Index

A

actions_to() (aizynthfinder.search.mcts.node.MctsNode method) add_stub() (aizynthfinder.search.breadth_first.nodes.MoleculeNode method) (aizynthfinder.search.retrostar.nodes.MoleculeNode method) AiZynthApp (class in aizynthfinder.interfaces.aizynthapp) AiZynthExpander (class in aizynthfinder.aizynthfinder) aizynthfinder module AiZynthFinder (class in aizynthfinder.aizynthfinder) aizynthfinder.aizynthfinder module aizynthfinder.analysis module aizynthfinder.analysis.routes module aizynthfinder.analysis.tree_analysis module aizynthfinder.analysis.utils module aizynthfinder.chem module aizynthfinder.chem.mol module aizynthfinder.chem.reaction module aizynthfinder.chem.serialization module aizynthfinder.context module aizynthfinder.context.collection module aizynthfinder.context.config module aizynthfinder.context.policy module aizynthfinder.context.policy.expansion_strategies module aizynthfinder.context.policy.filter_strategies module aizynthfinder.context.policy.policies module aizynthfinder.context.policy.utils module aizynthfinder.context.scoring module aizynthfinder.context.scoring.collection module aizynthfinder.context.scoring.scorers module aizynthfinder.context.scoring.scorers_base module aizynthfinder.context.scoring.scorers_mols module aizynthfinder.context.scoring.scorers_reactions module aizynthfinder.context.stock module aizynthfinder.context.stock.queries module aizynthfinder.context.stock.stock module aizynthfinder.interfaces module aizynthfinder.interfaces.aizynthapp module aizynthfinder.interfaces.aizynthcli module aizynthfinder.interfaces.gui module aizynthfinder.interfaces.gui.clustering module aizynthfinder.interfaces.gui.pareto_fronts module aizynthfinder.interfaces.gui.utils module aizynthfinder.reactiontree module aizynthfinder.search module aizynthfinder.search.andor_trees module

aizynthfinder.search.breadth_first module aizynthfinder.search.breadth_first.nodes module aizynthfinder.search.breadth_first.search_tree module aizynthfinder.search.dfpn module aizynthfinder.search.dfpn.nodes module aizynthfinder.search.dfpn.search_tree module aizynthfinder.search.mcts module aizynthfinder.search.mcts.node module aizynthfinder.search.mcts.search module aizynthfinder.search.mcts.state module aizynthfinder.search.mcts.utils module aizynthfinder.search.retrostar module aizynthfinder.search.retrostar.cost module aizynthfinder.search.retrostar.nodes module aizynthfinder.search.retrostar.search_tree module aizynthfinder.tools module aizynthfinder.tools.cat_output module aizynthfinder.tools.download_public_data module aizynthfinder.tools.make_stock module aizynthfinder.utils module aizynthfinder.utils.bonds module aizynthfinder.utils.exceptions module aizynthfinder.utils.files module aizynthfinder.utils.image module aizynthfinder.utils.loading module aizynthfinder.utils.logging module aizynthfinder.utils.math module aizynthfinder.utils.models module aizynthfinder.utils.mongo module aizynthfinder.utils.paths module aizynthfinder.utils.sc_score module aizynthfinder.utils.type_utils module amount() (aizynthfinder.context.stock.queries.StockQueryMixin method) (aizynthfinder.context.stock.stock.Stock method) ancestors() (aizynthfinder.search.breadth_first.nodes.MoleculeNode method) (aizynthfinder.search.retrostar.nodes.MoleculeNode method) AndOrSearchTreeBase (class in aizynthfinder.search.andor_trees) apply() (aizynthfinder.context.policy.filter_strategies.BondFilter method) (aizynthfinder.context.policy.filter_strategies.FilterStrategy method) (aizynthfinder.context.policy.filter_strategies.FrozenSubstructureFilter method) (aizynthfinder.context.policy.filter_strategies.QuickKerasFilter method) (aizynthfinder.context.policy.filter_strategies.ReactantsCountFilter method) (aizynthfinder.context.policy.policies.FilterPolicy method) availability_list() (aizynthfinder.context.stock.stock.Stock method) availability_string() (aizynthfinder.context.stock.queries.MongoDbInchiKeyQuery method) (aizynthfinder.context.stock.queries.StockQueryMixin method) (aizynthfinder.context.stock.stock.Stock method) AverageTemplateOccurrenceScorer (class in aizynthfinder.context.scoring.scorers_reactions)

