Index

A

act (torch_pgn.args.EncoderArgs attribute)

apply_dist_norm() (torch_pgn.data.dmpnn_utils.ProxGraph method)

B

basis_emb_size (torch_pgn.args.EncoderArgs attribute) batch_size (torch_pgn.args.TrainArgs attribute)

BatchProxGraph (class in torch_pgn.data.dmpnn_utils) BesselBasisLayer (class in torch_pgn.models.dimenet_utils)

C

construct_encoder() (torch_pgn.models.model.PGNNetwork method) construct_feed_forward() (torch_pgn.models.model.PGNNetwork method) construct_graphs (torch_pgn.args.DataArgs attribute) construct_nn_conv() (torch_pgn.models.pfp_encoder.PFPEncoder method)

covalent_only_depth (torch_pgn.args.EncoderArgs attribute) cross_validate (torch_pgn.args.DataArgs attribute) cross_validation() (in module torch_pgn.train.cross_validate_model) cutoff (torch_pgn.args.EncoderArgs attribute) cv_folds (torch_pgn.args.DataArgs attribute)

D

data_path (torch_pgn.args.DataArgs attribute) DataArgs (class in torch_pgn.args) dataset_type (torch_pgn.args.DataArgs attribute) decay_delay (torch_pgn.args.TrainArgs attribute) depth (torch_pgn.args.EncoderArgs attribute) device (torch_pgn.args.TrainArgs attribute) DimeNet (class in torch_pgn.models.DimeNet)

DimeNetPlusPlus (class in torch_pgn.models.DimeNet) directed (torch_pgn.args.DataArgs attribute) distance_mean (torch_pgn.args.DataArgs attribute) distance_std (torch_pgn.args.DataArgs attribute) download() (torch_pgn.data.FingerprintDataset.FingerprintDataset method) (torch_pgn.data.ProximityGraphDataset.ProximityGraphDataset method) dropout_prob (torch_pgn.args.FFArgs attribute)

E

edge_dim (torch_pgn.args.TrainArgs attribute) EmbeddingBlock (class in torch_pgn.models.dimenet_utils) enable_interacting_mask (torch_pgn.args.DataArgs attribute) enable_molgraph (torch_pgn.args.DataArgs attribute) encoder_type (torch_pgn.args.TrainArgs attribute)

EncoderArgs (class in torch_pgn.args) Envelope (class in torch_pgn.models.dimenet_utils) envelope_exponent (torch_pgn.args.EncoderArgs attribute) epochs (torch_pgn.args.TrainArgs attribute) evaluate() (in module torch_pgn.train.evaluate_model) extract_cross_edges() (in module torch_pgn.graphs.proximal_residues)

F

featurize_atoms_ECFP_like() (in module torch_pgn.featurization.simple_featurization) featurize_edges_simple() (in module torch_pgn.featurization.simple_featurization) ff_dim_1 (torch_pgn.args.FFArgs attribute) FFArgs (class in torch_pgn.args) fine_tuning_dir (torch_pgn.args.TrainArgs attribute) FingerprintDataset (class in torch_pgn.data.FingerprintDataset) format_batch() (in module torch_pgn.train.train_utils) format_data_directory() (in module torch_pgn.data.data_utils) forward() (torch_pgn.models.DimeNet.DimeNet method) (torch_pgn.models.dimenet_utils.BesselBasisLayer method) (torch_pgn.models.dimenet_utils.EmbeddingBlock method) (torch_pgn.models.dimenet_utils.Envelope method) (torch_pgn.models.dimenet_utils.InteractionBlock method) (torch_pgn.models.dimenet_utils.InteractionPPBlock method) (torch_pgn.models.dimenet_utils.OutputBlock method) (torch_pgn.models.dimenet_utils.OutputPPBlock method) (torch_pgn.models.dimenet_utils.ResidualLayer method) (torch_pgn.models.dimenet_utils.SphericalBasisLayer method) (torch_pgn.models.dmpnn_encoder.MPNEncoder method) (torch_pgn.models.FPEncoder.FPEncoder method) (torch_pgn.models.GGNet.GGNet method) (torch_pgn.models.model.PGNNetwork method) (torch_pgn.models.pfp_encoder.PFPEncoder method)

