Index

A

ABSTAINED (orthonym.metrics.coverage_metrics.RowClassification attribute) (orthonym.validation.reconstruct.Verdict attribute) abstention_code_for() (in module orthonym.metrics.abstention) AbstentionCode (class in orthonym.metrics.abstention) AbstentionRecord (class in orthonym.metrics.abstention) accounted_atoms (orthonym.assembly.composer.HandlerResult attribute) acid_fragment_has_ring() (in module orthonym.rules.esters) acid_is_more_senior() (in module orthonym.decomposition.fragment_ranker) acid_is_ring_acid() (in module orthonym.rules.esters) acid_name_to_acyl_prefix() (in module orthonym.assembly.substituent_naming) acid_name_to_amido_prefix() (in module orthonym.assembly.substituent_naming) active (orthonym.rules.pin_vocabulary.PromotionProbe attribute) ACYCLIC (orthonym.rules.phane.SkeletonClass attribute) acyl_amido_prefix_from_branch() (in module orthonym.assembly.substituent_naming) acyl_carbons_to_amido_prefix() (in module orthonym.assembly.substituent_naming) ACYL_CHALCOGENCHAIN_PSEUDOKETONE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) acyl_prefix_for() (in module orthonym.rules.functional_replacement) acyl_prefix_from_branch() (in module orthonym.assembly.substituent_naming) acyloxy_leaf_fired (orthonym.assembly.universal_substituent.UniversalResult attribute) add() (orthonym.assembly.candidate_pool.CandidatePool method) add_retained_name() (in module orthonym.data.retained_names) aggregate() (in module orthonym.metrics.breadth) (in module orthonym.metrics.coverage_metrics) aligned_batch_lines() (in module orthonym.jvm_flags) alkoxy_prefix_from_substituent() (in module orthonym.assembly.substituent_enumerator) all_candidates() (orthonym.assembly.candidate_pool.CandidatePool method) all_orientations() (in module orthonym.rules.fusion_orientation) all_orientations_general() (in module orthonym.rules.fusion_orientation) all_ring_atoms (orthonym.namer.MolecularFeatures attribute) (orthonym.rules.polycyclic_bridged.PolycyclicInfo attribute) allow_reduced() (in module orthonym.jars) alpha_beta_at() (in module orthonym.rules.steroid_stereo) alpha_sort_key() (in module orthonym.assembly.naming_utils) AlphaKey (class in orthonym.assembly.naming_utils) alt_het_tuple (orthonym.rules.fused_ring_selection.ComponentRank attribute) amide_type (orthonym.namer.MolecularFeatures attribute) amido_n_has_substituent() (in module orthonym.rules.inorganic_acids) AMINO_ACID (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) Amplificant (class in orthonym.rules.phane) amplificants (orthonym.rules.phane.PhaneStructure attribute) analyze() (orthonym.rules.polycyclic.VonBaeyerAnalyzer method) analyze_cage_universal() (in module orthonym.rules.vonbaeyer_universal) analyze_polycyclic_system() (in module orthonym.rules.polycyclic_bridged) analyze_saturation_for_naming() (in module orthonym.rules.partial_saturation) analyze_spiro_universal() (in module orthonym.rules.vonbaeyer_universal) anilino_preferred_prefix() (in module orthonym.rules.ring_substituents) anilino_prefix_from_aniline_name() (in module orthonym.rules.ring_substituents) anilino_prefix_from_n_branch() (in module orthonym.rules.ring_substituents) ANION_RETAINED (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) ANION_SMALL (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) another_ring_ketone_system_is_senior() (in module orthonym.rules.lactones)

apply_centres_labels() (in module orthonym.perception.centres_bridge) apply_enclosing_marks() (in module orthonym.assembly.naming_utils) apply_ion_suffix_modification() (in module orthonym.assembly.resolvers) apply_ion_suffix_to_name() (in module orthonym.rules.ions) apply_mononuclear_enclosing() (in module orthonym.assembly.composition_primitives) apply_triviality_controller() (in module orthonym.assembly.retained_substitution) apply_vowel_elision() (in module orthonym.assembly.naming_utils) ArityEstimate (class in orthonym.validation.name_morphemes) as_dict() (orthonym.errors.OrthonymLimitError method) assemble_fragment_name() (in module orthonym.decomposition.fragment_assembly) assemble_fused_ring_with_saturation() (in module orthonym.assembly.composer) assemble_ion_name() (in module orthonym.assembly.composer) assemble_name() (in module orthonym.assembly) (in module orthonym.assembly.composer) assemble_organometallic_name() (in module orthonym.rules.organometallics) assign_stereochemistry() (in module orthonym.perception.stereo) at_pin_tier() (in module orthonym.rules.pin_vocabulary) atom (orthonym.data.group_split_rules.SplitComponent attribute) atom_count (orthonym.assembly.resolvers.ParentInfo attribute) atom_ids (orthonym.assembly.general_engine.TokenBinding attribute) (orthonym.validation.binding_spine.SpineBinding attribute) atom_to_locant (orthonym.assembly.composer.ComplexRingResult attribute) (orthonym.assembly.coverage_scoring.CandidateName attribute) (orthonym.assembly.resolvers.ParentInfo attribute) (orthonym.namer.MolecularFeatures attribute) (orthonym.rules.bridged_fused_pin.BridgedParent attribute) (orthonym.rules.bridged_fused_pin.numbering.Numbering attribute) (orthonym.rules.polycyclics.PartialSatName attribute) (orthonym.rules.vonbaeyer_universal.RingAnalysis attribute) atom_to_locant_hint (orthonym.assembly.handlers.NamingResult attribute) (orthonym.assembly.name_tree.NamingResult attribute) atoms (orthonym.assembly.composer.NameFragment attribute) (orthonym.rules.p44_scorer.ParentCandidate attribute) (orthonym.rules.parent_ranking.ParentCandidate attribute) (orthonym.rules.phane.Amplificant attribute) (orthonym.rules.polycyclic.BridgeInfo attribute) (orthonym.rules.polycyclic_bridged.BridgeInfo attribute) (orthonym.rules.terminal_fragment.TerminalFragmentName attribute) atoms_in_same_ring() (in module orthonym.perception.rings) atoms_of() (in module orthonym.perception.molcache) ATTACH_LOCANT_UNKNOWN (in module orthonym.assembly.substituent_naming) attach_mol_idx (orthonym.assembly.substituent_enumerator.SubstituentInfo attribute) attachment (orthonym.validation.binding_spine.SpineBinding attribute) attachment_atoms (orthonym.rules.phane.Amplificant attribute) attachment_set (orthonym.rules.bridged_fused_pin.numbering.Numbering attribute) audit_coverage() (in module orthonym.assembly.coverage_audit) audit_monocycle_replacement_name() (in module orthonym.rules.terminal_ring) audit_record (orthonym.assembly.inner_dispatch.InnerDispatchResult attribute) (orthonym.routing.ClassDispatchResult attribute) (orthonym.routing.dispatch_table.ClassDispatchResult attribute) audit_spiro_descriptor() (in module orthonym.rules.vonbaeyer_universal) audit_von_baeyer_descriptor() (in module orthonym.rules.vonbaeyer_universal) AXIAL_GENERAL_FORM (in module orthonym.perception.stereo) AZINIC_DERIVATIVE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute)

