protac_degradation_predictor

• protac_degradation_predictor package
  • Subpackages
    • protac_degradation_predictor.optuna package
      • Submodules
      • protac_degradation_predictor.optuna.pytorch_models module
      • protac_degradation_predictor.optuna.sklearn_models module
      • protac_degradation_predictor.optuna.utils module
      • protac_degradation_predictor.optuna.xgboost_models module
      • Module contents
  • Submodules
  • protac_degradation_predictor.config module
    • Config
      • Config.morgan_radius
      • Config.fingerprint_size
      • Config.protein_embedding_size
      • Config.cell_embedding_size
      • Config.dmax_threshold
      • Config.pdc50_threshold
      • Config.active_label
      • Config.e3_ligase2uniprot
  • protac_degradation_predictor.data_utils module
    • avail_e3_ligases()
    • avail_cell_lines()
    • avail_uniprots()
    • get_fingerprint()
    • is_active()
    • load_curated_dataset()
  • protac_degradation_predictor.optuna_utils module
    • get_dataframe_stats()
    • get_majority_vote_metrics()
    • get_suggestion()
    • pytorch_model_objective()
    • hyperparameter_tuning_and_training()
  • protac_degradation_predictor.optuna_utils_xgboost module
    • get_confidence_scores()
    • train_and_evaluate_xgboost()
    • xgboost_model_objective()
    • xgboost_hyperparameter_tuning_and_training()
  • protac_degradation_predictor.protac_dataset module
    • PROTAC_Dataset
      • PROTAC_Dataset.get_smiles_emb_dim()
      • PROTAC_Dataset.get_protein_emb_dim()
      • PROTAC_Dataset.get_cell_emb_dim()
      • PROTAC_Dataset.apply_smote()
      • PROTAC_Dataset.fit_scaling()
      • PROTAC_Dataset.apply_scaling()
      • PROTAC_Dataset.get_numpy_arrays()
    • get_datasets()
    • PROTAC_DataModule
      • PROTAC_DataModule.setup()
      • PROTAC_DataModule.train_dataloader()
      • PROTAC_DataModule.val_dataloader()
      • PROTAC_DataModule.test_dataloader()
      • PROTAC_DataModule.get_random_split_indices()
      • PROTAC_DataModule.get_e3_ligase_split_indices()
      • PROTAC_DataModule.get_smiles2fp_and_avg_tanimoto()
      • PROTAC_DataModule.get_tanimoto_split_indices()
      • PROTAC_DataModule.get_target_split_indices()
  • protac_degradation_predictor.protac_degradation_predictor module
    • get_protac_active_proba()
    • is_protac_active()
    • get_protac_embedding()
  • protac_degradation_predictor.pytorch_models module
    • PROTAC_Predictor
      • PROTAC_Predictor.forward()
      • PROTAC_Predictor.T_destination
      • PROTAC_Predictor.add_module()
      • PROTAC_Predictor.apply()
      • PROTAC_Predictor.bfloat16()
      • PROTAC_Predictor.buffers()
      • PROTAC_Predictor.call_super_init
      • PROTAC_Predictor.children()
      • PROTAC_Predictor.cpu()
      • PROTAC_Predictor.cuda()
      • PROTAC_Predictor.double()
      • PROTAC_Predictor.dump_patches
      • PROTAC_Predictor.eval()
      • PROTAC_Predictor.extra_repr()
      • PROTAC_Predictor.float()
      • PROTAC_Predictor.get_buffer()
      • PROTAC_Predictor.get_extra_state()
      • PROTAC_Predictor.get_parameter()
      • PROTAC_Predictor.get_submodule()
      • PROTAC_Predictor.half()
      • PROTAC_Predictor.ipu()
      • PROTAC_Predictor.load_state_dict()
      • PROTAC_Predictor.modules()
      • PROTAC_Predictor.named_buffers()
      • PROTAC_Predictor.named_children()
      • PROTAC_Predictor.named_modules()
      • PROTAC_Predictor.named_parameters()
      • PROTAC_Predictor.parameters()
      • PROTAC_Predictor.register_backward_hook()
      • PROTAC_Predictor.register_buffer()
      • PROTAC_Predictor.register_forward_hook()
      • PROTAC_Predictor.register_forward_pre_hook()
      • PROTAC_Predictor.register_full_backward_hook()
      • PROTAC_Predictor.register_full_backward_pre_hook()
      • PROTAC_Predictor.register_load_state_dict_post_hook()
      • PROTAC_Predictor.register_module()
      • PROTAC_Predictor.register_parameter()
      • PROTAC_Predictor.register_state_dict_pre_hook()
      • PROTAC_Predictor.requires_grad_()
      • PROTAC_Predictor.set_extra_state()
      • PROTAC_Predictor.share_memory()
      • PROTAC_Predictor.state_dict()
      • PROTAC_Predictor.to()
      • PROTAC_Predictor.to_empty()
      • PROTAC_Predictor.train()
      • PROTAC_Predictor.type()
      • PROTAC_Predictor.xpu()
      • PROTAC_Predictor.zero_grad()
      • PROTAC_Predictor.training
    • PROTAC_Model
      • PROTAC_Model.initialize_scalers()
      • PROTAC_Model.apply_scalers()
      • PROTAC_Model.scale_tensor()
      • PROTAC_Model.forward()
      • PROTAC_Model.step()
      • PROTAC_Model.training_step()
      • PROTAC_Model.validation_step()
      • PROTAC_Model.test_step()
      • PROTAC_Model.configure_optimizers()
      • PROTAC_Model.predict_step()
      • PROTAC_Model.train_dataloader()
      • PROTAC_Model.val_dataloader()
      • PROTAC_Model.test_dataloader()
      • PROTAC_Model.on_save_checkpoint()
      • PROTAC_Model.on_load_checkpoint()
    • get_confidence_scores()
    • train_model()
    • evaluate_model()
    • load_model()
  • protac_degradation_predictor.sklearn_models module
    • train_sklearn_model()
    • suggest_random_forest()
    • suggest_logistic_regression()
    • suggest_svc()
    • suggest_gradient_boosting()
  • Module contents