fp_column (torch_pgn.args.DataArgs attribute) fp_dim (torch_pgn.args.DataArgs attribute) (torch_pgn.args.EncoderArgs attribute) fp_format (torch_pgn.args.DataArgs attribute) fp_norm (torch_pgn.args.EncoderArgs attribute) FPDataset (class in torch_pgn.datasets.FPDataset) FPEncoder (class in torch_pgn.models.FPEncoder)

G

get_a2a() (torch_pgn.data.dmpnn_utils.BatchProxGraph method) get_b2b() (torch_pgn.data.dmpnn_utils.BatchProxGraph method) get_components() (torch_pgn.data.dmpnn_utils.BatchProxGraph method) get_interacting_atoms() (in module torch_pgn.graphs.proximal_residues) get_labels() (in module torch_pgn.train.train_utils) get_metric_functions() (in module torch_pgn.train.train_utils)

get_molecule_graph() (in module torch_pgn.graphs.proximal_residues) get_pool_function() (in module torch_pgn.models.nn_utils) get_proximal_atoms() (in module torch_pgn.graphs.proximal_residues) get_score() (torch_pgn.train.Trainer.Trainer method) get_sparse_fnctn() (in module torch_pgn.models.nn_utils) GGNet (class in torch_pgn.models.GGNet)

H

hidden_dim (torch_pgn.args.FFArgs attribute) hyperopt() (in module torch_pgn.train.hyperopt)

HyperoptArgs (class in torch_pgn.args) hyperparameter_optimization() (in module torch_pgn.train.hyperopt)

I

include_dist (torch_pgn.args.DataArgs attribute) index_select_ND() (in module torch_pgn.models.nn_utils) int_emb_size (torch_pgn.args.EncoderArgs attribute)

interaction_edges_removed (torch_pgn.args.DataArgs attribute) InteractionBlock (class in torch_pgn.models.dimenet_utils) InteractionPPBlock (class in torch_pgn.models.dimenet_utils)

L

label_col (torch_pgn.args.DataArgs attribute) label_file (torch_pgn.args.DataArgs attribute) label_mean (torch_pgn.args.DataArgs attribute) label_std (torch_pgn.args.DataArgs attribute) ligand_depth (torch_pgn.args.DataArgs attribute) ligand_only (torch_pgn.args.DataArgs attribute) ligand_only_readout (torch_pgn.args.EncoderArgs attribute) LigandOnlyPretransform (class in torch_pgn.data.data_utils)

load_args() (in module torch_pgn.train.train_utils) load_checkpoint() (in module torch_pgn.train.train_utils) (torch_pgn.train.Trainer.Trainer method) load_data() (torch_pgn.train.Trainer.Trainer method) load_proximity_graphs() (in module torch_pgn.data.load_data) load_test (torch_pgn.args.DataArgs attribute) (torch_pgn.args.TrainArgs attribute) loss_function (torch_pgn.args.TrainArgs attribute) lr (torch_pgn.args.TrainArgs attribute)