B

backbone_atom_to_locant (orthonym.perception.lipids.BackboneMatch attribute) BackboneMatch (class in orthonym.perception.lipids) base (orthonym.rules.bridged_fused_pin.BridgedParent attribute) basis (orthonym.assembly.substituent_enumerator.FreeValencePrefix attribute) (orthonym.rules.terminal_fragment.TerminalFragmentName attribute) (orthonym.rules.terminal_ring.TerminalRingName attribute) (orthonym.validation.name_morphemes.ArityEstimate attribute) (orthonym.validation.name_morphemes.FreeValenceEstimate attribute) begins_with_italic_designator() (in module orthonym.assembly.naming_utils) benzene_prefix_citation_locants() (in module orthonym.rules.benzene) benzene_prefix_suffix_promotion() (in module orthonym.rules.benzene) benzene_ring (orthonym.namer.MolecularFeatures attribute) benzene_substituents (orthonym.namer.MolecularFeatures attribute) best() (orthonym.assembly.candidate_pool.CandidatePool method) BEST_EFFORT_MAX_CAGE_ATOMS (in module orthonym.rules.vonbaeyer_universal) best_orientations() (in module orthonym.rules.fusion_orientation) best_splits() (in module orthonym.rules.bridged_fused_pin.selection) beyond_pin_caps() (in module orthonym.rules.vonbaeyer_universal) BINDING_PROOF_MODES (in module orthonym.namer) BindingKind (class in orthonym.validation.binding_spine) bindings (orthonym.assembly.general_engine.GeneralEngineResult attribute) (orthonym.assembly.universal_substituent.UniversalResult attribute) BindingSpine (class in orthonym.validation.binding_spine) bond (orthonym.data.group_split_rules.SplitComponent attribute) bond_ids (orthonym.validation.binding_spine.SpineBinding attribute) bond_orders (orthonym.data.resonance_templates.ResonanceChainTemplate attribute) bonds_of() (in module orthonym.perception.molcache) BRANCH_UNNAMEABLE (orthonym.metrics.abstention.AbstentionCode attribute) bridge_atoms (orthonym.rules.phane.PhaneStructure attribute) bridge_info_list (orthonym.rules.polycyclic.PolycyclicDescriptor attribute) bridge_lengths (orthonym.rules.polycyclic.PolycyclicDescriptor attribute)

bridge_locants (orthonym.rules.bridged_fused_pin.numbering.Numbering attribute) bridge_prefix() (in module orthonym.rules.bridged_fused_pin.prefixes) bridge_text() (in module orthonym.rules.bridged_fused_pin.prefixes) BRIDGED_FUSED (orthonym.rules.ring_selection.RingSystemType attribute) BridgedParent (class in orthonym.rules.bridged_fused_pin) bridgehead_locants_stub (orthonym.rules.fused_ring_selection.ComponentRank attribute) bridgeheads (orthonym.rules.bridged_fused_pin.selection.Split attribute) (orthonym.rules.polycyclic_bridged.PolycyclicInfo attribute) BridgeInfo (class in orthonym.rules.polycyclic) (class in orthonym.rules.polycyclic_bridged) BridgePrefix (class in orthonym.rules.bridged_fused_pin.prefixes) bridges (orthonym.rules.bridged_fused_pin.BridgedParent attribute) (orthonym.rules.bridged_fused_pin.selection.Split attribute) BudgetTimeout build() (in module orthonym.rules.bridged_fused_pin) build_acyl_halide_name() (in module orthonym.rules.functional_replacement) build_atom_to_locant() (in module orthonym.rules.locants) build_carbonic_mono_frn() (in module orthonym.rules.functional_replacement) build_frn_acid_name() (in module orthonym.rules.functional_replacement) build_hw_name() (in module orthonym.rules.heterocycles) build_monocycle_replacement_name() (in module orthonym.rules.terminal_ring) build_multi_component_name() (in module orthonym.rules.fusion_descriptors) build_p_frn_acid_name() (in module orthonym.rules.functional_replacement) build_p_frn_acid_stem_word() (in module orthonym.rules.functional_replacement) build_p_frn_amide_name() (in module orthonym.rules.functional_replacement) build_p_frn_halide_name() (in module orthonym.rules.functional_replacement) build_phane_pin() (in module orthonym.rules.phane) build_polyacid_name() (in module orthonym.rules.functional_replacement) build_replacement_prefix() (in module orthonym.rules.ring_replacement) build_ring_fusion_graph() (in module orthonym.rules.fusion_orientation) build_systematic_fusion_name() (in module orthonym.rules.fusion_descriptors)