B

backpropagate() (aizynthfinder.search.mcts.node.MctsNode method) (aizynthfinder.search.mcts.node.ParetoMctsNode method) (aizynthfinder.search.mcts.search.MctsSearchTree method) base_coefficient (aizynthfinder.context.scoring.scorers_base.PowerScaler attribute) basic_compare() (aizynthfinder.chem.mol.Molecule method)

best() (aizynthfinder.analysis.tree_analysis.TreeAnalysis method) BondFilter (class in aizynthfinder.context.policy.filter_strategies) BrokenBonds (class in aizynthfinder.utils.bonds) BrokenBondsScorer (class in aizynthfinder.context.scoring.scorers) build_routes() (aizynthfinder.aizynthfinder.AiZynthFinder method)

C

cached_search() (aizynthfinder.context.stock.queries.StockQueryMixin method) calculate() (aizynthfinder.search.retrostar.cost.RetroStarCost method) (aizynthfinder.search.retrostar.cost.ZeroMoleculeCost method) cat_datafiles() (in module aizynthfinder.utils.files) cat_hdf_files() (in module aizynthfinder.utils.files) child_reactions() (aizynthfinder.reactiontree.ReactionTree method) children (aizynthfinder.search.andor_trees.TreeNodeMixin property) (aizynthfinder.search.breadth_first.nodes.MoleculeNode property) (aizynthfinder.search.breadth_first.nodes.ReactionNode property) (aizynthfinder.search.dfpn.nodes.ReactionNode property) (aizynthfinder.search.mcts.node.MctsNode property) (aizynthfinder.search.retrostar.nodes.MoleculeNode property) (aizynthfinder.search.retrostar.nodes.ReactionNode property) children_view() (aizynthfinder.search.mcts.node.MctsNode method) (aizynthfinder.search.mcts.node.ParetoMctsNode method) clear_cache() (aizynthfinder.context.stock.queries.StockQueryMixin method) close() (aizynthfinder.search.retrostar.nodes.MoleculeNode method) cluster() (aizynthfinder.analysis.routes.RouteCollection method)

ClusteringGui (class in aizynthfinder.interfaces.gui.clustering) combined_reaction_trees() (aizynthfinder.analysis.routes.RouteCollection method) CombinedReactionTrees (class in aizynthfinder.analysis.utils) CombinedScorer (class in aizynthfinder.context.scoring.scorers) compute_reward() (aizynthfinder.search.mcts.search.MctsSearchTree method) compute_scores() (aizynthfinder.analysis.routes.RouteCollection method) Configuration (class in aizynthfinder.context.config) ContextCollection (class in aizynthfinder.context.collection) copy() (aizynthfinder.chem.reaction.FixedRetroReaction method) (aizynthfinder.chem.reaction.RetroReaction method) CostException create_default_scorers() (aizynthfinder.context.scoring.collection.ScorerCollection method) create_root() (aizynthfinder.search.breadth_first.nodes.MoleculeNode class method) (aizynthfinder.search.dfpn.nodes.MoleculeNode class method) (aizynthfinder.search.mcts.node.MctsNode class method) (aizynthfinder.search.retrostar.nodes.MoleculeNode class method) create_stub() (aizynthfinder.search.breadth_first.nodes.ReactionNode class method) (aizynthfinder.search.retrostar.nodes.ReactionNode class method)

D

data_path() (in module aizynthfinder.utils.paths) DeepSetScorer (class in aizynthfinder.context.scoring.scorers) DeltaSyntheticComplexityScorer (class in aizynthfinder.context.scoring.scorers_mols) dense_layer_forward_pass() (in module aizynthfinder.utils.math) depth() (aizynthfinder.reactiontree.ReactionTree method) deselect() (aizynthfinder.context.collection.ContextCollection method) deserialize_action() (in module aizynthfinder.chem.serialization)

dict_with_extra() (aizynthfinder.analysis.routes.RouteCollection method) dict_with_scores() (aizynthfinder.analysis.routes.RouteCollection method) dicts (aizynthfinder.analysis.routes.RouteCollection property) disproven (aizynthfinder.search.dfpn.nodes.ReactionNode property) distance_matrix() (aizynthfinder.analysis.routes.RouteCollection method) distance_to() (aizynthfinder.reactiontree.ReactionTree method) do_expansion() (aizynthfinder.aizynthfinder.AiZynthExpander method)

