Index

A

active_label (protac_degradation_predictor.config.Config attribute) add_module() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) apply() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) apply_scalers() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)

apply_scaling() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method) apply_smote() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method) avail_cell_lines() (in module protac_degradation_predictor.data_utils) avail_e3_ligases() (in module protac_degradation_predictor.data_utils) avail_uniprots() (in module protac_degradation_predictor.data_utils)

B

bfloat16() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)

buffers() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)

C

call_super_init (protac_degradation_predictor.pytorch_models.PROTAC_Predictor attribute) cell_embedding_size (protac_degradation_predictor.config.Config attribute) children() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)

Config (class in protac_degradation_predictor.config) configure_optimizers() (protac_degradation_predictor.pytorch_models.PROTAC_Model method) cpu() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) cuda() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)

D

dmax_threshold (protac_degradation_predictor.config.Config attribute)

double() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) dump_patches (protac_degradation_predictor.pytorch_models.PROTAC_Predictor attribute)

E

e3_ligase2uniprot (protac_degradation_predictor.config.Config attribute) eval() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)

evaluate_model() (in module protac_degradation_predictor.pytorch_models) extra_repr() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)

F

fingerprint_size (protac_degradation_predictor.config.Config attribute) fit_scaling() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method)

float() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) forward() (protac_degradation_predictor.pytorch_models.PROTAC_Model method) (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)

G

get_buffer() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) get_cell_emb_dim() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method) get_confidence_scores() (in module protac_degradation_predictor.optuna_utils_xgboost) (in module protac_degradation_predictor.pytorch_models) get_dataframe_stats() (in module protac_degradation_predictor.optuna_utils) get_datasets() (in module protac_degradation_predictor.protac_dataset) get_e3_ligase_split_indices() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule static method) get_extra_state() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) get_fingerprint() (in module protac_degradation_predictor.data_utils) get_majority_vote_metrics() (in module protac_degradation_predictor.optuna_utils) get_numpy_arrays() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method)

get_parameter() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) get_protac_active_proba() (in module protac_degradation_predictor.protac_degradation_predictor) get_protac_embedding() (in module protac_degradation_predictor.protac_degradation_predictor) get_protein_emb_dim() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method) get_random_split_indices() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule static method) get_smiles2fp_and_avg_tanimoto() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule static method) get_smiles_emb_dim() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method) get_submodule() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) get_suggestion() (in module protac_degradation_predictor.optuna_utils) get_tanimoto_split_indices() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule static method) get_target_split_indices() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule static method)

H

half() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)

hyperparameter_tuning_and_training() (in module protac_degradation_predictor.optuna_utils)

I

initialize_scalers() (protac_degradation_predictor.pytorch_models.PROTAC_Model method) ipu() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)

is_active() (in module protac_degradation_predictor.data_utils) is_protac_active() (in module protac_degradation_predictor.protac_degradation_predictor)

L

load_curated_dataset() (in module protac_degradation_predictor.data_utils)

load_model() (in module protac_degradation_predictor.pytorch_models) load_state_dict() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)

M

module protac_degradation_predictor protac_degradation_predictor.config protac_degradation_predictor.data_utils protac_degradation_predictor.optuna_utils protac_degradation_predictor.optuna_utils_xgboost protac_degradation_predictor.protac_dataset protac_degradation_predictor.protac_degradation_predictor protac_degradation_predictor.pytorch_models protac_degradation_predictor.sklearn_models

modules() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) morgan_radius (protac_degradation_predictor.config.Config attribute)

N

named_buffers() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) named_children() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)

named_modules() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) named_parameters() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)

O

on_load_checkpoint() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)

on_save_checkpoint() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)

P

parameters() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) pdc50_threshold (protac_degradation_predictor.config.Config attribute) predict_step() (protac_degradation_predictor.pytorch_models.PROTAC_Model method) PROTAC_DataModule (class in protac_degradation_predictor.protac_dataset) PROTAC_Dataset (class in protac_degradation_predictor.protac_dataset) protac_degradation_predictor module protac_degradation_predictor.config module protac_degradation_predictor.data_utils module protac_degradation_predictor.optuna_utils module

protac_degradation_predictor.optuna_utils_xgboost module protac_degradation_predictor.protac_dataset module protac_degradation_predictor.protac_degradation_predictor module protac_degradation_predictor.pytorch_models module protac_degradation_predictor.sklearn_models module PROTAC_Model (class in protac_degradation_predictor.pytorch_models) PROTAC_Predictor (class in protac_degradation_predictor.pytorch_models) protein_embedding_size (protac_degradation_predictor.config.Config attribute) pytorch_model_objective() (in module protac_degradation_predictor.optuna_utils)

R

register_backward_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) register_buffer() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) register_forward_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) register_forward_pre_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) register_full_backward_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)

register_full_backward_pre_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) register_load_state_dict_post_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) register_module() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) register_parameter() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) register_state_dict_pre_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) requires_grad_() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)

S

scale_tensor() (protac_degradation_predictor.pytorch_models.PROTAC_Model method) set_extra_state() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) setup() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule method) share_memory() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) state_dict() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)

step() (protac_degradation_predictor.pytorch_models.PROTAC_Model method) suggest_gradient_boosting() (in module protac_degradation_predictor.sklearn_models) suggest_logistic_regression() (in module protac_degradation_predictor.sklearn_models) suggest_random_forest() (in module protac_degradation_predictor.sklearn_models) suggest_svc() (in module protac_degradation_predictor.sklearn_models)

T

T_destination (protac_degradation_predictor.pytorch_models.PROTAC_Predictor attribute) test_dataloader() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule method) (protac_degradation_predictor.pytorch_models.PROTAC_Model method) test_step() (protac_degradation_predictor.pytorch_models.PROTAC_Model method) to() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) to_empty() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method) train() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)

train_and_evaluate_xgboost() (in module protac_degradation_predictor.optuna_utils_xgboost) train_dataloader() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule method) (protac_degradation_predictor.pytorch_models.PROTAC_Model method) train_model() (in module protac_degradation_predictor.pytorch_models) train_sklearn_model() (in module protac_degradation_predictor.sklearn_models) training (protac_degradation_predictor.pytorch_models.PROTAC_Predictor attribute) training_step() (protac_degradation_predictor.pytorch_models.PROTAC_Model method) type() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)

V

val_dataloader() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule method) (protac_degradation_predictor.pytorch_models.PROTAC_Model method)

validation_step() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)

X

xgboost_hyperparameter_tuning_and_training() (in module protac_degradation_predictor.optuna_utils_xgboost)

xgboost_model_objective() (in module protac_degradation_predictor.optuna_utils_xgboost) xpu() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)

Z

zero_grad() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)