C

cache_or_compute() (in module orthonym.assembly.memo) cached_by_key() (in module orthonym.perception.molcache) cached_is_complex_ring_system() (in module orthonym.assembly.handlers._handler_shared) cached_nested_call() (in module orthonym.assembly.nested_memo) cage_atoms (orthonym.rules.vonbaeyer_universal.RingAnalysis attribute) cage_caps() (in module orthonym.rules.vonbaeyer_universal) can_limit() (in module orthonym.wallclock) CandidateName (class in orthonym.assembly.coverage_scoring) CandidatePool (class in orthonym.assembly.candidate_pool) canon_match (orthonym.rules.vonbaeyer_universal.RingAnalysis attribute) canon_smiles() (in module orthonym.perception.molcache) canonical_smiles (orthonym.assembly.retained_substitution.ControllerEvent attribute) (orthonym.data.triviality_controller_seed.SeedEntry attribute) (orthonym.namer.MolecularFeatures attribute) carbocyclic_ring_yl_attachment_descriptor() (in module orthonym.assembly.substituent_naming) CARBOHYDRATE_LOOKUP (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) carbon_free_phospho_prefix() (in module orthonym.rules.phosphorus) carbon_free_valence_prefix() (in module orthonym.assembly.substituent_enumerator) carveout_outcome() (in module orthonym.metrics.provenance) CATENATED_HYDRIDE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) CATION_QUATERNARY (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) CATION_RETAINED (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) cation_to_prefix() (in module orthonym.assembly.substituent_naming) centres_available() (in module orthonym.jvm_bridge) centres_label_batch() (in module orthonym.perception.centres_bridge) centres_label_mol() (in module orthonym.perception.centres_bridge) centres_stdout() (in module orthonym.jvm_bridge) certify_general_result() (in module orthonym.validation.coverage_gate) chain_is_parent (orthonym.namer.MolecularFeatures attribute) chain_vector() (in module orthonym.data.resonance_templates) CHALCOGEN_CHAIN (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) chalcogen_oxide_fc_covers_molecule() (in module orthonym.rules.sulfur) chalcogen_rooted_acyl_amino_core() (in module orthonym.assembly.substituent_enumerator) CHALCOGENS (in module orthonym.assembly.locant_omission) CHARGE (orthonym.validation.binding_spine.BindingKind attribute) charge_atom_ids (orthonym.assembly.general_engine.TokenBinding attribute) (orthonym.validation.binding_spine.SpineBinding attribute) charge_dropped() (in module orthonym.perception.structure_conservation) charges (orthonym.data.resonance_templates.ResonanceChainTemplate attribute) children (orthonym.validation.binding_spine.SpineBinding attribute) choose_indicated_hydrogen() (in module orthonym.rules.bridged_fused_pin.hydro) cip (orthonym.perception.lipids.BackboneMatch attribute) cip_descriptor_rank_key() (in module orthonym.assembly.naming_utils) cip_locant_rank_key() (in module orthonym.assembly.naming_utils) citation_order (orthonym.rules.bridged_fused_pin.numbering.Numbering attribute) cite_organyl_in_composed_prefix() (in module orthonym.assembly.substituent_enumerator) claimed_atom_indices (orthonym.validation.atom_coverage.CoverageResult attribute) (orthonym.validation.CoverageResult attribute) claimed_atoms (orthonym.validation.atom_coverage.CoverageResult attribute) (orthonym.validation.CoverageResult attribute) class_id (orthonym.assembly.handlers.NameTreeNode attribute) (orthonym.assembly.name_tree.NameTreeNode attribute) (orthonym.routing.ClassDispatchEntry attribute) (orthonym.routing.ClassDispatchResult attribute) (orthonym.routing.dispatch_table.ClassDispatchEntry attribute) (orthonym.routing.dispatch_table.ClassDispatchResult attribute) ClassDispatchEntry (class in orthonym.routing) (class in orthonym.routing.dispatch_table) ClassDispatchResult (class in orthonym.routing) (class in orthonym.routing.dispatch_table) ClassFirstRouter (class in orthonym.routing) (class in orthonym.routing.dispatcher) classify_and_name_fragment() (in module orthonym.assembly.substituent_enumerator) classify_anion() (in module orthonym.rules.ions) classify_bridged_system() (in module orthonym.rules.polycyclic_bridged) classify_cation() (in module orthonym.rules.ions) classify_charged_pcg() (in module orthonym.rules.charged_router) classify_compound_class() (in module orthonym.namer) classify_conjugate() (in module orthonym.rules.conjugate_controller) classify_failure_limit() (in module orthonym.errors) classify_fused_system() (in module orthonym.rules.fused_rings) classify_heterocycle() (in module orthonym.rules.heterocycles) classify_heterocycle_priority() (in module orthonym.rules.ortho_fused) classify_limit() (in module orthonym) (in module orthonym.namer) classify_multi_ester() (in module orthonym.rules.esters) classify_outcome() (in module orthonym.metrics.breadth) classify_radical() (in module orthonym.rules.radicals) classify_resonance_chain() (in module orthonym.data.resonance_templates) classify_ring() (in module orthonym.perception.rings) classify_ring_system() (in module orthonym.rules.fusion_orientation) classify_ring_system_type() (in module orthonym.rules.ring_selection) classify_row() (in module orthonym.metrics.coverage_metrics) classify_scope_limit() (in module orthonym.errors) classify_substituent() (in module orthonym.perception.chains) clear_abstention() (in module orthonym.metrics.abstention) clear_confidence() (in module orthonym.assembly.coverage_scoring) clear_leaked_naming_state() (in module orthonym.wallclock) clear_ledger() (in module orthonym.metrics.candidate_ledger) (in module orthonym.validation.proof_ledger)