E

exclude() (aizynthfinder.context.stock.stock.Stock method) expand() (aizynthfinder.search.dfpn.nodes.MoleculeNode method) (aizynthfinder.search.dfpn.nodes.ReactionNode method) (aizynthfinder.search.mcts.node.MctsNode method) expansion_policy (aizynthfinder.context.config.Configuration attribute) ExpansionPolicy (class in aizynthfinder.context.policy.policies)

ExpansionStrategy (class in aizynthfinder.context.policy.expansion_strategies) ExternalModelAPIError ExternalModelViaGRPC (class in aizynthfinder.utils.models) ExternalModelViaREST (class in aizynthfinder.utils.models) extract_plain_smiles() (in module aizynthfinder.tools.make_stock) extract_smiles_from_module() (in module aizynthfinder.tools.make_stock) extract_statistics() (aizynthfinder.aizynthfinder.AiZynthFinder method)

F

feasibility() (aizynthfinder.context.policy.filter_strategies.QuickKerasFilter method) filter_policy (aizynthfinder.context.config.Configuration attribute) FilterPolicy (class in aizynthfinder.context.policy.policies) FilterStrategy (class in aizynthfinder.context.policy.filter_strategies) fingerprint() (aizynthfinder.chem.mol.Molecule method) FixedRetroReaction (class in aizynthfinder.chem.reaction) forward() (aizynthfinder.utils.sc_score.SCScore method) FractionInSourceStockScorer (class in aizynthfinder.context.scoring.scorers_mols) FractionInStockScorer (class in aizynthfinder.context.scoring.scorers_mols) FractionOfIntermediatesInStockScorer (class in aizynthfinder.context.scoring.scorers_mols) from_analysis() (aizynthfinder.analysis.routes.RouteCollection class method) from_app() (aizynthfinder.interfaces.gui.clustering.ClusteringGui class method) (aizynthfinder.interfaces.gui.pareto_fronts.ParetoFrontsGUI class method)

from_dict() (aizynthfinder.context.config.Configuration class method) (aizynthfinder.reactiontree.ReactionTree class method) (aizynthfinder.search.breadth_first.nodes.MoleculeNode class method) (aizynthfinder.search.breadth_first.nodes.ReactionNode class method) (aizynthfinder.search.mcts.node.MctsNode class method) (aizynthfinder.search.mcts.state.MctsState class method) (aizynthfinder.search.retrostar.nodes.MoleculeNode class method) (aizynthfinder.search.retrostar.nodes.ReactionNode class method) from_file() (aizynthfinder.context.config.Configuration class method) from_json() (aizynthfinder.search.breadth_first.search_tree.SearchTree class method) (aizynthfinder.search.mcts.search.MctsSearchTree class method) (aizynthfinder.search.retrostar.search_tree.SearchTree class method) from_serialization() (aizynthfinder.chem.reaction.RetroReaction class method) FrozenSubstructureFilter (class in aizynthfinder.context.policy.filter_strategies)

G

get_actions() (aizynthfinder.context.policy.expansion_strategies.ExpansionStrategy method) (aizynthfinder.context.policy.expansion_strategies.MultiExpansionStrategy method) (aizynthfinder.context.policy.expansion_strategies.TemplateBasedDirectExpansionStrategy method) (aizynthfinder.context.policy.expansion_strategies.TemplateBasedExpansionStrategy method) (aizynthfinder.context.policy.policies.ExpansionPolicy method)

get_bonds_in_molecule() (aizynthfinder.chem.mol.TreeMolecule method) get_mongo_client() (in module aizynthfinder.utils.mongo) get_tree_molecules() (aizynthfinder.chem.serialization.MoleculeDeserializer method) graph() (aizynthfinder.search.mcts.search.MctsSearchTree method)

H

has_all_focussed_bonds() (aizynthfinder.chem.mol.TreeMolecule method) has_atom_mapping() (aizynthfinder.chem.mol.Molecule method)

hash_key() (aizynthfinder.reactiontree.ReactionTree method) hash_reactions() (in module aizynthfinder.chem.reaction)

I

images (aizynthfinder.analysis.routes.RouteCollection property) in_stock() (aizynthfinder.reactiontree.ReactionTree method) inchi (aizynthfinder.chem.mol.Molecule property) inchi_key (aizynthfinder.chem.mol.Molecule property) index_to_mapping (aizynthfinder.chem.mol.Molecule property)

