├── .gitignore ├── README.md ├── assets ├── conditional-ligand-pocket-sampling-trajectory.gif ├── conditional-sampling-maximized-polarizability.gif ├── conditional-sampling-minimized-polarizability.gif ├── unconditional-sampling-trajectory.gif └── unconditional-sampling-trajectory.mp4 ├── data ├── README.md ├── geom.zip ├── geom │ └── .gitkeep ├── qm9.zip └── qm9 │ └── .gitkeep ├── eqgat_diff ├── .gitignore ├── .ipynb_checkpoints │ └── Untitled-checkpoint.ipynb ├── README.md ├── callbacks │ └── ema.py ├── e3moldiffusion │ ├── README.md │ ├── __init__.py │ ├── chem.py │ ├── convs.py │ ├── coordsatomsbonds.py │ ├── gnn.py │ ├── modules.py │ └── molfeat.py ├── environment.yml ├── experiments │ ├── __init__.py │ ├── data │ │ ├── __init__.py │ │ ├── abstract_dataset.py │ │ ├── adaptive_loader.py │ │ ├── calculate_dipoles.py │ │ ├── calculate_energies.py │ │ ├── config_file.py │ │ ├── data_info.py │ │ ├── distributions.py │ │ ├── geom │ │ │ ├── calculate_energies.py │ │ │ ├── geom_dataset_adaptive.py │ │ │ ├── geom_dataset_adaptive_qm.py │ │ │ ├── geom_dataset_energy.py │ │ │ └── geom_dataset_nonadaptive.py │ │ ├── ligand │ │ │ ├── __init__.py │ │ │ ├── constants.py │ │ │ ├── geometry_utils.py │ │ │ ├── ligand_dataset_adaptive.py │ │ │ ├── ligand_dataset_nonadaptive.py │ │ │ ├── molecule_builder.py │ │ │ ├── process_bindingmoad.py │ │ │ ├── process_crossdocked.py │ │ │ └── utils.py │ │ ├── metrics.py │ │ ├── pubchem │ │ │ ├── download_pubchem.py │ │ │ ├── preprocess_pubchem.py │ │ │ ├── process_pubchem.py │ │ │ ├── pubchem_dataset_adaptive.py │ │ │ └── pubchem_dataset_nonadaptive.py │ │ ├── qm9 │ │ │ └── qm9_dataset.py │ │ └── utils.py │ ├── diffusion │ │ ├── __init__.py │ │ ├── categorical.py │ │ ├── continuous.py │ │ └── utils.py │ ├── diffusion_continuous.py │ ├── diffusion_continuous_pocket.py │ ├── diffusion_discrete.py │ ├── diffusion_discrete_addfeats.py │ ├── diffusion_discrete_pocket.py │ ├── diffusion_discrete_pocket_addfeats.py │ ├── diffusion_pretrain_discrete.py │ ├── diffusion_pretrain_discrete_addfeats.py │ ├── docking.py │ ├── docking_mgl.py │ ├── generate_ligands.py │ ├── hparams.py │ ├── losses.py │ ├── molecule_utils.py │ ├── run_evaluation.py │ ├── run_evaluation_ligand.py │ ├── run_train.py │ ├── sampling │ │ ├── __init__.py │ │ ├── analyze.py │ │ ├── analyze_strict.py │ │ ├── fpscores.pkl.gz │ │ └── utils.py │ ├── utils.py │ ├── xtb_energy.py │ ├── xtb_relaxation.py │ └── xtb_wrapper.py ├── setup.cfg └── setup.py ├── inference ├── README.md ├── run_eval_geom.sh ├── run_eval_qm9.sh ├── sampling_geom.ipynb ├── sampling_qm9.ipynb └── tmp │ ├── .gitkeep │ └── geom │ └── .gitkeep └── weights ├── README.md ├── geom └── .gitkeep └── qm9 └── .gitkeep /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tuanle618/eqgat-diff/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: 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