clear_pool() (in module orthonym.assembly.candidate_pool) clear_process_cache() (in module orthonym.assembly.memo) clear_provenance() (in module orthonym.metrics.provenance) clear_reference_name() (in module orthonym.rules.parent_correctness) cleave_and_cap() (in module orthonym.decomposition) (in module orthonym.decomposition.fragment_capping) close() (orthonym.validation.opsin_server.PersistentOpsin method) code (orthonym.metrics.abstention.AbstentionRecord attribute) (orthonym.validation.binding_spine.Finding attribute) codes() (orthonym.validation.binding_spine.SpineProof method) collect_ring_junction_stereo() (in module orthonym.rules.stereochemistry) collect_ring_stereodescriptors() (in module orthonym.rules.stereochemistry) collect_stereodescriptors() (in module orthonym.rules.stereochemistry) collect_steroid_alpha_beta() (in module orthonym.rules.steroid_stereo) collect_substituent_atom_set() (in module orthonym.assembly.substituent_enumerator) combine_identical_prefix_groups() (in module orthonym.assembly.composition_primitives) combined_rt (orthonym.validation.dual_validator.DualResult attribute) (orthonym.validation.DualResult attribute) compare_by_node_scores() (in module orthonym.assembly.per_substring_scoring) compare_heteroatom_priority() (in module orthonym.data.hw_heteroatoms) compare_lambda_locant_sets() (in module orthonym.assembly.name_comparison) compare_locant_sets() (in module orthonym.rules.locants) compare_locant_str_sets() (in module orthonym.assembly.name_comparison) compare_locant_strings() (in module orthonym.assembly.name_comparison) compare_names() (in module orthonym.assembly.name_comparison) compare_numbering() (in module orthonym.rules.locants) compare_parent_candidates() (in module orthonym.rules.p44_scorer) compare_scores() (in module orthonym.assembly.per_substring_scoring) compare_seniority() (in module orthonym.rules.seniority) compare_with_reason() (in module orthonym.rules.p44_scorer) compiled() (in module orthonym.perception.smarts_cache) complete (orthonym.assembly.coverage_audit.CoverageVerdict attribute) (orthonym.assembly.offer_pool.Offer attribute) ComplexRingResult (class in orthonym.assembly.composer) component_sort_key() (in module orthonym.rules.adducts) ComponentRank (class in orthonym.rules.fused_ring_selection) components (orthonym.data.group_split_rules.SplitRule attribute) composed_alkoxy_prefix() (in module orthonym.assembly.substituent_enumerator) composed_chalcogen_group_prefix() (in module orthonym.assembly.substituent_enumerator) composed_prefix_multiplier() (in module orthonym.assembly.substituent_enumerator) composed_prefix_organyl_name() (in module orthonym.assembly.substituent_enumerator) composite_smarts (orthonym.data.group_split_rules.SplitRule attribute) compound_aware_multibond_set() (in module orthonym.rules.locants) compulsory_prefix_smarts (orthonym.data.triviality_controller_seed.SeedEntry attribute) compute_chain_candidate() (in module orthonym.assembly.candidate_pool) compute_confidence() (in module orthonym.assembly.coverage_scoring) compute_features() (in module orthonym.namer) compute_fused_numbering() (in module orthonym.rules.fusion_numbering) compute_hapticity() (in module orthonym.perception.metals) compute_nesting_depth() (in module orthonym.assembly.naming_utils) confidence (orthonym.assembly.coverage_scoring.CandidateName attribute) confident (orthonym.validation.name_morphemes.ArityEstimate attribute) (orthonym.validation.name_morphemes.FreeValenceEstimate attribute) CONFIDENTLY_WRONG (orthonym.metrics.coverage_metrics.RowClassification attribute) CONFIRMED (orthonym.validation.reconstruct.Verdict attribute) constitution_match (orthonym.validation.atom_coverage.CoverageResult attribute) (orthonym.validation.CoverageResult attribute) ControllerEvent (class in orthonym.assembly.retained_substitution) core_atoms (orthonym.perception.lipids.BackboneMatch attribute) core_numberings() (in module orthonym.data.fused_heterocycles) count (orthonym.assembly.composer.NameFragment attribute) (orthonym.assembly.group_splitting.SplitComponent attribute) (orthonym.assembly.resolvers.SuffixInfo attribute) count_cuts_to_open() (in module orthonym.rules.polycyclic_bridged) count_defined_stereo_elements() (in module orthonym.rules.stereochemistry) count_defined_stereo_in_fragment() (in module orthonym.rules.stereochemistry) count_double_bond_stereo() (in module orthonym.perception.stereo) count_expressed_stereo_descriptors() (in module orthonym.rules.stereochemistry) count_functional_groups() (in module orthonym.perception.functional_groups) count_naming_pass() (in module orthonym.assembly.fragment_naming) count_peptide_bonds() (in module orthonym.rules.amino_acids) count_ring_double_bonds() (in module orthonym.perception.rings) count_ring_sp3_atoms() (in module orthonym.rules.partial_saturation) count_rings_at_least() (in module orthonym.perception.mancude) count_stereocenters() (in module orthonym.perception.stereo) coverage (orthonym.assembly.composer.HandlerResult property) COVERAGE_DOWNGRADE (orthonym.metrics.abstention.AbstentionCode attribute) coverage_provenance (orthonym.assembly.coverage_scoring.CandidateName attribute) coverage_ratio (orthonym.validation.atom_coverage.CoverageResult attribute) (orthonym.validation.CoverageResult attribute) CoverageResult (class in orthonym.validation) (class in orthonym.validation.atom_coverage) CoverageVerdict (class in orthonym.assembly.coverage_audit) covers (orthonym.assembly.universal_substituent.UniversalResult attribute) CUMULATIVE_ZWITTERION (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) cycle_rank() (in module orthonym.rules.bridged_fused_pin.selection) CYCLIC_PHANE (orthonym.rules.ring_selection.RingSystemType attribute) CYCLIC_POLYESTER (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) cyclo_ring_count_word() (in module orthonym.rules.polycyclic) CYCLOPHANE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute)

D

DECOMPOSITION_PRE_GENERAL (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) decorate_isotopic_name() (in module orthonym.rules.isotopes) decorated_ring_substituent_name() (in module orthonym.rules.ring_substituents) DEFAULT_ATOM_WORK_BUDGET (in module orthonym.assembly.universal_substituent) defers (orthonym.assembly.substituent_enumerator.FreeValencePrefix property) depth (orthonym.metrics.candidate_ledger.LedgerEntry attribute) description (orthonym.assembly.handlers.InnerDispatchEntry attribute) (orthonym.assembly.inner_dispatch.InnerDispatchEntry attribute) (orthonym.routing.ClassDispatchEntry attribute) (orthonym.routing.dispatch_table.ClassDispatchEntry attribute) descriptor (orthonym.rules.vonbaeyer_universal.RingAnalysis attribute) descriptor_string (orthonym.rules.polycyclic.PolycyclicDescriptor attribute) detail (orthonym.assembly.coverage_audit.CoverageVerdict attribute) (orthonym.metrics.abstention.AbstentionRecord attribute) (orthonym.metrics.candidate_ledger.LedgerEntry attribute) (orthonym.validation.binding_spine.Finding attribute) detect_amino_acid() (in module orthonym.rules.amino_acids) detect_axial_chirality() (in module orthonym.perception.stereo) detect_bicyclo_unsaturation() (in module orthonym.rules.bicyclo) detect_bridged_fused() (in module orthonym.rules.bridged_fused) detect_carbocyclic_partial_saturation() (in module orthonym.rules.partial_saturation) detect_exocyclic_esters() (in module orthonym.rules.esters) detect_features() (in module orthonym.perception.functional_groups) detect_functional_groups() (in module orthonym.perception.functional_groups) detect_lactone() (in module orthonym.rules.ortho_fused) detect_lipid_backbone() (in module orthonym.perception.lipids) detect_locant_collisions() (in module orthonym.rules.locant_validation) detect_metal_complex() (in module orthonym.perception.metals)