InMemoryInchiKeyQuery (class in aizynthfinder.context.stock.queries) is_branched() (aizynthfinder.reactiontree.ReactionTree method) is_solved (aizynthfinder.search.mcts.node.MctsNode property) is_terminal() (aizynthfinder.search.mcts.node.MctsNode method) items (aizynthfinder.context.collection.ContextCollection property)

J

jsons (aizynthfinder.analysis.routes.RouteCollection property)

L

leafs() (aizynthfinder.reactiontree.ReactionTree method) load() (aizynthfinder.context.collection.ContextCollection method) (aizynthfinder.context.policy.policies.ExpansionPolicy method) (aizynthfinder.context.policy.policies.FilterPolicy method) (aizynthfinder.context.scoring.collection.ScorerCollection method) (aizynthfinder.context.stock.stock.Stock method) load_dynamic_class() (in module aizynthfinder.utils.loading) load_from_config() (aizynthfinder.context.collection.ContextCollection method) (aizynthfinder.context.policy.policies.ExpansionPolicy method) (aizynthfinder.context.policy.policies.FilterPolicy method) (aizynthfinder.context.scoring.collection.ScorerCollection method) (aizynthfinder.context.stock.stock.Stock method)

load_model() (in module aizynthfinder.utils.models) LocalKerasModel (class in aizynthfinder.utils.models) LocalOnnxModel (class in aizynthfinder.utils.models) logger() (in module aizynthfinder.utils.logging)

M

main() (in module aizynthfinder.interfaces.aizynthapp) (in module aizynthfinder.interfaces.aizynthcli) (in module aizynthfinder.tools.cat_output) (in module aizynthfinder.tools.download_public_data) (in module aizynthfinder.tools.make_stock) make_dicts() (aizynthfinder.analysis.routes.RouteCollection method) make_hdf5_stock() (in module aizynthfinder.tools.make_stock) make_images() (aizynthfinder.analysis.routes.RouteCollection method) make_jsons() (aizynthfinder.analysis.routes.RouteCollection method) make_molbloom() (in module aizynthfinder.tools.make_stock) make_molbloom_inchi() (in module aizynthfinder.tools.make_stock) make_mongo_stock() (in module aizynthfinder.tools.make_stock) make_rxnutils_route() (in module aizynthfinder.context.scoring.scorers_base) make_subset() (aizynthfinder.context.scoring.collection.ScorerCollection method) make_unique() (aizynthfinder.chem.mol.Molecule method) make_visjs_page() (in module aizynthfinder.utils.image) mapped_atom_bonds (aizynthfinder.chem.mol.TreeMolecule property) mapped_reaction_smiles() (aizynthfinder.chem.reaction.RetroReaction method) mapping_to_index (aizynthfinder.chem.mol.Molecule property) (aizynthfinder.chem.mol.TreeMolecule property) max_val (aizynthfinder.context.scoring.scorers_base.MinMaxScaler attribute) MaxTransformScorer (class in aizynthfinder.context.scoring.scorers_reactions) MctsNode (class in aizynthfinder.search.mcts.node) MctsSearchTree (class in aizynthfinder.search.mcts.search) MctsState (class in aizynthfinder.search.mcts.state) metadata (aizynthfinder.reactiontree.ReactionTree property) min_val (aizynthfinder.context.scoring.scorers_base.MinMaxScaler attribute) MinMaxScaler (class in aizynthfinder.context.scoring.scorers_base) module aizynthfinder aizynthfinder.aizynthfinder aizynthfinder.analysis aizynthfinder.analysis.routes aizynthfinder.analysis.tree_analysis aizynthfinder.analysis.utils aizynthfinder.chem aizynthfinder.chem.mol aizynthfinder.chem.reaction aizynthfinder.chem.serialization aizynthfinder.context aizynthfinder.context.collection aizynthfinder.context.config aizynthfinder.context.policy aizynthfinder.context.policy.expansion_strategies aizynthfinder.context.policy.filter_strategies aizynthfinder.context.policy.policies aizynthfinder.context.policy.utils aizynthfinder.context.scoring aizynthfinder.context.scoring.collection aizynthfinder.context.scoring.scorers aizynthfinder.context.scoring.scorers_base aizynthfinder.context.scoring.scorers_mols aizynthfinder.context.scoring.scorers_reactions aizynthfinder.context.stock aizynthfinder.context.stock.queries aizynthfinder.context.stock.stock aizynthfinder.interfaces aizynthfinder.interfaces.aizynthapp aizynthfinder.interfaces.aizynthcli aizynthfinder.interfaces.gui aizynthfinder.interfaces.gui.clustering aizynthfinder.interfaces.gui.pareto_fronts aizynthfinder.interfaces.gui.utils aizynthfinder.reactiontree aizynthfinder.search aizynthfinder.search.andor_trees aizynthfinder.search.breadth_first aizynthfinder.search.breadth_first.nodes aizynthfinder.search.breadth_first.search_tree aizynthfinder.search.dfpn aizynthfinder.search.dfpn.nodes aizynthfinder.search.dfpn.search_tree aizynthfinder.search.mcts aizynthfinder.search.mcts.node aizynthfinder.search.mcts.search aizynthfinder.search.mcts.state aizynthfinder.search.mcts.utils aizynthfinder.search.retrostar aizynthfinder.search.retrostar.cost aizynthfinder.search.retrostar.nodes aizynthfinder.search.retrostar.search_tree aizynthfinder.tools aizynthfinder.tools.cat_output aizynthfinder.tools.download_public_data aizynthfinder.tools.make_stock aizynthfinder.utils aizynthfinder.utils.bonds aizynthfinder.utils.exceptions aizynthfinder.utils.files aizynthfinder.utils.image aizynthfinder.utils.loading aizynthfinder.utils.logging aizynthfinder.utils.math aizynthfinder.utils.models aizynthfinder.utils.mongo aizynthfinder.utils.paths aizynthfinder.utils.sc_score aizynthfinder.utils.type_utils

