_data.py └── train.py └── src └── genmol ├── __init__.py ├── model.py ├── sampler.py └── utils ├── __init__.py ├── bracket_safe_converter.py ├── ema.py ├── utils_chem.py ├── utils_data.py ├── 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