Index

A

add_small_mols() (in module synplan.chem.reaction) algorithm (synplan.utils.config.TreeConfig attribute) apply_reaction_rule() (in module synplan.chem.reaction) as_query_container (synplan.utils.config.RuleExtractionConfig attribute) atom_indices (synplan.route_quality.FunctionalGroupMatch attribute) (synplan.route_quality.HalogenMatch attribute) (synplan.route_quality.protection.functional_groups.FunctionalGroupMatch attribute) (synplan.route_quality.protection.functional_groups.HalogenMatch attribute)

atom_info_retention (synplan.utils.config.RuleExtractionConfig attribute) attn_dropout (synplan.utils.config.PolicyNetworkConfig attribute) attn_type (synplan.utils.config.PolicyNetworkConfig attribute) automorphism_filter (synplan.utils.config.ReactorConfig attribute)

B

backprop_type (synplan.utils.config.TreeConfig attribute) BaseConfigModel (class in synplan.utils.config) batch_size (synplan.utils.config.PolicyNetworkConfig attribute) (synplan.utils.config.TuningConfig attribute) (synplan.utils.config.ValueNetworkConfig attribute)

beam_width (synplan.utils.config.TreeConfig attribute) building_blocks (synplan.utils.config.RolloutEvaluationConfig attribute) building_blocks_from_rdkit() (in module synplan.chem.rdkit_compat)

C

c_ucb (synplan.utils.config.TreeConfig attribute) category (synplan.route_quality.FunctionalGroupMatch attribute) (synplan.route_quality.protection.functional_groups.FunctionalGroupMatch attribute) cgr_from_reaction_rule() (in module synplan.chem.utils) classify_interactions() (synplan.route_quality.protection.scanner.RouteScanner static method) (synplan.route_quality.RouteScanner static method) classify_reaction_type() (in module synplan.route_quality) (in module synplan.route_quality.protection.reaction_classifier) classify_reaction_type_broad() (in module synplan.route_quality) (in module synplan.route_quality.protection.reaction_classifier) classify_reaction_type_detailed() (in module synplan.route_quality) (in module synplan.route_quality.protection.reaction_classifier) clear_cache() (synplan.route_quality.FunctionalGroupDetector method) (synplan.route_quality.protection.functional_groups.FunctionalGroupDetector method) close() (synplan.utils.files.FileHandler method) (synplan.utils.files.SMILESRead method)

CombinedPolicyConfig (class in synplan.utils.config) competing_groups_path (synplan.route_quality.protection.config.ProtectionConfig attribute) (synplan.route_quality.ProtectionConfig attribute) CompetingInteraction (class in synplan.route_quality) (class in synplan.route_quality.protection.scanner) CompetingSitesScore (class in synplan.route_quality) (class in synplan.route_quality.protection.scorer) compose_precursors() (in module synplan.chem.precursor) count() (synplan.utils.files.RawReactionReader method) count_rdf_records() (in module synplan.utils.files) count_same_family_competing() (synplan.route_quality.HalogenDetector method) (synplan.route_quality.protection.functional_groups.HalogenDetector method) count_sdf_records() (in module synplan.utils.files) count_smiles_records() (in module synplan.utils.files)

D

delete_atoms (synplan.utils.config.ReactorConfig attribute) detect_all() (synplan.route_quality.FunctionalGroupDetector method) (synplan.route_quality.HalogenDetector method) (synplan.route_quality.protection.functional_groups.FunctionalGroupDetector method) (synplan.route_quality.protection.functional_groups.HalogenDetector method) detect_competing() (synplan.route_quality.FunctionalGroupDetector method) (synplan.route_quality.protection.functional_groups.FunctionalGroupDetector method) detect_competing_halogens() (synplan.route_quality.HalogenDetector method) (synplan.route_quality.protection.functional_groups.HalogenDetector method)

detect_reacting() (synplan.route_quality.FunctionalGroupDetector method) (synplan.route_quality.protection.functional_groups.FunctionalGroupDetector method) detect_reaction_center_halogens() (synplan.route_quality.HalogenDetector method) (synplan.route_quality.protection.functional_groups.HalogenDetector method) DisableLogger (class in synplan.utils.logging) dropout (synplan.utils.config.PolicyNetworkConfig attribute) (synplan.utils.config.ValueNetworkConfig attribute)