mol_nodes (aizynthfinder.search.andor_trees.AndOrSearchTreeBase property) (aizynthfinder.search.breadth_first.search_tree.SearchTree property) (aizynthfinder.search.dfpn.search_tree.SearchTree property) (aizynthfinder.search.retrostar.search_tree.SearchTree property) MolbloomFilterQuery (class in aizynthfinder.context.stock.queries) Molecule (class in aizynthfinder.chem.mol) MoleculeCost (class in aizynthfinder.search.retrostar.cost) MoleculeDeserializer (class in aizynthfinder.chem.serialization) MoleculeException MoleculeNode (class in aizynthfinder.search.breadth_first.nodes) (class in aizynthfinder.search.dfpn.nodes) (class in aizynthfinder.search.retrostar.nodes) molecules() (aizynthfinder.reactiontree.ReactionTree method) MoleculeSerializer (class in aizynthfinder.chem.serialization) MongoDbInchiKeyQuery (class in aizynthfinder.context.stock.queries) MultiExpansionStrategy (class in aizynthfinder.context.policy.expansion_strategies)

N

names() (aizynthfinder.context.scoring.collection.ScorerCollection method) nmax (aizynthfinder.analysis.utils.RouteSelectionArguments attribute) nmin (aizynthfinder.analysis.utils.RouteSelectionArguments attribute) nodes() (aizynthfinder.search.mcts.search.MctsSearchTree method)

NodeUnexpectedBehaviourException none_molecule() (in module aizynthfinder.chem.mol) NumberOfPrecursorsInStockScorer (class in aizynthfinder.context.scoring.scorers_mols) NumberOfPrecursorsScorer (class in aizynthfinder.context.scoring.scorers_mols) NumberOfReactionsScorer (class in aizynthfinder.context.scoring.scorers_reactions)

O

objects() (aizynthfinder.context.scoring.collection.ScorerCollection method) one_iteration() (aizynthfinder.search.andor_trees.AndOrSearchTreeBase method) (aizynthfinder.search.breadth_first.search_tree.SearchTree method) (aizynthfinder.search.dfpn.search_tree.SearchTree method) (aizynthfinder.search.mcts.search.MctsSearchTree method) (aizynthfinder.search.retrostar.search_tree.SearchTree method)

