├── AE_Geometry_and_Conditional_Latent_Diffusion ├── commons │ ├── geometry_utils.py │ ├── logger.py │ ├── losses.py │ ├── process_mols.py │ └── utils.py ├── configs │ ├── prop │ │ ├── pdbbind_general_egnn.yml │ │ └── pdbbind_general_egnn_enc_final_h.yml │ ├── sampling.yml │ └── training.yml ├── custom_data │ ├── arbitary_ligand.sdf │ ├── index.txt │ └── target_protein.pdb ├── datasets │ ├── __init__.py │ ├── pdbbind.py │ ├── pl_data.py │ ├── pl_pair_dataset.py │ └── protein_ligand.py ├── geometric_gnn_dojo_utils │ ├── __init__.py │ ├── egnn_layers.py │ ├── gvp_layers.py │ ├── models.py │ ├── modules │ │ ├── __init__.py │ │ ├── blocks.py │ │ ├── cg.py │ │ ├── irreps_tools.py │ │ ├── model.py │ │ ├── radial.py │ │ └── symmetric_contraction.py │ ├── tfn_layers.py │ └── utils │ │ ├── __init__.py │ │ ├── plot_utils.py │ │ └── train_utils.py ├── hgraph │ ├── __init__.py │ ├── chemutils.py │ ├── dataset.py │ ├── decoder.py │ ├── encoder.py │ ├── hgnn.py │ ├── inc_graph.py │ ├── mol_graph.py │ ├── nnutils.py │ ├── rnn.py │ └── vocab.py ├── models │ ├── common.py │ ├── egnn.py │ ├── molopt_score_model.py │ ├── property_pred │ │ ├── prop_egnn.py │ │ └── prop_model.py │ └── uni_transformer.py ├── models_diffusion │ ├── ddpm.py │ ├── ddpm_conditional.py │ ├── ddpm_conditional_pocket.py │ ├── ddpm_utils.py │ ├── ddpm_utils_conditional.py │ ├── ddpm_utils_conditional_pocket.py │ ├── ncsn.py │ └── vae.py ├── scripts │ ├── batch_sample_diffusion.sh │ ├── data_preparation │ │ ├── clean_crossdocked.py │ │ ├── extract_pockets.py │ │ └── split_pl_dataset.py │ ├── dock_baseline.py │ ├── dock_testset.py │ ├── evaluate.py │ ├── evaluate_from_meta.py │ ├── generate_embedding.py │ ├── likelihood_est_diffusion.py │ ├── property_prediction │ │ ├── eval_prop.py │ │ ├── extract_pockets.py │ │ ├── inference.py │ │ ├── pdbbind_split.py │ │ └── train_prop.py │ ├── read_mol_custom.py │ ├── sample_2d.py │ ├── sample_2d_custom.py │ ├── sample_3d.py │ ├── sample_3d_custom.py │ ├── sample_diffusion.py │ ├── sample_for_pocket.py │ ├── sample_z.py │ ├── sample_z_custom.py │ ├── train_ae.py │ └── train_latent_diffusion.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 ├── AE_Geometry_and_Unconditional_Latent_Diffusion ├── datasets │ ├── datasets_molecule3d.py │ ├── datasets_molecule3d_new.py │ ├── datasets_molecule3d_v2.py │ ├── datasets_molecule3d_v3.py │ ├── datasets_utils.py │ └── moses_data │ │ ├── 11_p0.smi.gz │ │ ├── dataset_v1.csv │ │ ├── samples │ │ ├── .gitattributes │ │ ├── aae │ │ │ ├── aae_1.csv │ │ │ ├── aae_2.csv │ │ │ ├── aae_3.csv │ │ │ ├── aae_all.csv │ │ │ ├── metrics_aae_1.csv │ │ │ ├── metrics_aae_2.csv │ │ │ └── metrics_aae_3.csv │ │ ├── char_rnn │ │ │ ├── char_rnn_1.csv │ │ │ ├── char_rnn_2.csv │ │ │ ├── char_rnn_3.csv │ │ │ ├── char_rnn_all.csv │ │ │ ├── metrics_char_rnn_1.csv │ │ │ ├── metrics_char_rnn_2.csv │ │ │ └── metrics_char_rnn_3.csv │ │ ├── combinatorial │ │ │ ├── combinatorial_1.csv │ │ │ ├── combinatorial_2.csv │ │ │ ├── combinatorial_3.csv │ │ │ ├── combinatorial_all.csv │ │ │ ├── metrics_combinatorial_1.csv │ │ │ ├── metrics_combinatorial_2.csv │ │ │ └── metrics_combinatorial_3.csv │ │ ├── hmm │ │ │ ├── hmm_1.csv │ │ │ ├── hmm_2.csv │ │ │ ├── hmm_3.csv │ │ │ ├── hmm_all.csv │ │ │ ├── metrics_hmm_1.csv │ │ │ ├── metrics_hmm_2.csv │ │ │ └── metrics_hmm_3.csv │ │ ├── jtn │ │ │ ├── jtn_1.csv │ │ │ ├── jtn_2.csv │ │ │ ├── jtn_3.csv │ │ │ ├── jtn_all.csv │ │ │ ├── metrics_jtn_1.csv │ │ │ ├── metrics_jtn_2.csv │ │ │ └── metrics_jtn_3.csv │ │ ├── latent_gan │ │ │ ├── latent_gan_1.csv │ │ │ ├── latent_gan_2.csv │ │ │ ├── latent_gan_3.csv │ │ │ ├── latent_gan_all.csv │ │ │ ├── metrics_latent_gan_1.csv │ │ │ ├── metrics_latent_gan_2.csv │ │ │ └── metrics_latent_gan_3.csv │ │ ├── ngram │ │ │ ├── metrics_ngram_1.csv │ │ │ ├── metrics_ngram_2.csv │ │ │ ├── metrics_ngram_3.csv │ │ │ ├── ngram_1.csv │ │ │ ├── ngram_2.csv │ │ │ ├── ngram_3.csv │ │ │ └── ngram_all.csv │ │ ├── train_metrics.csv │ │ └── vae │ │ │ ├── metrics_vae_1.csv │ │ │ ├── metrics_vae_2.csv │ │ │ ├── metrics_vae_3.csv │ │ │ ├── vae_1.csv │ │ │ ├── vae_2.csv │ │ │ ├── vae_3.csv │ │ │ └── vae_all.csv │ │ ├── test.csv │ │ ├── test_scaffolds.csv │ │ ├── test_scaffolds_stats.npz │ │ ├── test_stats.npz │ │ └── train.csv ├── dmcg_utils │ ├── e2c │ │ └── dataset.py │ ├── model │ │ ├── conv.py │ │ ├── gnn.py │ │ └── gnn_v2.py │ ├── molecule │ │ ├── .gt.py.swp │ │ ├── features.py │ │ ├── graph.py │ │ └── gt.py │ └── utils │ │ ├── psi4_utils.py │ │ └── utils.py ├── edm_qm9_utils │ ├── __init__.py │ ├── analyze.py │ ├── bond_analyze.py │ ├── data │ │ ├── __init__.py │ │ ├── args.py │ │ ├── collate.py │ │ ├── dataset_class.py │ │ ├── prepare │ │ │ ├── __init__.py │ │ │ ├── download.py │ │ │ ├── md17.py │ │ │ ├── process.py │ │ │ ├── qm9.py │ │ │ └── utils.py │ │ └── utils.py │ ├── dataset.py │ ├── losses.py │ ├── models.py │ ├── property_prediction │ │ ├── README.md │ │ ├── __init__.py │ │ ├── main_qm9_prop.py │ │ ├── models │ │ │ ├── __init__.py │ │ │ └── gcl.py │ │ ├── models_property.py │ │ └── prop_utils.py │ ├── rdkit_functions.py │ ├── sampling.py │ ├── utils.py │ └── visualizer.py ├── evaluate_conditional.ipynb ├── evaluate_unconditional.ipynb ├── geometric_gnn_dojo_utils │ ├── __init__.py │ ├── egnn_layers.py │ ├── gvp_layers.py │ ├── models.py │ ├── modules │ │ ├── __init__.py │ │ ├── blocks.py │ │ ├── cg.py │ │ ├── irreps_tools.py │ │ ├── model.py │ │ ├── radial.py │ │ └── symmetric_contraction.py │ ├── tfn_layers.py │ └── utils │ │ ├── __init__.py │ │ ├── plot_utils.py │ │ └── train_utils.py ├── hgraph │ ├── __init__.py │ ├── chemutils.py │ ├── dataset.py │ ├── decoder.py │ ├── encoder.py │ ├── hgnn.py │ ├── inc_graph.py │ ├── mol_graph.py │ ├── nnutils.py │ ├── rnn.py │ └── vocab.py ├── main_2dto3d_encoder_decoder.py ├── main_2dto3d_encoder_decoder_gssl.py ├── main_latent_ddpm_drug.py ├── main_latent_ddpm_qm9.py ├── main_latent_ddpm_qm9_conditional.py ├── models_diffusion │ ├── ddpm.py │ ├── ddpm_conditional.py │ ├── ddpm_utils.py │ ├── ddpm_utils_conditional.py │ ├── ncsn.py │ └── vae.py ├── sample1_latent_ddpm_qm9_latent.py ├── sample1_latent_ddpm_qm9_latent_conditional.py ├── sample2_latent_ddpm_qm9_2d.py ├── sample3_latent_ddpm_qm9_3d.py └── utils_yy │ ├── README.md │ ├── debug.png │ └── utils.py ├── AE_Topology ├── common_atoms │ ├── Al_0.pt │ ├── Ar_0.pt │ ├── As_0.pt │ ├── Be_0.pt │ ├── Bi_0.pt │ ├── Bi_2.pt │ ├── Br_1.pt │ ├── Ca_0.pt │ ├── Co_0.pt │ ├── Cr_0.pt │ ├── Cu_0.pt │ ├── Fe_0.pt │ ├── Ga_0.pt │ ├── Ge_0.pt │ ├── He_0.pt │ ├── Hg_0.pt │ ├── K_0.pt │ ├── Kr_0.pt │ ├── Li_0.pt │ ├── 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