E

embedder_type (synplan.utils.config.PolicyNetworkConfig attribute) emit() (synplan.utils.logging.TqdmHandler method) enable_pruning (synplan.utils.config.TreeConfig attribute) enable_reranking (synplan.route_quality.protection.config.ProtectionConfig attribute) (synplan.route_quality.ProtectionConfig attribute)

environment_atom_count (synplan.utils.config.RuleExtractionConfig attribute) epsilon (synplan.utils.config.TreeConfig attribute) evaluation_agg (synplan.utils.config.TreeConfig attribute) exclude_small (synplan.utils.config.TreeConfig attribute) extract_routes_rdkit() (in module synplan.chem.rdkit_compat)

F

family (synplan.route_quality.HalogenMatch attribute) (synplan.route_quality.protection.functional_groups.HalogenMatch attribute) fg_atoms (synplan.route_quality.CompetingInteraction attribute) (synplan.route_quality.protection.scanner.CompetingInteraction attribute) fg_name (synplan.route_quality.CompetingInteraction attribute) (synplan.route_quality.protection.scanner.CompetingInteraction attribute) FileHandler (class in synplan.utils.files) filtering_weights_path (synplan.utils.config.CombinedPolicyConfig attribute) fix_aromatic_rings (synplan.utils.config.ReactorConfig attribute)

fix_tautomers (synplan.utils.config.ReactorConfig attribute) from_config() (synplan.route_quality.ProtectionRouteScorer class method) from_dict() (synplan.utils.config.BaseConfigModel class method) from_tsv() (synplan.chem.reaction_rules.RuleSet class method) from_yaml() (synplan.utils.config.BaseConfigModel class method) func_groups_list (synplan.utils.config.RuleExtractionConfig attribute) FunctionalGroupDetector (class in synplan.route_quality) (class in synplan.route_quality.protection.functional_groups) FunctionalGroupMatch (class in synplan.route_quality) (class in synplan.route_quality.protection.functional_groups)

G

get_reaction_center_atoms() (in module synplan.route_quality) (in module synplan.route_quality.protection.reaction_classifier)

H

halogen_groups_path (synplan.route_quality.protection.config.ProtectionConfig attribute) (synplan.route_quality.ProtectionConfig attribute) HalogenDetector (class in synplan.route_quality) (class in synplan.route_quality.protection.functional_groups)

HalogenMatch (class in synplan.route_quality) (class in synplan.route_quality.protection.functional_groups) hash_from_reaction_rule() (in module synplan.chem.utils) heads (synplan.utils.config.PolicyNetworkConfig attribute) HiddenPrints (class in synplan.utils.logging)

I

include_func_groups (synplan.utils.config.RuleExtractionConfig attribute) include_rings (synplan.utils.config.RuleExtractionConfig attribute) incompatibility_path (synplan.route_quality.protection.config.ProtectionConfig attribute) (synplan.route_quality.ProtectionConfig attribute) IncompatibilityMatrix (class in synplan.route_quality) (class in synplan.route_quality.protection.scanner) init_logger() (in module synplan.utils.logging) init_node_value (synplan.utils.config.TreeConfig attribute) init_parse_worker() (in module synplan.utils.files)

is_building_block() (synplan.chem.precursor.Precursor method) is_solved() (synplan.mcts.node.Node method) iter_chunks() (synplan.utils.files.RawReactionReader method) iter_csv_smiles() (in module synplan.utils.files) iter_csv_smiles_blocks() (in module synplan.utils.files) iter_rdf_text_blocks() (in module synplan.utils.files) iter_sdf_text_blocks() (in module synplan.utils.files) iter_smiles() (in module synplan.utils.files) iter_smiles_blocks() (in module synplan.utils.files)