P

package_path() (in module aizynthfinder.utils.paths) parent (aizynthfinder.search.mcts.node.MctsNode property) parent_molecule() (aizynthfinder.reactiontree.ReactionTree method) pareto_front() (aizynthfinder.analysis.tree_analysis.TreeAnalysis method) pareto_fronts_plot() (in module aizynthfinder.interfaces.gui.utils) ParetoFrontsGUI (class in aizynthfinder.interfaces.gui.pareto_fronts) ParetoMctsNode (class in aizynthfinder.search.mcts.node) path_to() (aizynthfinder.search.mcts.node.MctsNode method) PolicyException post_processing (aizynthfinder.context.config.Configuration attribute) PowerScaler (class in aizynthfinder.context.scoring.scorers_base) predict() (aizynthfinder.utils.models.ExternalModelViaGRPC method) (aizynthfinder.utils.models.ExternalModelViaREST method) (aizynthfinder.utils.models.LocalKerasModel method) (aizynthfinder.utils.models.LocalOnnxModel method)

prepare_tree() (aizynthfinder.aizynthfinder.AiZynthFinder method) price() (aizynthfinder.context.stock.queries.InMemoryInchiKeyQuery method) (aizynthfinder.context.stock.queries.StockQueryMixin method) (aizynthfinder.context.stock.stock.Stock method) PriceSumScorer (class in aizynthfinder.context.scoring.scorers_mols) promising_child() (aizynthfinder.search.dfpn.nodes.MoleculeNode method) (aizynthfinder.search.dfpn.nodes.ReactionNode method) (aizynthfinder.search.mcts.node.MctsNode method) prop (aizynthfinder.search.andor_trees.TreeNodeMixin property) (aizynthfinder.search.breadth_first.nodes.MoleculeNode property) (aizynthfinder.search.breadth_first.nodes.ReactionNode property) (aizynthfinder.search.dfpn.nodes.MoleculeNode property) (aizynthfinder.search.dfpn.nodes.ReactionNode property) (aizynthfinder.search.retrostar.nodes.MoleculeNode property) (aizynthfinder.search.retrostar.nodes.ReactionNode property) proven (aizynthfinder.search.dfpn.nodes.ReactionNode property)

Q

QuickKerasFilter (class in aizynthfinder.context.policy.filter_strategies)

R

rd_reaction (aizynthfinder.chem.reaction.TemplatedRetroReaction property) reactants (aizynthfinder.chem.reaction.RetroReaction property) ReactantsCountFilter (class in aizynthfinder.context.policy.filter_strategies) ReactionClassMembershipScorer (class in aizynthfinder.context.scoring.scorers_reactions) ReactionClassRankScorer (class in aizynthfinder.context.scoring.scorers_reactions) ReactionNode (class in aizynthfinder.search.breadth_first.nodes) (class in aizynthfinder.search.dfpn.nodes) (class in aizynthfinder.search.retrostar.nodes) reactions() (aizynthfinder.reactiontree.ReactionTree method) ReactionTree (class in aizynthfinder.reactiontree) ReactionTreeFromAndOrTrace (class in aizynthfinder.search.andor_trees) ReactionTreeFromDict (class in aizynthfinder.reactiontree) ReactionTreeFromExpansion (class in aizynthfinder.reactiontree) ReactionTreeFromSuperNode (class in aizynthfinder.search.mcts.utils) ReactionTreeLoader (class in aizynthfinder.reactiontree) read_datafile() (in module aizynthfinder.utils.files) rectified_linear_unit() (in module aizynthfinder.utils.math) RejectionException remove_atom_mapping() (aizynthfinder.chem.mol.Molecule method)

rescore() (aizynthfinder.analysis.routes.RouteCollection method) reset_cache() (aizynthfinder.context.policy.expansion_strategies.ExpansionStrategy method) (aizynthfinder.context.policy.expansion_strategies.TemplateBasedExpansionStrategy method) (aizynthfinder.context.policy.policies.ExpansionPolicy method) (aizynthfinder.context.policy.policies.FilterPolicy method) reset_exclusion_list() (aizynthfinder.context.stock.stock.Stock method) RetroReaction (class in aizynthfinder.chem.reaction) RetroStarCost (class in aizynthfinder.search.retrostar.cost) return_all (aizynthfinder.analysis.utils.RouteSelectionArguments attribute) reverse (aizynthfinder.context.scoring.scorers_base.MinMaxScaler attribute) route_display() (in module aizynthfinder.interfaces.gui.utils) route_to_node() (in module aizynthfinder.search.mcts.utils) RouteCollection (class in aizynthfinder.analysis.routes) RouteCostScorer (class in aizynthfinder.context.scoring.scorers) routes() (aizynthfinder.search.andor_trees.AndOrSearchTreeBase method) (aizynthfinder.search.breadth_first.search_tree.SearchTree method) (aizynthfinder.search.dfpn.search_tree.SearchTree method) (aizynthfinder.search.retrostar.search_tree.SearchTree method) RouteSelectionArguments (class in aizynthfinder.analysis.utils) RouteSimilarityScorer (class in aizynthfinder.context.scoring.scorers)

