├── .gitignore ├── DrawGraph └── totalmodel.png ├── FeatureDefine ├── Conformer3DFeature.py ├── FinerprintsFeature.py ├── LineGraph.py ├── MolFeature.py ├── RDKitFeature.py ├── distribution │ ├── __init__.py │ ├── mordred_dist.py │ └── padel_dist.py └── pubchemfp.py ├── LoadData ├── LoadDataset.py ├── __init__.py ├── qm8_loader.py └── qm9_loader.py ├── Models ├── AblationModel.py ├── BasicGNN.py ├── CrossAttention.py ├── FPN.py ├── FP_GNN_NET.py ├── GCN_Net.py ├── GCN_layer.py ├── GIN.py ├── Layers │ ├── GN_block_tsfm.py │ ├── GraphAttentionReadout.py │ ├── GraphSequenceAttention.py │ ├── Readout.py │ ├── __init__.py │ ├── attention.py │ ├── comenet.py │ ├── comenet_feature.py │ ├── dimenetpp.py │ ├── dimenetpp_feature.py │ ├── painn.py │ ├── pnaConv.py │ ├── schnet.py │ ├── sphere_feature.py │ └── spherenet.py ├── Loss │ ├── MV_GNN_MSE.py │ └── __init__.py ├── MV_GNN.py ├── ModelGetter.py ├── PNA.py ├── PNANet.py ├── Schnet_GNN_Interact.py ├── SphereNet_GNN_Interact.py ├── Sphere_Net.py ├── TSFM.py ├── Transformer │ ├── Tsfm_interface.py │ ├── pretrain_trfm.py │ └── utils │ │ └── Smiles2token.py ├── Transformer_official │ ├── pretrain_trfm.py │ ├── tsfm_fp.py │ └── utils.py ├── Uni_MPNN.py ├── __init__.py └── dig │ ├── __init__.py │ ├── ggraph │ ├── __init__.py │ ├── dataset │ │ ├── PygDataset.py │ │ ├── __init__.py │ │ ├── config.csv │ │ └── ggraph_dataset.py │ ├── evaluation │ │ ├── __init__.py │ │ └── metric.py │ ├── method │ │ ├── GraphAF │ │ │ ├── __init__.py │ │ │ ├── graphaf.py │ │ │ ├── model │ │ │ │ ├── __init__.py │ │ │ │ ├── graphaf.py │ │ │ │ ├── graphflow.py │ │ │ │ ├── graphflow_con_rl.py │ │ │ │ ├── graphflow_rl.py │ │ │ │ ├── model_utils.py │ │ │ │ ├── rgcn.py │ │ │ │ └── st_net.py │ │ │ └── train_utils.py │ │ ├── GraphDF │ │ │ ├── __init__.py │ │ │ ├── graphdf.py │ │ │ ├── model │ │ │ │ ├── __init__.py │ │ │ │ ├── df_utils.py │ │ │ │ ├── disgraphaf.py │ │ │ │ ├── graphflow.py │ │ │ │ ├── graphflow_con_rl.py │ │ │ │ ├── graphflow_rl.py │ │ │ │ ├── rgcn.py │ │ │ │ └── st_net.py │ │ │ └── train_utils.py │ │ ├── GraphEBM │ │ │ ├── __init__.py │ │ │ ├── energy_func.py │ │ │ ├── graphebm.py │ │ │ └── util.py │ │ ├── JTVAE │ │ │ ├── __init__.py │ │ │ ├── fast_jtnn │ │ │ │ ├── __init__.py │ │ │ │ ├── chemutils.py │ │ │ │ ├── datautils.py │ │ │ │ ├── jtmpn.py │ │ │ │ ├── jtmpn_bo.py │ │ │ │ ├── jtnn_dec.py │ │ │ │ ├── jtnn_enc.py │ │ │ │ ├── jtnn_enc_bo.py │ │ │ │ ├── jtnn_vae.py │ │ │ │ ├── jtnn_vae_bo.py │ │ │ │ ├── jtprop_vae.py │ │ │ │ ├── mol_tree.py │ │ │ │ ├── mpn.py │ │ │ │ ├── nnutils.py │ │ │ │ ├── sascorer.py │ │ │ │ └── vocab.py │ │ │ └── jtvae.py │ │ ├── __init__.py │ │ └── generator.py │ └── utils │ │ ├── __init__.py │ │ ├── environment.py │ │ ├── fpscores.pkl.gz │ │ ├── gen_mol_from_one_shot_tensor.py │ │ └── sascorer.py │ ├── ggraph3D │ ├── __init__.py │ ├── dataset │ │ ├── __init__.py │ │ └── ggraph3D_dataset.py │ ├── evaluation │ │ ├── __init__.py │ │ └── metric.py │ ├── method │ │ ├── G_SphereNet │ │ │ ├── __init__.py │ │ │ ├── gspherenet.py │ │ │ └── model │ │ │ │ ├── __init__.py │ │ │ │ ├── att.py │ │ │ │ ├── features.py │ │ │ │ ├── geometric_computing.py │ │ │ │ ├── net_utils.py │ │ │ │ ├── spherenet.py │ │ │ │ └── sphgen.py │ │ └── __init__.py │ └── utils │ │ ├── __init__.py │ │ ├── eval_bond_mmd_utils.py │ │ ├── eval_prop_utils.py │ │ └── eval_validity_utils.py │ ├── lsgraph │ ├── __init__.py │ ├── dataset │ │ ├── __init__.py │ │ ├── get_data.py │ │ └── loader.py │ └── method │ │ ├── FM.py │ │ ├── GraphFMOB │ │ ├── __init__.py │ │ ├── csrc │ │ │ ├── cpu │ │ │ │ ├── relabel_cpu.cpp │ │ │ │ └── relabel_cpu.h │ │ │ ├── cuda │ │ │ │ ├── sync_cuda.cu │ │ │ │ └── sync_cuda.h │ │ │ ├── relabel.cpp │ │ │ ├── sync.cpp │ │ │ └── thread.h │ │ ├── history.py │ │ ├── loader.py │ │ ├── metis.py │ │ ├── models │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── gcn.py │ │ │ ├── gcn2.py │ │ │ ├── pna.py │ │ │ └── pna_jk.py │ │ ├── pool.py │ │ └── utils.py │ │ └── __init__.py │ ├── model_storage │ ├── prop_opt_alpha.pth │ ├── prop_opt_gap.pth │ └── rand_gen.pth │ ├── oodgraph │ ├── __init__.py │ ├── good_arxiv.py │ ├── good_cbas.py │ ├── good_cmnist.py │ ├── good_cora.py │ ├── good_hiv.py │ ├── good_motif.py │ ├── good_pcba.py │ └── good_zinc.py │ ├── sslgraph │ ├── __init__.py │ ├── dataset │ │ ├── TUDataset.py │ │ ├── __init__.py │ │ ├── datasets.py │ │ └── feat_expansion.py │ ├── evaluation │ │ ├── __init__.py │ │ ├── eval_graph.py │ │ └── eval_node.py │ ├── method │ │ ├── __init__.py │ │ └── contrastive │ │ │ ├── __init__.py │ │ │ ├── model │ │ │ ├── __init__.py │ │ │ ├── contrastive.py │ │ │ ├── grace.py │ │ │ ├── graphcl.py │ │ │ ├── infograph.py │ │ │ ├── mvgrl.py │ │ │ └── pgrace.py │ │ │ ├── objectives │ │ │ ├── __init__.py │ │ │ ├── infonce.py │ │ │ └── jse.py │ │ │ └── views_fn │ │ │ ├── __init__.py │ │ │ ├── combination.py │ │ │ ├── feature.py │ │ │ ├── sample.py │ │ │ └── structure.py │ └── utils │ │ ├── __init__.py │ │ ├── adaptive.py │ │ ├── encoders.py │ │ └── seed.py │ ├── threedgraph │ ├── __init__.py │ ├── dataset │ │ ├── ECdataset.py │ │ ├── FOLDdataset.py │ │ ├── PygMD17.py │ │ ├── PygQM93D.py │ │ ├── README.md │ │ └── __init__.py │ ├── evaluation │ │ ├── __init__.py │ │ └── eval.py │ ├── method │ │ ├── __init__.py │ │ ├── comenet │ │ │ ├── __init__.py │ │ │ ├── comenet.py │ │ │ ├── features.py │ │ │ └── ocp │ │ │ │ ├── README.md │ │ │ │ ├── comenet-ocp.py │ │ │ │ ├── comenet.yml │ │ │ │ └── utils.py │ │ ├── dimenetpp │ │ │ ├── __init__.py │ │ │ ├── dimenetpp.py │ │ │ └── features.py │ │ ├── pronet │ │ │ ├── __init__.py │ │ │ ├── features.py │ │ │ └── pronet.py │ │ ├── run.py │ │ ├── schnet │ │ │ ├── __init__.py │ │ │ └── schnet.py │ │ └── spherenet │ │ │ ├── __init__.py │ │ │ ├── features.py │ │ │ └── spherenet.py │ └── utils │ │ ├── __init__.py │ │ └── geometric_computing.py │ ├── version.py │ └── xgraph │ ├── __init__.py │ ├── dataset │ ├── __init__.py │ ├── mol_dataset.py │ ├── nlp_dataset.py │ ├── syn_dataset.py │ └── utils_dataset.py │ ├── evaluation │ ├── Readme.md │ ├── __init__.py │ ├── defi.py │ └── metrics.py │ ├── method │ ├── __init__.py │ ├── base_explainer.py │ ├── deeplift.py │ ├── flowx.py │ ├── gnn_gi.py │ ├── gnn_lrp.py │ ├── gnnexplainer.py │ ├── gradcam.py │ ├── pgexplainer.py │ ├── shapley.py │ ├── subgraphx.py │ └── utils │ │ ├── __init__.py │ │ └── symmetric_edge_mask.py │ ├── models │ ├── __init__.py │ ├── ext │ │ ├── __init__.py │ │ └── deeplift │ │ │ ├── __init__.py │ │ │ ├── deep_lift.py │ │ │ └── layer_deep_lift.py │ ├── gradient_utils.py │ ├── model_manager.py │ ├── models.py │ └── utils.py │ └── utils │ ├── __init__.py │ ├── compatibility.py │ └── init.py ├── README.md ├── Transformer1D ├── Dataloader.py ├── Match.py ├── SMILES-Transformer │ ├── build_corpus.py │ ├── build_vocab.py │ ├── dataset.py │ ├── enumerator.py │ ├── pretrain_rnn.py │ ├── sample.py │ ├── sdf2csv.py │ ├── smi2csv.py │ └── utils.py ├── SmilesEnumerator.py ├── Tsfm_interface.py ├── pretrain_trfm.py ├── tsfm_finetune.py └── utils │ ├── DataReader.py │ └── Smiles2token.py ├── UnifiedMolPretrain ├── .idea │ ├── .gitignore │ ├── UnifiedMolPretrain.iml │ ├── deployment.xml │ ├── inspectionProfiles │ │ ├── Project_Default.xml │ │ └── profiles_settings.xml │ ├── misc.xml │ ├── modules.xml │ └── vcs.xml ├── Test.py ├── finetune.py ├── finetunew3d.py ├── others │ └── checkxyz.py ├── pretrain3d │ ├── __init__.py │ ├── data │ │ ├── MolFeature.py │ │ ├── With3dPropPredDataset │ │ │ ├── __init__.py │ │ │ └── dataset.py │ │ ├── __init__.py │ │ └── pcqm4m.py │ ├── model │ │ ├── __init__.py │ │ ├── conv.py │ │ └── gnn.py │ └── utils │ │ ├── PreProcessor.py │ │ ├── __init__.py │ │ ├── dist.py │ │ ├── evaluate.py │ │ ├── features.py │ │ ├── graph.py │ │ ├── gt.py │ │ ├── master.csv │ │ ├── misc.py │ │ ├── torch_util.py │ │ └── url.py └── train.py ├── Utils ├── Accumulator.py ├── NoamLR.py ├── PreProcessor.py ├── change_config_to_yaml.py ├── check_3dpos.py ├── geometric_computing.py ├── get_models.py 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