K

keep_incoming_groups (synplan.utils.config.RuleExtractionConfig attribute) keep_leaving_groups (synplan.utils.config.RuleExtractionConfig attribute)

keep_metadata (synplan.utils.config.RuleExtractionConfig attribute) keep_reagents (synplan.utils.config.RuleExtractionConfig attribute)

L

learning_rate (synplan.utils.config.PolicyNetworkConfig attribute) (synplan.utils.config.ValueNetworkConfig attribute) lnmcs_ratio (synplan.utils.config.TreeConfig attribute) load_rule_index_mapping_tsv() (in module synplan.utils.files)

log_grad_norm (synplan.utils.config.PolicyNetworkConfig attribute) logger (synplan.utils.config.PolicyNetworkConfig attribute) lookup() (synplan.route_quality.IncompatibilityMatrix method) (synplan.route_quality.protection.scanner.IncompatibilityMatrix method)

M

max_depth (synplan.utils.config.RolloutEvaluationConfig attribute) (synplan.utils.config.TreeConfig attribute) max_iterations (synplan.utils.config.TreeConfig attribute) max_rules_applied (synplan.utils.config.TreeConfig attribute) max_time (synplan.utils.config.TreeConfig attribute) max_tree_size (synplan.utils.config.TreeConfig attribute) min_mol_size (synplan.utils.config.RolloutEvaluationConfig attribute) (synplan.utils.config.TreeConfig attribute) min_popularity (synplan.utils.config.RuleExtractionConfig attribute) model_config (synplan.route_quality.CompetingInteraction attribute) (synplan.route_quality.FunctionalGroupMatch attribute) (synplan.route_quality.HalogenMatch attribute) (synplan.route_quality.protection.config.ProtectionConfig attribute) (synplan.route_quality.protection.functional_groups.FunctionalGroupMatch attribute) (synplan.route_quality.protection.functional_groups.HalogenMatch attribute) (synplan.route_quality.protection.scanner.CompetingInteraction attribute) (synplan.route_quality.ProtectionConfig attribute) (synplan.utils.config.BaseConfigModel attribute) (synplan.utils.config.CombinedPolicyConfig attribute) (synplan.utils.config.PolicyEvaluationConfig attribute) (synplan.utils.config.PolicyNetworkConfig attribute) (synplan.utils.config.RandomEvaluationConfig attribute) (synplan.utils.config.RDKitEvaluationConfig attribute) (synplan.utils.config.ReactorConfig attribute) (synplan.utils.config.RolloutEvaluationConfig attribute) (synplan.utils.config.RuleExtractionConfig attribute) (synplan.utils.config.TreeConfig attribute) (synplan.utils.config.TuningConfig attribute) (synplan.utils.config.ValueNetworkConfig attribute) (synplan.utils.config.ValueNetworkEvaluationConfig attribute)

module synplan synplan.chem synplan.chem.precursor synplan.chem.rdkit_compat synplan.chem.reaction synplan.chem.reaction_rules synplan.chem.utils synplan.interfaces synplan.mcts.node synplan.ml synplan.ml.networks synplan.route_quality synplan.route_quality.protection.config synplan.route_quality.protection.functional_groups synplan.route_quality.protection.reaction_classifier synplan.route_quality.protection.scanner synplan.route_quality.protection.scorer synplan.utils synplan.utils.config synplan.utils.files synplan.utils.logging mol_from_smiles() (in module synplan.chem.utils) MoleculeReader (class in synplan.utils.files) MoleculeWriter (class in synplan.utils.files) multicenter_rules (synplan.utils.config.RuleExtractionConfig attribute)