S

sanitize() (aizynthfinder.chem.mol.Molecule method) save_datafile() (in module aizynthfinder.utils.files) save_molecule_images() (in module aizynthfinder.utils.image) sc_deltas() (aizynthfinder.context.scoring.scorers_mols.DeltaSyntheticComplexityScorer method) scale_factor (aizynthfinder.context.scoring.scorers_base.MinMaxScaler attribute) score_vector() (aizynthfinder.context.scoring.collection.ScorerCollection method) Scorer (class in aizynthfinder.context.scoring.scorers_base) scorer_name (aizynthfinder.context.scoring.scorers.BrokenBondsScorer attribute) (aizynthfinder.context.scoring.scorers.DeepSetScorer attribute) (aizynthfinder.context.scoring.scorers.RouteCostScorer attribute) (aizynthfinder.context.scoring.scorers.RouteSimilarityScorer attribute) (aizynthfinder.context.scoring.scorers.StateScorer attribute) (aizynthfinder.context.scoring.scorers_base.Scorer attribute) (aizynthfinder.context.scoring.scorers_mols.DeltaSyntheticComplexityScorer attribute) (aizynthfinder.context.scoring.scorers_mols.FractionInSourceStockScorer attribute) (aizynthfinder.context.scoring.scorers_mols.FractionInStockScorer attribute) (aizynthfinder.context.scoring.scorers_mols.NumberOfPrecursorsInStockScorer attribute) (aizynthfinder.context.scoring.scorers_mols.NumberOfPrecursorsScorer attribute) (aizynthfinder.context.scoring.scorers_mols.PriceSumScorer attribute) (aizynthfinder.context.scoring.scorers_reactions.AverageTemplateOccurrenceScorer attribute) (aizynthfinder.context.scoring.scorers_reactions.MaxTransformScorer attribute) (aizynthfinder.context.scoring.scorers_reactions.NumberOfReactionsScorer attribute) (aizynthfinder.context.scoring.scorers_reactions.ReactionClassRankScorer attribute) ScorerCollection (class in aizynthfinder.context.scoring.collection) ScorerException scorers (aizynthfinder.context.config.Configuration attribute) SCScore (class in aizynthfinder.utils.sc_score) search (aizynthfinder.context.config.Configuration attribute) SearchTree (class in aizynthfinder.search.breadth_first.search_tree) (class in aizynthfinder.search.dfpn.search_tree) (class in aizynthfinder.search.retrostar.search_tree) select() (aizynthfinder.context.collection.ContextCollection method) (aizynthfinder.context.stock.stock.Stock method) select_all() (aizynthfinder.context.collection.ContextCollection method) select_first() (aizynthfinder.context.collection.ContextCollection method) select_last() (aizynthfinder.context.collection.ContextCollection method) select_leaf() (aizynthfinder.search.mcts.search.MctsSearchTree method) selection (aizynthfinder.context.collection.ContextCollection property) serialize() (aizynthfinder.search.breadth_first.nodes.MoleculeNode method) (aizynthfinder.search.breadth_first.nodes.ReactionNode method) (aizynthfinder.search.breadth_first.search_tree.SearchTree method) (aizynthfinder.search.mcts.node.MctsNode method) (aizynthfinder.search.mcts.node.ParetoMctsNode method) (aizynthfinder.search.mcts.search.MctsSearchTree method) (aizynthfinder.search.mcts.state.MctsState method) (aizynthfinder.search.retrostar.nodes.MoleculeNode method) (aizynthfinder.search.retrostar.nodes.ReactionNode method) (aizynthfinder.search.retrostar.search_tree.SearchTree method)