detect_metallacycle() (in module orthonym.perception.metals) detect_natural_product() (in module orthonym.perception.natural_products) detect_np_modifications() (in module orthonym.rules.natural_products) detect_partial_saturation() (in module orthonym.rules.partial_saturation) detect_polycyclic_lactone() (in module orthonym.rules.polycyclic) detect_polyfunctional() (in module orthonym.rules.polyfunctional) detect_ring_assembly() (in module orthonym.rules.ring_assemblies) detect_species_type() (in module orthonym.perception.ions) determine_base_component() (in module orthonym.rules.ortho_fused) determine_ring_cis_trans() (in module orthonym.rules.stereochemistry) determine_simple_cis_trans() (in module orthonym.rules.stereochemistry) didehydro_benzene_name() (in module orthonym.rules.benzene) DINUCLEAR_HYDRIDE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) direct_return (orthonym.assembly.candidate_pool.HandlerPolicy attribute) disable() (in module orthonym.metrics.candidate_ledger) disarm_hang_budgets() (in module orthonym.assembly.fragment_naming) discover_substituents() (in module orthonym.assembly.substituent_enumerator) dispatch() (in module orthonym.routing) (in module orthonym.routing.dispatcher) (orthonym.routing.ClassFirstRouter method) (orthonym.routing.dispatcher.ClassFirstRouter method) dispatch_inner() (in module orthonym.assembly.handlers) (in module orthonym.assembly.inner_dispatch) double_bond_stereo (orthonym.namer.MolecularFeatures attribute) double_bonds (orthonym.namer.MolecularFeatures attribute) double_locants (orthonym.rules.ring_unsaturation.RingUnsaturation attribute) double_pairs (orthonym.rules.ring_unsaturation.RingUnsaturation attribute) DualResult (class in orthonym.validation) (class in orthonym.validation.dual_validator)

E

E1Verdict (class in orthonym.validation.e1_certificate) edge_position_to_letter() (in module orthonym.rules.fusion_descriptors) element_seniority_rank() (in module orthonym.rules.locants) eligible (orthonym.rules.bridged_fused_pin.hydro.HydroState attribute) embed_atoms_on_hex_lattice() (in module orthonym.rules.fusion_orientation) embed_general() (in module orthonym.rules.fusion_orientation) emit_acylium() (in module orthonym.rules.charged_router) emit_bis_quaternary_aminium() (in module orthonym.rules.ions) emit_bis_quaternary_ammonium() (in module orthonym.rules.ions) emit_catenated_hydride_cation() (in module orthonym.rules.ions) emit_chalcogen_ylium() (in module orthonym.rules.ions) emit_cumulative_ium_ide() (in module orthonym.rules.ions) emit_halogen_onium() (in module orthonym.rules.ions) emit_mono_ionized_polyfunctional() (in module orthonym.rules.ions) emit_onium_hydride_parent() (in module orthonym.rules.ions) emit_parent_hydride_cumulative_suffix() (in module orthonym.rules.ions) emit_parent_hydride_polyvalent_suffixes() (in module orthonym.rules.ions) emit_poly_carbanion_ide() (in module orthonym.rules.ions) emit_poly_cation_ylium() (in module orthonym.rules.ions) emit_primary_amine_anide() (in module orthonym.rules.charged_router) emit_secondary_amine_azanide() (in module orthonym.rules.charged_router) emit_uronium() (in module orthonym.rules.ions) emit_ylide() (in module orthonym.rules.ions) emit_zwitterion_ring_carboxylate() (in module orthonym.rules.ions) EMITTED (orthonym.metrics.candidate_ledger.Stage attribute) emitted (orthonym.metrics.coverage_metrics.RowResult attribute) enable() (in module orthonym.metrics.candidate_ledger)

enable_crash_traceback() (in module orthonym.diagnostics) enclose_if_compound() (in module orthonym.assembly.naming_utils) encoding (orthonym.assembly.group_splitting.SplitEvent attribute) (orthonym.data.group_split_rules.SplitRule attribute) end_bh (orthonym.rules.polycyclic.BridgeInfo attribute) (orthonym.rules.polycyclic_bridged.BridgeInfo attribute) end_naming_session() (in module orthonym.assembly.fragment_naming) enrich_handler_name() (in module orthonym.assembly.handlers._enrichment) enter_name_scope() (in module orthonym.assembly.fragment_naming) enumerate_metal_ligand_groups() (in module orthonym.perception.metals) enumerate_parent_candidates() (in module orthonym.rules.parent_ranking) env_var (orthonym.jars.JarSpec attribute) ERROR (orthonym.validation.reconstruct.Verdict attribute) ESTER_ANION_ZWITTERION (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) ester_carbonyl_atoms() (in module orthonym.rules.esters) ester_carbonyls_share_an_acid_parent() (in module orthonym.rules.esters) ester_match (orthonym.namer.MolecularFeatures attribute) ester_shares_its_acid_with_another_ester() (in module orthonym.rules.esters) estimate_parent_coverage() (in module orthonym.assembly.coverage_utils) exit_name_scope() (in module orthonym.assembly.fragment_naming) exocyclic_atom_indices (orthonym.perception.metals.MetallacycleInfo attribute) express_junior_anionic_chalcogens() (in module orthonym.rules.ions) extra (orthonym.perception.lipids.BackboneMatch attribute) extra_atoms (orthonym.validation.atom_coverage.CoverageResult attribute) (orthonym.validation.CoverageResult attribute) extract_chain_substituents() (in module orthonym.assembly.substituent_enumerator) extract_ring_substituents() (in module orthonym.assembly.substituent_enumerator)