N

name (synplan.route_quality.FunctionalGroupMatch attribute) (synplan.route_quality.HalogenMatch attribute) (synplan.route_quality.protection.functional_groups.FunctionalGroupMatch attribute) (synplan.route_quality.protection.functional_groups.HalogenMatch attribute) nmcs_level (synplan.utils.config.TreeConfig attribute) nmcs_playout_mode (synplan.utils.config.TreeConfig attribute) Node (class in synplan.mcts.node) normalize (synplan.utils.config.PolicyEvaluationConfig attribute) (synplan.utils.config.RandomEvaluationConfig attribute) (synplan.utils.config.RDKitEvaluationConfig attribute) (synplan.utils.config.RolloutEvaluationConfig attribute) (synplan.utils.config.ValueNetworkEvaluationConfig attribute)

normalize_scores (synplan.utils.config.TreeConfig attribute) num_conv_layers (synplan.utils.config.PolicyNetworkConfig attribute) (synplan.utils.config.ValueNetworkConfig attribute) num_epoch (synplan.utils.config.PolicyNetworkConfig attribute) (synplan.utils.config.ValueNetworkConfig attribute) num_simulations (synplan.utils.config.TuningConfig attribute)

O

one_shot (synplan.utils.config.ReactorConfig attribute)

open_text() (in module synplan.utils.files)

P

parse_one() (in module synplan.utils.files) parse_reaction() (in module synplan.utils.files) policy_network (synplan.utils.config.RolloutEvaluationConfig attribute) policy_type (synplan.utils.config.PolicyNetworkConfig attribute) PolicyEvaluationConfig (class in synplan.utils.config) PolicyNetworkConfig (class in synplan.utils.config)

popularity (synplan.chem.reaction_rules.RuleSet attribute) Precursor (class in synplan.chem.precursor) priority_rules_fraction (synplan.utils.config.PolicyNetworkConfig attribute) ProtectionConfig (class in synplan.route_quality) (class in synplan.route_quality.protection.config) ProtectionRouteScorer (class in synplan.route_quality)

Q

query_to_mol() (in module synplan.chem.utils)

R

RandomEvaluationConfig (class in synplan.utils.config) rank_routes() (synplan.route_quality.CompetingSitesScore method) (synplan.route_quality.protection.scorer.CompetingSitesScore method) ranking_weight (synplan.utils.config.CombinedPolicyConfig attribute) ranking_weights_path (synplan.utils.config.CombinedPolicyConfig attribute) RawReactionReader (class in synplan.utils.files) RDKitEvaluationConfig (class in synplan.utils.config) reacting_fg (synplan.route_quality.CompetingInteraction attribute) (synplan.route_quality.protection.scanner.CompetingInteraction attribute) Reaction (class in synplan.chem.reaction) reaction_indices (synplan.chem.reaction_rules.RuleSet attribute) reaction_query_to_reaction() (in module synplan.chem.utils) reaction_rules (synplan.utils.config.RolloutEvaluationConfig attribute) ReactionReader (class in synplan.utils.files) ReactionWriter (class in synplan.utils.files) reactor_validation (synplan.utils.config.RuleExtractionConfig attribute)

ReactorConfig (class in synplan.utils.config) read() (synplan.utils.files.SMILESRead method) Reader (class in synplan.utils.files) rescore() (synplan.route_quality.ProtectionRouteScorer method) (synplan.route_quality.RouteScorer method) reverse_reaction() (in module synplan.chem.utils) reverse_rule (synplan.utils.config.RuleExtractionConfig attribute) RolloutEvaluationConfig (class in synplan.utils.config) route_to_rdkit() (in module synplan.chem.rdkit_compat) RouteScanner (class in synplan.route_quality) (class in synplan.route_quality.protection.scanner) RouteScorer (class in synplan.route_quality) rule_prob_threshold (synplan.utils.config.CombinedPolicyConfig attribute) (synplan.utils.config.PolicyNetworkConfig attribute) RuleExtractionConfig (class in synplan.utils.config) rules (synplan.chem.reaction_rules.RuleSet attribute) RuleSet (class in synplan.chem.reaction_rules)