serialize_action() (in module aizynthfinder.chem.serialization) set_stop_criteria() (aizynthfinder.context.stock.stock.Stock method) setup() (aizynthfinder.interfaces.aizynthapp.AiZynthApp method) setup_logger() (in module aizynthfinder.utils.logging) sigmoid() (in module aizynthfinder.utils.math) slope (aizynthfinder.context.scoring.scorers_base.SquashScaler attribute) smiles (aizynthfinder.chem.reaction.RetroReaction property) smiles_in_stock() (aizynthfinder.context.stock.stock.Stock method) SmilesBasedRetroReaction (class in aizynthfinder.chem.reaction) softmax() (in module aizynthfinder.utils.math) sort() (aizynthfinder.analysis.tree_analysis.TreeAnalysis method) (aizynthfinder.context.scoring.scorers_base.Scorer method) sort_bonds() (in module aizynthfinder.utils.bonds) split_file() (in module aizynthfinder.utils.files) SplitAndOrTree (class in aizynthfinder.search.andor_trees) SquashScaler (class in aizynthfinder.context.scoring.scorers_base) start_processes() (in module aizynthfinder.utils.files) state (aizynthfinder.search.mcts.node.MctsNode property) StateScorer (class in aizynthfinder.context.scoring.scorers) stock (aizynthfinder.context.config.Configuration attribute) Stock (class in aizynthfinder.context.stock.stock) stock_availability (aizynthfinder.search.mcts.state.MctsState property) stock_inchikeys (aizynthfinder.context.stock.queries.InMemoryInchiKeyQuery property) stock_info() (aizynthfinder.aizynthfinder.AiZynthFinder method) StockAvailabilityScorer (class in aizynthfinder.context.scoring.scorers_mols) StockException StockQueryMixin (class in aizynthfinder.context.stock.queries) stop_criteria (aizynthfinder.context.stock.stock.Stock property) store (aizynthfinder.chem.serialization.MoleculeSerializer property) subtrees() (aizynthfinder.reactiontree.ReactionTree method)

T

target_mol (aizynthfinder.aizynthfinder.AiZynthFinder property) target_smiles (aizynthfinder.aizynthfinder.AiZynthFinder property) target_value (aizynthfinder.search.retrostar.nodes.MoleculeNode property) TemplateBasedDirectExpansionStrategy (class in aizynthfinder.context.policy.expansion_strategies) TemplateBasedExpansionStrategy (class in aizynthfinder.context.policy.expansion_strategies) TemplatedRetroReaction (class in aizynthfinder.chem.reaction) to_dict() (aizynthfinder.analysis.utils.CombinedReactionTrees method) (aizynthfinder.chem.reaction.RetroReaction method) (aizynthfinder.chem.reaction.SmilesBasedRetroReaction method) (aizynthfinder.chem.reaction.TemplatedRetroReaction method) (aizynthfinder.reactiontree.ReactionTree method)

to_image() (aizynthfinder.reactiontree.ReactionTree method) (aizynthfinder.search.mcts.state.MctsState method) to_json() (aizynthfinder.reactiontree.ReactionTree method) to_reaction_tree() (aizynthfinder.search.mcts.node.MctsNode method) to_smiles_based_retroreaction() (aizynthfinder.chem.reaction.FixedRetroReaction method) to_visjs_page() (aizynthfinder.analysis.utils.CombinedReactionTrees method) tree_search() (aizynthfinder.aizynthfinder.AiZynthFinder method) tree_statistics() (aizynthfinder.analysis.tree_analysis.TreeAnalysis method) TreeAnalysis (class in aizynthfinder.analysis.tree_analysis) TreeAnalysisException TreeMolecule (class in aizynthfinder.chem.mol) TreeNodeMixin (class in aizynthfinder.search.andor_trees)

U

UniqueMolecule (class in aizynthfinder.chem.mol) unqueried (aizynthfinder.chem.reaction.RetroReaction property) update() (aizynthfinder.search.dfpn.nodes.MoleculeNode method) (aizynthfinder.search.dfpn.nodes.ReactionNode method) (aizynthfinder.search.retrostar.nodes.MoleculeNode method) (aizynthfinder.search.retrostar.nodes.ReactionNode method)

W

weight (aizynthfinder.chem.mol.Molecule property)

weighted_score() (aizynthfinder.context.scoring.collection.ScorerCollection method)

X

xoffset (aizynthfinder.context.scoring.scorers_base.SquashScaler attribute)

Y

yoffset (aizynthfinder.context.scoring.scorers_base.SquashScaler attribute)

Z

ZeroMoleculeCost (class in aizynthfinder.search.retrostar.cost)