F

factors (orthonym.assembly.coverage_scoring.CandidateName attribute) family (orthonym.perception.lipids.BackboneMatch attribute) features_for_candidate() (in module orthonym.rules.parent_ranking) fetch_all() (in module orthonym.jars) fg_name (orthonym.assembly.group_splitting.SplitEvent attribute) (orthonym.data.group_split_rules.SplitRule attribute) FGFilterMismatchError filename (orthonym.jars.JarSpec attribute) finalize() (in module orthonym.validation.proof_ledger) find_all_bridge_paths() (in module orthonym.rules.polycyclic_bridged) find_all_bridgeheads() (in module orthonym.rules.polycyclic_bridged) find_all_carbon_chains() (in module orthonym.perception.chains) find_all_skeletal_chains() (in module orthonym.perception.chains) find_bridge_paths() (in module orthonym.rules.bicyclo) find_cleavable_bonds() (in module orthonym.decomposition) (in module orthonym.decomposition.bond_cleavage) find_ester_match() (in module orthonym.rules.esters) find_jar() (in module orthonym.jars) find_longest_carbon_chain() (in module orthonym.perception.chains) find_longest_path() (in module orthonym.rules.polycyclic) find_longest_skeletal_chain() (in module orthonym.perception.chains) find_main_ring() (in module orthonym.rules.polycyclic_bridged) find_masked_spiro_atoms() (in module orthonym.rules.spiro) find_maximal_carbon_chains() (in module orthonym.perception.chains) find_monospiro_separation_atom() (in module orthonym.rules.spiro) find_opsin_jar() (in module orthonym.validation.atom_coverage) find_principal_chain() (in module orthonym.perception.chains) find_resonance_chains() (in module orthonym.data.resonance_templates) find_ring_bridgeheads() (in module orthonym.perception.rings) find_true_bridgeheads() (in module orthonym.rules.bicyclo) Finding (class in orthonym.validation.binding_spine) findings (orthonym.validation.binding_spine.SpineProof attribute) forced_locant_reason() (in module orthonym.assembly.locant_omission) forced_locant_scope() (in module orthonym.assembly.locant_omission) formal_charges (orthonym.perception.metals.MetalComplex attribute) format_complex_fusion() (in module orthonym.rules.fusion_descriptors) format_fg_prefix() (in module orthonym.rules.polyfunctional)

format_isotope_descriptor() (in module orthonym.rules.isotopes) format_lambda_token() (in module orthonym.rules.lambda_convention) format_locants() (in module orthonym.assembly.composer) format_n_substitution() (in module orthonym.rules.amides) format_np_modification_prefix() (in module orthonym.rules.natural_products) format_ring_junction_stereo() (in module orthonym.rules.stereochemistry) format_ring_stereo_with_descriptors() (in module orthonym.rules.stereochemistry) format_saturation_prefix() (in module orthonym.rules.partial_saturation) format_stereodescriptor_string() (in module orthonym.rules.stereochemistry) format_substituent_prefix() (in module orthonym.assembly.naming_utils) (in module orthonym.rules.ortho_fused) format_suffix_with_locants() (in module orthonym.assembly.naming_utils) frag_atoms (orthonym.assembly.substituent_enumerator.SubstituentInfo attribute) frag_mol (orthonym.assembly.substituent_enumerator.SubstituentInfo attribute) FRAGMENT (orthonym.metrics.candidate_ledger.Scope attribute) fragment_acid_name_verified() (in module orthonym.assembly.substituent_naming) fragment_attachment_atom() (in module orthonym.assembly.composition_tier) fragment_is_linear_terminal_alkyl() (in module orthonym.assembly.substituent_naming) fragment_legacy (orthonym.assembly.handlers.NameTreeNode attribute) (orthonym.assembly.name_tree.NameTreeNode attribute) fragment_type (orthonym.assembly.composer.NameFragment attribute) fragments_to_tree() (in module orthonym.assembly.name_tree_builder) FREE_HOMONUCLEAR_G14_HYDRIDE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) free_valence (orthonym.assembly.substituent_enumerator.FreeValencePrefix attribute) free_valence_morphology() (in module orthonym.validation.name_morphemes) free_valences (orthonym.validation.name_morphemes.FreeValenceEstimate attribute) FreeValenceEstimate (class in orthonym.validation.name_morphemes) FreeValencePrefix (class in orthonym.assembly.substituent_enumerator) freeze_inner_table() (in module orthonym.assembly.inner_dispatch) from_token_bindings() (orthonym.validation.binding_spine.BindingSpine class method) functional_groups (orthonym.namer.MolecularFeatures attribute) FUSED (orthonym.rules.ring_selection.RingSystemType attribute) fused_ring_atom_drop() (in module orthonym.perception.structure_conservation) fused_rings() (in module orthonym.rules.bridged_fused_pin.selection) FUSION (orthonym.validation.binding_spine.BindingKind attribute) fusion_nomenclature_applies() (in module orthonym.rules.polycyclic) fusion_pin_class() (in module orthonym.perception.mancude)