M

make_save_directories() (in module torch_pgn.train.train_utils) ManyVsManyDataset (class in torch_pgn.datasets.ManyVsManyDataset) max_num_neighbors (torch_pgn.args.EncoderArgs attribute) metrics (torch_pgn.args.TrainArgs attribute) minimize_score (torch_pgn.args.HyperoptArgs attribute) mode (torch_pgn.args.DataArgs attribute) module torch_pgn torch_pgn.args torch_pgn.data torch_pgn.data.data_utils torch_pgn.data.dmpnn_utils torch_pgn.data.FingerprintDataset torch_pgn.data.load_data torch_pgn.data.ProximityGraphDataset torch_pgn.datasets torch_pgn.datasets.FPDataset torch_pgn.datasets.ManyVsManyDataset torch_pgn.datasets.OneVsManyDataset torch_pgn.datasets.PGDataset torch_pgn.evaluate torch_pgn.evaluate.plot_utils torch_pgn.featurization torch_pgn.featurization.simple_featurization torch_pgn.graphs torch_pgn.graphs.graph_utils torch_pgn.graphs.proximal_residues torch_pgn.graphs.proximity_graph torch_pgn.load_data torch_pgn.models torch_pgn.models.DimeNet torch_pgn.models.dimenet_utils torch_pgn.models.dmpnn_encoder torch_pgn.models.FPEncoder torch_pgn.models.GGNet torch_pgn.models.model torch_pgn.models.nn_utils torch_pgn.models.pfp_encoder torch_pgn.train torch_pgn.train.cross_validate_model torch_pgn.train.evaluate_model torch_pgn.train.hyperopt torch_pgn.train.run_training torch_pgn.train.train torch_pgn.train.train_model torch_pgn.train.train_utils torch_pgn.train.Trainer

MolGraphTransform (class in torch_pgn.data.dmpnn_utils) MPNEncoder (class in torch_pgn.models.dmpnn_encoder) mpnn_directed (torch_pgn.args.EncoderArgs attribute) mse_loss() (in module torch_pgn.train.train_utils) multi_gpu (torch_pgn.args.TrainArgs attribute)

N

nn_conv_aggr (torch_pgn.args.EncoderArgs attribute) nn_conv_dropout_prob (torch_pgn.args.EncoderArgs attribute) nn_conv_in_dim (torch_pgn.args.EncoderArgs attribute) nn_conv_internal_dim (torch_pgn.args.EncoderArgs attribute) nn_conv_out_dim (torch_pgn.args.EncoderArgs attribute) node_dim (torch_pgn.args.TrainArgs attribute) normalize_dist (torch_pgn.args.DataArgs attribute) normalize_distance() (in module torch_pgn.data.data_utils) normalize_targets (torch_pgn.args.DataArgs attribute) normalize_targets() (in module torch_pgn.data.data_utils) num_after_skip (torch_pgn.args.EncoderArgs attribute)

num_before_skip (torch_pgn.args.EncoderArgs attribute) num_bilinear (torch_pgn.args.EncoderArgs attribute) num_blocks (torch_pgn.args.EncoderArgs attribute) num_classes (torch_pgn.args.FFArgs attribute) num_iters (torch_pgn.args.HyperoptArgs attribute) num_layers (torch_pgn.args.FFArgs attribute) num_output_layers (torch_pgn.args.EncoderArgs attribute) num_radial (torch_pgn.args.EncoderArgs attribute) num_spherical (torch_pgn.args.EncoderArgs attribute) num_workers (torch_pgn.args.DataArgs attribute) (torch_pgn.args.TrainArgs attribute)

O

one_step_convolution (torch_pgn.args.EncoderArgs attribute) OneHotTransform (class in torch_pgn.data.data_utils) OneVsManyDataset (class in torch_pgn.datasets.OneVsManyDataset)

out_channels (torch_pgn.args.EncoderArgs attribute) out_emb_channels (torch_pgn.args.EncoderArgs attribute) OutputBlock (class in torch_pgn.models.dimenet_utils) OutputPPBlock (class in torch_pgn.models.dimenet_utils)