S

safe_canonicalization() (in module synplan.chem.utils) scan_route() (synplan.route_quality.protection.scanner.RouteScanner method) (synplan.route_quality.RouteScanner method) score() (synplan.route_quality.ProtectionRouteScorer method) (synplan.route_quality.RouteScorer method) score_function (synplan.utils.config.RDKitEvaluationConfig attribute) score_route() (synplan.route_quality.CompetingSitesScore method) (synplan.route_quality.protection.scorer.CompetingSitesScore method) score_weight (synplan.route_quality.protection.config.ProtectionConfig attribute) (synplan.route_quality.ProtectionConfig attribute) search_strategy (synplan.utils.config.TreeConfig attribute) severity (synplan.route_quality.CompetingInteraction attribute) (synplan.route_quality.protection.scanner.CompetingInteraction attribute) silence_logger() (in module synplan.utils.logging) silent (synplan.utils.config.TreeConfig attribute) single_product_only (synplan.utils.config.RuleExtractionConfig attribute) smarts_strings (synplan.chem.reaction_rules.RuleSet attribute) SMILESRead (class in synplan.utils.files) standardize_building_blocks() (in module synplan.chem.utils) step_id (synplan.route_quality.CompetingInteraction attribute) (synplan.route_quality.protection.scanner.CompetingInteraction attribute) stochastic (synplan.utils.config.RolloutEvaluationConfig attribute) stop_at_first (synplan.utils.config.TreeConfig attribute) synplan module synplan.chem module synplan.chem.precursor module synplan.chem.rdkit_compat module synplan.chem.reaction module

synplan.chem.reaction_rules module synplan.chem.utils module synplan.interfaces module synplan.mcts.node module synplan.ml module synplan.ml.networks module synplan.route_quality module synplan.route_quality.protection.config module synplan.route_quality.protection.functional_groups module synplan.route_quality.protection.reaction_classifier module synplan.route_quality.protection.scanner module synplan.route_quality.protection.scorer module synplan.utils module synplan.utils.config module synplan.utils.files module synplan.utils.logging module

T

target_from_rdkit() (in module synplan.chem.rdkit_compat) temperature (synplan.utils.config.CombinedPolicyConfig attribute) to_dataframe() (synplan.chem.reaction_rules.RuleSet method) to_dict() (synplan.utils.config.BaseConfigModel method) to_reaction_smiles_record() (in module synplan.utils.files) to_reactor_kwargs() (synplan.utils.config.ReactorConfig method)

to_yaml() (synplan.utils.config.BaseConfigModel method) top_rules (synplan.utils.config.CombinedPolicyConfig attribute) (synplan.utils.config.PolicyNetworkConfig attribute) TqdmHandler (class in synplan.utils.logging) trainer (synplan.utils.config.PolicyNetworkConfig attribute) TreeConfig (class in synplan.utils.config) TuningConfig (class in synplan.utils.config)

U

ucb_type (synplan.utils.config.TreeConfig attribute)

unite_molecules() (in module synplan.chem.utils)

V

ValueNetworkConfig (class in synplan.utils.config) ValueNetworkEvaluationConfig (class in synplan.utils.config)

vector_dim (synplan.utils.config.PolicyNetworkConfig attribute) (synplan.utils.config.ValueNetworkConfig attribute)

W

weights_path (synplan.utils.config.PolicyNetworkConfig attribute) (synplan.utils.config.ValueNetworkConfig attribute) (synplan.utils.config.ValueNetworkEvaluationConfig attribute)

write() (synplan.utils.files.MoleculeWriter method) (synplan.utils.files.ReactionWriter method) Writer (class in synplan.utils.files)