G

gate_nonsuffix_nacyl_float() (in module orthonym.decomposition.engine) GATE_OUTCOME_BYPASSED (in module orthonym.metrics.provenance) GATE_OUTCOME_CARVEOUT_PREFIX (in module orthonym.metrics.provenance) GATE_OUTCOME_DESCRIPTIVE_FALLBACK (in module orthonym.metrics.provenance) GATE_OUTCOME_DISABLED (in module orthonym.metrics.provenance) GATE_OUTCOME_FULL_KEY_VERIFIED (in module orthonym.metrics.provenance) GATE_OUTCOME_NOT_RUN (in module orthonym.metrics.provenance) GATE_OUTCOME_SELF01 (in module orthonym.metrics.provenance) GATE_OUTCOME_SELF01_CONSTITUTION_ONLY (in module orthonym.metrics.provenance) GATE_OUTCOME_SELF01_INCONCLUSIVE (in module orthonym.metrics.provenance) GATE_OUTCOME_SELF01_SKIPPED (in module orthonym.metrics.provenance) GATE_OUTCOME_SELF01_WARN_MISMATCH (in module orthonym.metrics.provenance) GATE_OUTCOME_STEREO_RECOMPOSED (in module orthonym.metrics.provenance) GATE_OUTCOME_SUPPRESSED (in module orthonym.metrics.provenance) GATE_OUTCOME_UNAVAILABLE (in module orthonym.metrics.provenance) GATE_REJECTED (orthonym.metrics.candidate_ledger.Stage attribute) GATE_SUPPRESSED (orthonym.metrics.abstention.AbstentionCode attribute) gate_token_for_gate_outcome() (in module orthonym.metrics.provenance) GENERAL (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) general_engine_stereo_complete() (in module orthonym.rules.stereochemistry) GENERAL_ONLY_AMINO_ACIDS (in module orthonym.data.amino_acids) GENERAL_ONLY_BRIDGE_PREFIXES (in module orthonym.rules.bridged_fused) GENERAL_ONLY_NATURAL_PRODUCTS (in module orthonym.data.natural_products) GeneralEngineResult (class in orthonym.assembly.general_engine) generate_bicyclo_descriptor() (in module orthonym.rules.bicyclo) generate_fusion_descriptor() (in module orthonym.rules.fusion_descriptors) generate_multi_fusion_descriptor() (in module orthonym.rules.fusion_descriptors) generate_multi_fusion_name() (in module orthonym.rules.fusion_descriptors) generate_polycyclic_name() (in module orthonym.rules.polycyclic) generate_polycyclo_descriptor() (in module orthonym.rules.tricyclo) generate_spiro_descriptor() (in module orthonym.rules.spiro) generate_systematic_name_for_fused_pair() (in module orthonym.rules.fusion_descriptors) generate_tricyclo_descriptor() (in module orthonym.rules.tricyclo) GENERIC_CYCLOPHANE (orthonym.rules.phane.PhaneTopology attribute) get_acid_fragment_name() (in module orthonym.rules.esters) get_acid_halide_consumed_atoms() (in module orthonym.rules.acid_halides) get_acid_name() (in module orthonym.data.chain_names) get_acid_stem() (in module orthonym.data.chain_names) get_acylate_name() (in module orthonym.data.trivial_acids) get_acyloxy_prefix() (in module orthonym.rules.esters) get_alkoxy_prefix() (in module orthonym.assembly.substituent_prefix_forms) get_alkoxycarbonimidoyl_prefix() (in module orthonym.assembly.substituent_prefix_forms) get_alkoxycarbonyl_prefix() (in module orthonym.assembly.substituent_prefix_forms) get_alkoxysulfinyl_prefix() (in module orthonym.assembly.substituent_prefix_forms) get_alkyl_fragment_name() (in module orthonym.rules.esters) get_alkyl_name() (in module orthonym.assembly.naming_utils) (in module orthonym.data.chain_names) get_all_edge_letters() (in module orthonym.data.polycyclic_data) get_all_prefix_groups() (in module orthonym.rules.seniority) get_amide_chain_length() (in module orthonym.rules.amides) get_amide_parent_name() (in module orthonym.rules.amides) get_amide_type() (in module orthonym.rules.amides) get_amino_acid_acyl_name() (in module orthonym.data.amino_acids) get_amino_acid_ate_stem() (in module orthonym.data.amino_acids) get_amino_acid_atoms() (in module orthonym.rules.amino_acids) get_amino_acid_name() (in module orthonym.data.amino_acids) get_anhydride_consumed_atoms() (in module orthonym.rules.anhydrides) get_anion_name() (in module orthonym.data.ion_retained_names) get_anion_suffix() (in module orthonym.rules.ions) get_anoate_name() (in module orthonym.data.chain_names) get_aromatic_reference() (in module orthonym.data.partial_saturation_refs) get_aromatic_rings() (in module orthonym.perception.rings) get_benzene_ring() (in module orthonym.rules.benzene) get_benzene_substituents() (in module orthonym.rules.benzene) get_bicyclo_by_descriptor() (in module orthonym.data.bicyclo_systems) get_bicyclo_descriptor() (in module orthonym.rules.ortho_fused) get_bicyclo_numbering() (in module orthonym.rules.bicyclo) get_bicyclo_ring_atoms() (in module orthonym.rules.bicyclo) get_bicyclo_substituents() (in module orthonym.rules.bicyclo) get_bond_locants() (in module orthonym.rules.locants) get_bracket_depth() (in module orthonym.assembly.naming_utils) get_bridge_lengths() (in module orthonym.rules.bicyclo) get_bridge_prefix() (in module orthonym.rules.bridged_fused) get_bridged_fused_info() (in module orthonym.rules.bridged_fused) get_bridgehead_atoms() (in module orthonym.perception.rings) (in module orthonym.rules.stereochemistry) get_carbamoyloxy_prefix() (in module orthonym.assembly.substituent_prefix_forms) get_carbocyclic_aromatic_reference() (in module orthonym.data.partial_saturation_refs) get_carotene_parent_name() (in module orthonym.data.natural_products) get_cation_name() (in module orthonym.data.ion_retained_names) get_cation_suffix() (in module orthonym.rules.ions) get_cation_word() (in module orthonym.data.cation_words) get_chain_atoms_with_locants() (in module orthonym.perception.chains) get_chain_excluded_atoms() (in module orthonym.perception.functional_groups) get_chain_name() (in module orthonym.data.chain_names) get_chain_prefix() (in module orthonym.data.chain_names) get_child_locants() (in module orthonym.rules.fusion_descriptors) get_complete_bicyclo_data() (in module orthonym.rules.bicyclo) get_complete_ring_atom_set() (in module orthonym.perception.rings) get_complex_fusion_by_name() (in module orthonym.data.polycyclic_data) get_complex_fusion_info() (in module orthonym.data.polycyclic_data) get_component_by_pattern() (in module orthonym.data.fusion_components) get_component_info() (in module orthonym.data.fusion_components) get_component_prefix() (in module orthonym.data.fusion_components) get_component_seniority() (in module orthonym.data.fusion_components) get_containing_ring_system() (in module orthonym.perception.rings) get_current_pool() (in module orthonym.assembly.candidate_pool) get_dispatch_stats() (in module orthonym.routing) (in module orthonym.routing.dispatcher) (orthonym.namer.Orthonym method) (orthonym.routing.ClassFirstRouter method) (orthonym.routing.dispatcher.ClassFirstRouter method) get_double_bond_locant() (in module orthonym.rules.stereochemistry) get_double_bond_stereo() (in module orthonym.perception.stereo) get_edge_letter() (in module orthonym.data.polycyclic_data) get_enoate_name() (in module orthonym.data.chain_names) get_fg_prefix_form() (in module orthonym.rules.polyfunctional) get_functional_group_atoms() (in module orthonym.perception.functional_groups) get_functional_group_locants() (in module orthonym.rules.locants) get_fused_aromatic_core() (in module orthonym.rules.polycyclics) get_fused_heterocycle_info() (in module orthonym.data.fused_heterocycles) get_fused_heterocycle_name() (in module orthonym.data.fused_heterocycles) get_fused_heterocycle_prefix() (in module orthonym.data.fused_heterocycles) get_fused_heterocycle_substituents() (in module orthonym.rules.fused_rings) get_fused_ring_sizes() (in module orthonym.rules.fused_rings) get_fusion_edge() (in module orthonym.rules.fusion_descriptors) get_fusion_letter() (in module orthonym.rules.fusion_descriptors) get_fusion_prefix() (in module orthonym.rules.fusion_descriptors) get_general_retained_name() (in module orthonym.data) get_guanidine_prefix() (in module orthonym.assembly.substituent_prefix_forms) get_heteroatom_locants() (in module orthonym.rules.heterocycles) get_heteroatom_prefix() (in module orthonym.rules.polycyclic_bridged) get_heteroatom_priority() (in module orthonym.data.hw_heteroatoms)