P

parse_loss() (in module torch_pgn.train.train_utils) parse_pre_transforms() (torch_pgn.data.ProximityGraphDataset.ProximityGraphDataset method) parse_transforms() (in module torch_pgn.data.data_utils) patience (torch_pgn.args.TrainArgs attribute) PFPEncoder (class in torch_pgn.models.pfp_encoder) PGDataset (class in torch_pgn.datasets.PGDataset) PGNNetwork (class in torch_pgn.models.model) plot_correlation() (in module torch_pgn.evaluate.plot_utils) plot_correlations (torch_pgn.args.TrainArgs attribute) pool_type (torch_pgn.args.EncoderArgs attribute) predict() (in module torch_pgn.train.train_utils) process() (torch_pgn.data.FingerprintDataset.FingerprintDataset method) (torch_pgn.data.ProximityGraphDataset.ProximityGraphDataset method) process_args() (torch_pgn.args.DataArgs method) (torch_pgn.args.FFArgs method) (torch_pgn.args.HyperoptArgs method) (torch_pgn.args.TrainArgs method)

process_raw() (in module torch_pgn.load_data) process_raw_data() (in module torch_pgn.load_data) (torch_pgn.datasets.FPDataset.FPDataset method) (torch_pgn.datasets.ManyVsManyDataset.ManyVsManyDataset method) (torch_pgn.datasets.OneVsManyDataset.OneVsManyDataset method) (torch_pgn.datasets.PGDataset.PGDataset method) processed_file_names (torch_pgn.data.FingerprintDataset.FingerprintDataset property) (torch_pgn.data.ProximityGraphDataset.ProximityGraphDataset property) prox2graph() (in module torch_pgn.data.dmpnn_utils) ProxGraph (class in torch_pgn.data.dmpnn_utils) proximity_radius (torch_pgn.args.DataArgs attribute) ProximityGraphDataset (class in torch_pgn.data.ProximityGraphDataset)

R

RandomLigandTranslationTransform (class in torch_pgn.data.data_utils) raw_data_path (torch_pgn.args.DataArgs attribute) raw_file_names (torch_pgn.data.FingerprintDataset.FingerprintDataset property) (torch_pgn.data.ProximityGraphDataset.ProximityGraphDataset property) raw_mol_path (torch_pgn.args.DataArgs attribute) raw_pdb_path (torch_pgn.args.DataArgs attribute) receptor_depth (torch_pgn.args.DataArgs attribute) remove_dist_norm() (torch_pgn.data.dmpnn_utils.ProxGraph method) RemoveProximityEdgesPretransform (class in torch_pgn.data.data_utils)

reset_parameters() (torch_pgn.models.DimeNet.DimeNet method) (torch_pgn.models.dimenet_utils.BesselBasisLayer method) (torch_pgn.models.dimenet_utils.EmbeddingBlock method) (torch_pgn.models.dimenet_utils.InteractionBlock method) (torch_pgn.models.dimenet_utils.InteractionPPBlock method) (torch_pgn.models.dimenet_utils.ResidualLayer method) ResidualLayer (class in torch_pgn.models.dimenet_utils) rmse_loss() (in module torch_pgn.train.train_utils) run_training() (in module torch_pgn.train.run_training) (torch_pgn.train.Trainer.Trainer method)

S

save_checkpoint() (in module torch_pgn.train.train_utils) save_dir (torch_pgn.args.TrainArgs attribute) save_graphs (torch_pgn.args.DataArgs attribute) save_plots (torch_pgn.args.DataArgs attribute) save_splits (torch_pgn.args.DataArgs attribute) search_keys (torch_pgn.args.HyperoptArgs attribute) seed (torch_pgn.args.DataArgs attribute) (torch_pgn.args.TrainArgs attribute)

set_hyperopt_args() (torch_pgn.train.Trainer.Trainer method) skip_connections (torch_pgn.args.EncoderArgs attribute) sparse_type (torch_pgn.args.EncoderArgs attribute) SphericalBasisLayer (class in torch_pgn.models.dimenet_utils) split_conv (torch_pgn.args.EncoderArgs attribute) split_dir (torch_pgn.args.DataArgs attribute) split_test_graphs() (in module torch_pgn.data.data_utils) split_type (torch_pgn.args.DataArgs attribute) straw_model (torch_pgn.args.DataArgs attribute)

