Index

A

accumulate_stats() (in module route_distances.lstm.utils) add_fingerprints() (in module route_distances.lstm.features)

add_node_index() (in module route_distances.lstm.utils) AptedConfig (class in route_distances.ted.utils)

B

BOTH (route_distances.ted.utils.TreeContent attribute)

C

children (route_distances.validation.MoleculeNode attribute) (route_distances.validation.ReactionNode attribute) children() (route_distances.ted.utils.AptedConfig method) cluster() (route_distances.clustering.ClusteringHelper static method)

ClusteringHelper (class in route_distances.clustering) collate_batch() (in module route_distances.lstm.utils) collate_trees() (in module route_distances.lstm.utils) configure_optimizers() (route_distances.lstm.models.RouteDistanceModel method)

D

distance_iter() (route_distances.ted.reactiontree.ReactionTreeWrapper method) distance_matrix() (in module route_distances.ted.distances)

distance_to() (route_distances.ted.reactiontree.ReactionTreeWrapper method) distance_to_with_sorting() (route_distances.ted.reactiontree.ReactionTreeWrapper method) distances_calculator() (in module route_distances.lstm.inference)

F

first_tree (route_distances.ted.reactiontree.ReactionTreeWrapper property)

fixed_clustering() (route_distances.clustering.ClusteringHelper method) forward() (route_distances.lstm.models.RouteDistanceModel method)

G

gather_adjacency_list() (in module route_distances.lstm.utils)

gather_node_attributes() (in module route_distances.lstm.utils)

I

info (route_distances.ted.reactiontree.ReactionTreeWrapper property)

InMemoryTreeDataset (class in route_distances.lstm.data)

L

labels (route_distances.clustering.ClusteringHelper property)

linkage_matrix() (route_distances.clustering.ClusteringHelper method)

M

main() (in module route_distances.tools.cluster_aizynth_output) (in module route_distances.tools.prepare_aizynthfinder_output) (in module route_distances.tools.train_lstm_model) module route_distances route_distances.clustering route_distances.lstm route_distances.lstm.data route_distances.lstm.defaults route_distances.lstm.features route_distances.lstm.inference route_distances.lstm.models route_distances.lstm.optim route_distances.lstm.utils route_distances.route_distances route_distances.ted route_distances.ted.distances route_distances.ted.reactiontree route_distances.ted.utils route_distances.tools route_distances.tools.cluster_aizynth_output route_distances.tools.prepare_aizynthfinder_output route_distances.tools.train_lstm_model route_distances.validation

MoleculeNode (class in route_distances.validation) MOLECULES (route_distances.ted.utils.TreeContent attribute)

O

optimize() (route_distances.clustering.ClusteringHelper method)

OptunaObjective (class in route_distances.lstm.optim)

P

preprocess_reaction_tree() (in module route_distances.lstm.features)

R

ReactionNode (class in route_distances.validation) REACTIONS (route_distances.ted.utils.TreeContent attribute) ReactionTreeWrapper (class in route_distances.ted.reactiontree) remove_reactions() (in module route_distances.lstm.features) rename() (route_distances.ted.utils.AptedConfig method) route_distances module route_distances.clustering module route_distances.lstm module route_distances.lstm.data module route_distances.lstm.defaults module route_distances.lstm.features module route_distances.lstm.inference module route_distances.lstm.models module route_distances.lstm.optim module

route_distances.lstm.utils module route_distances.route_distances module route_distances.ted module route_distances.ted.distances module route_distances.ted.reactiontree module route_distances.ted.utils module route_distances.tools module route_distances.tools.cluster_aizynth_output module route_distances.tools.prepare_aizynthfinder_output module route_distances.tools.train_lstm_model module route_distances.validation module route_distances_calculator() (in module route_distances.route_distances) RouteDistanceModel (class in route_distances.lstm.models)

S

setup() (route_distances.lstm.data.TreeDataModule method)

smiles (route_distances.validation.MoleculeNode attribute) StandardFingerprintFactory (class in route_distances.ted.utils)

T

test_dataloader() (route_distances.lstm.data.TreeDataModule method) test_epoch_end() (route_distances.lstm.models.RouteDistanceModel method) test_step() (route_distances.lstm.models.RouteDistanceModel method) train_dataloader() (route_distances.lstm.data.TreeDataModule method) training_step() (route_distances.lstm.models.RouteDistanceModel method)

TreeContent (class in route_distances.ted.utils) TreeDataModule (class in route_distances.lstm.data) trees (route_distances.ted.reactiontree.ReactionTreeWrapper property) type (route_distances.validation.MoleculeNode attribute) (route_distances.validation.ReactionNode attribute)

V

val_dataloader() (route_distances.lstm.data.TreeDataModule method) validate_dict() (in module route_distances.validation)

validation_epoch_end() (route_distances.lstm.models.RouteDistanceModel method) validation_step() (route_distances.lstm.models.RouteDistanceModel method)