├── .gitignore ├── LICENSE ├── MolCRAFT ├── LICENSE ├── README.md ├── configs │ └── default.yaml ├── core │ ├── callbacks │ │ ├── basic.py │ │ ├── validation_callback.py │ │ └── validation_callback_for_sample.py │ ├── config │ │ └── config.py │ ├── datasets │ │ ├── __init__.py │ │ ├── pdbbind.py │ │ ├── pl_data.py │ │ ├── pl_pair_dataset.py │ │ ├── protein_ligand.py │ │ └── utils.py │ ├── evaluation │ │ ├── basic_results.py │ │ ├── docking_qvina.py │ │ ├── docking_vina.py │ │ ├── metrics.py │ │ ├── utils │ │ │ ├── __init__.py │ │ │ ├── atom_num.py │ │ │ ├── atom_num_config.py │ │ │ ├── bond_analyze.py │ │ │ ├── eval_atom_type.py │ │ │ ├── eval_bond_angle.py │ │ │ ├── eval_bond_length.py │ │ │ ├── eval_bond_length_config.py │ │ │ ├── eval_rmsd.py │ │ │ ├── eval_torsion_angle.py │ │ │ ├── fpscores.pkl.gz │ │ │ ├── sascorer.py │ │ │ ├── scoring_func.py │ │ │ └── similarity.py │ │ └── visualization.py │ ├── models │ │ ├── bfn4sbdd.py │ │ ├── bfn_base.py │ │ ├── common.py │ │ ├── sbdd_train_loop.py │ │ └── uni_transformer.py │ └── utils │ │ ├── misc.py │ │ ├── reconstruct.py │ │ ├── train.py │ │ ├── transforms.py │ │ ├── transforms_prop.py │ │ ├── visualize.py │ │ └── warmup.py ├── docker │ ├── Dockerfile │ ├── Makefile │ ├── README.md │ ├── asset │ │ ├── apt_packages.txt │ │ ├── download-vs-code-server.sh │ │ └── requirements.txt │ ├── environment.yml │ └── setup_docker_for_host.sh ├── sample_for_pocket.py ├── scripts.mk ├── test │ ├── eval_distribution.ipynb │ ├── eval_dock_vina.py │ ├── eval_posecheck.py │ ├── eval_rmsd.py │ └── eval_utils.py └── train_bfn.py ├── MolJO ├── LICENSE ├── README.md ├── configs │ ├── test_opt.yaml │ ├── test_opt_dcmp.yaml │ ├── test_opt_pb.yaml │ └── train_prop.yaml ├── core │ ├── callbacks │ │ ├── basic.py │ │ └── validation_callback.py │ ├── config │ │ └── config.py │ ├── datasets │ │ ├── __init__.py │ │ ├── pdbbind.py │ │ ├── pl_data.py │ │ ├── pl_pair_dataset.py │ │ ├── protein_ligand.py │ │ └── utils.py │ ├── evaluation │ │ ├── bond_analyze.py │ │ ├── docking_qvina.py │ │ ├── docking_smina.py │ │ ├── docking_vina.py │ │ ├── metrics.py │ │ ├── utils │ │ │ ├── __init__.py │ │ │ ├── analyze.py │ │ │ ├── atom_num.py │ │ │ ├── atom_num_config.py │ │ │ ├── atom_num_config_PDBLigAug.py │ │ │ ├── atom_num_config_crossdock.py │ │ │ ├── docking_qvina.py │ │ │ ├── docking_vina.py │ │ │ ├── eval_atom_type.py │ │ │ ├── eval_bond_angle.py │ │ │ ├── eval_bond_length.py │ │ │ ├── eval_bond_length_config.py │ │ │ ├── eval_torsion_angle.py │ │ │ ├── fpscores.pkl.gz │ │ │ ├── sascorer.py │ │ │ ├── scoring_func.py │ │ │ └── similarity.py │ │ └── visualization.py │ ├── models │ │ ├── bfn4sbdd.py │ │ ├── bfn_base.py │ │ ├── common.py │ │ ├── egnn.py │ │ ├── train_loop.py │ │ └── uni_transformer.py │ └── utils │ │ ├── misc.py │ │ ├── misc_prop.py │ │ ├── reconstruct.py │ │ ├── train.py │ │ ├── transforms.py │ │ ├── transforms_prop.py │ │ ├── visualize.py │ │ └── warmup.py ├── docker │ ├── Dockerfile │ ├── Makefile │ ├── README.md │ ├── asset │ │ ├── apt_packages.txt │ │ ├── download-vs-code-server.sh │ │ └── requirements.txt │ ├── environment.yml │ └── setup_docker_for_host.sh ├── sample_for_pocket_guided.py ├── sample_guided.py ├── test │ ├── pearson_r.ipynb │ ├── radar.ipynb │ ├── rgroup.ipynb │ └── visualize_traj.ipynb └── train_classifier.py ├── MolPilot ├── LICENSE ├── README.md ├── configs │ ├── crossdock_train_test.yaml │ ├── posebusters_dock.yaml │ └── posebusters_test.yaml ├── core │ ├── callbacks │ │ ├── basic.py │ │ ├── ema.py │ │ └── validation_callback.py │ ├── config │ │ └── config.py │ ├── datasets │ │ ├── __init__.py │ │ ├── embed_rdkit.py │ │ ├── merge_dataset.py │ │ ├── pdbbind.py │ │ ├── pl_data.py │ │ ├── pl_pair_dataset.py │ │ ├── pl_pair_dataset_hit.py │ │ ├── pl_pretrain_dataset.py │ │ ├── protein_ligand.py │ │ └── utils.py │ ├── evaluation │ │ ├── bond_analyze.py │ │ ├── docking_qvina.py │ │ ├── docking_smina.py │ │ ├── docking_vina.py │ │ ├── metrics.py │ │ ├── utils │ │ │ ├── __init__.py │ │ │ ├── analyze.py │ │ │ ├── atom_num.py │ │ │ ├── atom_num_config.py │ │ │ ├── docking_qvina.py │ │ │ ├── docking_vina.py │ │ │ ├── eval_atom_type.py │ │ │ ├── eval_bond_angle.py │ │ │ ├── eval_bond_length.py │ │ │ ├── eval_bond_length_config.py │ │ │ ├── eval_rmsd.py │ │ │ ├── eval_torsion_angle.py │ │ │ ├── fpscores.pkl.gz │ │ │ ├── sascorer.py │ │ │ ├── scoring_func.py │ │ │ └── similarity.py │ │ └── visualization.py │ ├── examples │ │ ├── 1h36_A_rec_1h36_r88_lig_tt_docked_0.sdf │ │ ├── 1h36_A_rec_1h36_r88_lig_tt_docked_0_pocket10.pdb │ │ ├── 3ug2_ligand.sdf │ │ └── 3ug2_protein.pdb │ ├── models │ │ ├── bfn4sbdd.py │ │ ├── bfn_base.py │ │ ├── common.py │ │ ├── layers.py │ │ ├── sbdd4train.py │ │ ├── sbdd4train_timewarp.py │ │ ├── time_scheduler_mono.py │ │ ├── time_warp.py │ │ ├── uni_transformer.py │ │ ├── uni_transformer_edge.py │ │ └── utils.py │ └── utils │ │ ├── misc.py │ │ ├── misc_prop.py │ │ ├── reconstruct.py │ │ ├── train.py │ │ ├── transforms.py │ │ ├── transforms_prop.py │ │ ├── visualize.py │ │ └── warmup.py ├── docker │ ├── Dockerfile │ ├── Makefile │ ├── README.md │ ├── asset │ │ ├── apt_packages.txt │ │ ├── download-vs-code-server.sh │ │ └── requirements.txt │ ├── environment.yml │ └── setup_docker_for_host.sh ├── eval │ ├── aio.py │ ├── batch.py │ ├── mover.py │ ├── plot.py │ ├── stats.py │ ├── update.py │ └── validate.py ├── sample_for_pocket.py ├── targetdiff │ ├── .gitattributes │ ├── .gitignore │ ├── LICIENCE │ ├── README.md │ ├── configs │ │ ├── prop │ │ │ ├── pdbbind_general_egnn.yml │ │ │ └── pdbbind_general_egnn_enc_final_h.yml │ │ ├── sampling.yml │ │ ├── sampling_rect.yml │ │ ├── sampling_rect_scheduler.yml │ │ ├── sampling_rect_scheduler_last.yml │ │ └── training.yml │ ├── datasets │ │ ├── __init__.py │ │ ├── pdbbind.py │ │ ├── pl_data.py │ │ ├── pl_pair_dataset.py │ │ └── protein_ligand.py │ ├── environment.yaml │ ├── examples │ │ ├── 1h36_A_rec_1h36_r88_lig_tt_docked_0.sdf │ │ ├── 1h36_A_rec_1h36_r88_lig_tt_docked_0_pocket10.pdb │ │ ├── 3ug2_ligand.sdf │ │ └── 3ug2_protein.pdb │ ├── models │ │ ├── common.py │ │ ├── egnn.py │ │ ├── molopt_score_model.py │ │ ├── property_pred │ │ │ ├── prop_egnn.py │ │ │ └── prop_model.py │ │ └── uni_transformer.py │ ├── notebooks │ │ ├── affinity_inference.ipynb │ │ ├── analyze_affinity.ipynb │ │ └── summary.ipynb │ ├── pretrained_models │ │ └── .gitignore │ ├── sampling_results │ │ └── .gitignore │ ├── scripts │ │ ├── batch_sample_diffusion.sh │ │ ├── data_preparation │ │ │ ├── clean_crossdocked.py │ │ │ ├── extract_pockets.py │ │ │ └── split_pl_dataset.py │ │ ├── dock_baseline.py │ │ ├── dock_testset.py │ │ ├── evaluate_diffusion.py │ │ ├── evaluate_from_meta.py │ │ ├── likelihood_est_diffusion.py │ │ ├── likelihood_est_diffusion_surface.py │ │ ├── property_prediction │ │ │ ├── eval_prop.py │ │ │ ├── extract_pockets.py │ │ │ ├── inference.py │ │ │ ├── pdbbind_split.py │ │ │ └── train_prop.py │ │ ├── sample_diffusion.py │ │ ├── sample_diffusion_surface.py │ │ ├── sample_for_pocket.py │ │ └── train_diffusion.py │ ├── test_loss_geodesic_budget.py │ └── utils │ │ ├── data.py │ │ ├── evaluation │ │ ├── analyze.py │ │ ├── atom_num.py │ │ ├── atom_num_config.py │ │ ├── docking_qvina.py │ │ ├── docking_vina.py │ │ ├── eval_atom_type.py │ │ ├── eval_bond_length.py │ │ ├── eval_bond_length_config.py │ │ ├── fpscores.pkl.gz │ │ ├── sascorer.py │ │ ├── scoring_func.py │ │ └── similarity.py │ │ ├── misc.py │ │ ├── misc_prop.py │ │ ├── reconstruct.py │ │ ├── train.py │ │ ├── transforms.py │ │ ├── transforms_prop.py │ │ ├── visualize.py │ │ └── warmup.py ├── test │ ├── eval_distribution.ipynb │ ├── loss_preliminary.ipynb │ └── test_loss_geodesic_budget.py └── train_bfn_twisted.py ├── README.md └── asset ├── molcraft.gif ├── molcraft_baseline_failure.png ├── molcraft_efficiency.png ├── molcraft_framework.png ├── molcraft_trajectory.png ├── moljo_framework.png ├── moljo_framework_all.png ├── moljo_rgroup.png ├── 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