T

tensorboard_logging (torch_pgn.args.TrainArgs attribute) test_percent (torch_pgn.args.DataArgs attribute) torch_pgn module torch_pgn.args module torch_pgn.data module torch_pgn.data.data_utils module torch_pgn.data.dmpnn_utils module torch_pgn.data.FingerprintDataset module torch_pgn.data.load_data module torch_pgn.data.ProximityGraphDataset module torch_pgn.datasets module torch_pgn.datasets.FPDataset module torch_pgn.datasets.ManyVsManyDataset module torch_pgn.datasets.OneVsManyDataset module torch_pgn.datasets.PGDataset module torch_pgn.evaluate module torch_pgn.evaluate.plot_utils module torch_pgn.featurization module torch_pgn.featurization.simple_featurization module torch_pgn.graphs module torch_pgn.graphs.graph_utils module torch_pgn.graphs.proximal_residues module torch_pgn.graphs.proximity_graph module torch_pgn.load_data module torch_pgn.models module torch_pgn.models.DimeNet module torch_pgn.models.dimenet_utils module torch_pgn.models.dmpnn_encoder module

torch_pgn.models.FPEncoder module torch_pgn.models.GGNet module torch_pgn.models.model module torch_pgn.models.nn_utils module torch_pgn.models.pfp_encoder module torch_pgn.train module torch_pgn.train.cross_validate_model module torch_pgn.train.evaluate_model module torch_pgn.train.hyperopt module torch_pgn.train.run_training module torch_pgn.train.train module torch_pgn.train.train_model module torch_pgn.train.train_utils module torch_pgn.train.Trainer module torch_seed (torch_pgn.args.TrainArgs attribute) train() (in module torch_pgn.train.run_training) (in module torch_pgn.train.train) train_index (torch_pgn.args.DataArgs attribute) train_model() (in module torch_pgn.train.train_model) TrainArgs (class in torch_pgn.args) Trainer (class in torch_pgn.train.Trainer) training (torch_pgn.models.DimeNet.DimeNet attribute) (torch_pgn.models.DimeNet.DimeNetPlusPlus attribute) (torch_pgn.models.dimenet_utils.BesselBasisLayer attribute) (torch_pgn.models.dimenet_utils.EmbeddingBlock attribute) (torch_pgn.models.dimenet_utils.Envelope attribute) (torch_pgn.models.dimenet_utils.InteractionBlock attribute) (torch_pgn.models.dimenet_utils.InteractionPPBlock attribute) (torch_pgn.models.dimenet_utils.OutputBlock attribute) (torch_pgn.models.dimenet_utils.OutputPPBlock attribute) (torch_pgn.models.dimenet_utils.ResidualLayer attribute) (torch_pgn.models.dimenet_utils.SphericalBasisLayer attribute) (torch_pgn.models.dmpnn_encoder.MPNEncoder attribute) (torch_pgn.models.FPEncoder.FPEncoder attribute) (torch_pgn.models.GGNet.GGNet attribute) (torch_pgn.models.model.PGNNetwork attribute) (torch_pgn.models.pfp_encoder.PFPEncoder attribute) transforms (torch_pgn.args.DataArgs attribute) triplets() (torch_pgn.models.DimeNet.DimeNet method)

U

url (torch_pgn.models.DimeNet.DimeNet attribute) (torch_pgn.models.DimeNet.DimeNetPlusPlus attribute)

V

validation_percent (torch_pgn.args.DataArgs attribute)

W

weight_decay (torch_pgn.args.TrainArgs attribute)

write_fps() (torch_pgn.datasets.FPDataset.FPDataset method) write_graphs() (torch_pgn.datasets.PGDataset.PGDataset method)

Y

yield_full_interaction_graph() (in module torch_pgn.graphs.proximity_graph)

yield_tree_reduction() (in module torch_pgn.graphs.proximity_graph)