get_heteroatom_replacement_prefix() (in module orthonym.rules.polycyclic) get_heterocycle_substituents() (in module orthonym.rules.heterocycles) get_higher_polycyclo_iupac_locants() (in module orthonym.rules.polycyclic_von_baeyer) get_hw_prefix() (in module orthonym.data.hw_heteroatoms) get_hw_stem() (in module orthonym.data.hw_stems) get_inner_dispatch_stats() (in module orthonym.assembly.inner_dispatch) (orthonym.namer.Orthonym method) get_ion_name() (in module orthonym.data.ion_retained_names) get_ion_sites() (in module orthonym.perception.ions) get_junction_locants_for_fused_system() (in module orthonym.rules.stereochemistry) get_mixed_spiro_fused_iupac_locants() (in module orthonym.rules.spiro) get_multiplier() (in module orthonym.assembly.composer) get_multiplier_prefix() (in module orthonym.assembly.naming_utils) get_n_alkyl_carbamoyl_prefix() (in module orthonym.assembly.substituent_prefix_forms) get_n_n_dialkyl_carbamoyl_prefix() (in module orthonym.assembly.substituent_prefix_forms) get_n_substituents() (in module orthonym.rules.amides) get_n_substituted_carbamothioylamino_prefix() (in module orthonym.assembly.substituent_prefix_forms) get_n_substituted_carbamoylamino_prefix() (in module orthonym.assembly.substituent_prefix_forms) get_naming_depth() (in module orthonym.assembly.fragment_naming) get_natural_product_name() (in module orthonym.data.natural_products) get_nitrile_locant() (in module orthonym.rules.nitriles) get_nitrile_parent_chain() (in module orthonym.rules.nitriles) get_non_principal_fg_locants() (in module orthonym.rules.polyfunctional) get_non_principal_groups() (in module orthonym.rules.polyfunctional) get_non_scaffold_atoms() (in module orthonym.perception.natural_products) get_pah_core_atoms() (in module orthonym.data.polycyclic_data) get_pah_names() (in module orthonym.data.polycyclic_data) get_pah_substituent_locants() (in module orthonym.rules.polycyclics) get_pah_substituent_positions() (in module orthonym.data.polycyclic_data) get_pah_type() (in module orthonym.rules.polycyclics) get_parent_name() (in module orthonym.rules.ortho_fused) get_persistent_opsin() (in module orthonym.validation.opsin_server) get_phosphanyl_prefix() (in module orthonym.rules.phosphorus) get_phosphorus_prefix() (in module orthonym.rules.phosphorus) get_phosphoryl_prefix() (in module orthonym.assembly.substituent_prefix_forms) get_polycyclic_by_name() (in module orthonym.data.polycyclic_data) get_polycyclic_by_smiles() (in module orthonym.data.polycyclic_data) get_polycyclic_core_atoms() (in module orthonym.rules.polycyclics) get_polycyclic_iupac_locants() (in module orthonym.rules.polycyclics) get_polycyclic_stereo() (in module orthonym.rules.polycyclic) get_polycyclic_substituents() (in module orthonym.rules.polycyclic) (in module orthonym.rules.polycyclics) get_polycyclic_unsaturation() (in module orthonym.rules.polycyclic) get_prefix() (in module orthonym.rules) (in module orthonym.rules.seniority) get_principal_group() (in module orthonym.rules) (in module orthonym.rules.seniority) get_proof() (in module orthonym.validation.proof_ledger) get_provenance() (in module orthonym.metrics.provenance) get_radical_sites() (in module orthonym.perception.ions) get_radical_suffix() (in module orthonym.rules.radicals) get_reference_ring_atoms() (in module orthonym.data.partial_saturation_refs) get_reference_smiles() (in module orthonym.data.partial_saturation_refs) get_retained_bicyclo_name() (in module orthonym.data.bicyclo_systems) get_retained_metallocene_name() (in module orthonym.data.organometallics) get_retained_name() (in module orthonym.data) (in module orthonym.data.retained_names) get_retained_tricyclo_name() (in module orthonym.rules.tricyclo) get_ring_acid_name() (in module orthonym.rules.esters) get_ring_assembly_iupac_locants() (in module orthonym.rules.ring_assemblies) get_ring_atoms() (in module orthonym.rules.polycyclic_bridged) get_ring_attachment_atom() (in module orthonym.rules.ring_substituents) get_ring_attachment_locant() (in module orthonym.rules.ring_substituents) get_ring_canonical_smiles() (in module orthonym.rules.heterocycles) get_ring_count() (in module orthonym.rules.polycyclic_bridged) get_ring_double_bond_atoms() (in module orthonym.perception.rings) get_ring_double_bonds() (in module orthonym.rules.cycloalkanes) get_ring_heteroatoms() (in module orthonym.perception.rings) (in module orthonym.rules.polycyclic_bridged) get_ring_info() (in module orthonym.perception.rings) get_ring_junction_stereo_prefix() (in module orthonym.rules.fused_rings) get_ring_parent_name() (in module orthonym.rules.nitriles) get_ring_saturation_level() (in module orthonym.rules.partial_saturation) get_ring_size() (in module orthonym.perception.rings) get_ring_substituent_name() (in module orthonym.rules.ring_substituents) get_ring_substituents() (in module orthonym.rules.cycloalkanes) get_ring_system_type() (in module orthonym.data.fused_heterocycles) get_ring_systems() (in module orthonym.perception.rings) get_rings_from_spiro_center() (in module orthonym.rules.spiro) get_saturated_position_locants() (in module orthonym.rules.partial_saturation) get_saturated_stem() (in module orthonym.data.hw_stems) get_saturation_locants() (in module orthonym.rules.partial_saturation) get_saturation_prefix() (in module orthonym.rules.heterocycles) (in module orthonym.rules.partial_saturation) get_saturation_prefix_for_fused_ring() (in module orthonym.assembly.composer) get_scaffold_numbering() (in module orthonym.data.natural_products) get_scaffold_patterns() (in module orthonym.data.natural_products) get_scaffold_substituents() (in module orthonym.perception.natural_products) get_shared_atoms() (in module orthonym.rules.fused_rings) get_simple_cis_trans_prefix() (in module orthonym.rules.fused_rings) get_simple_ring_stereo() (in module orthonym.rules.stereochemistry) get_simple_ring_stereo_from_atoms() (in module orthonym.rules.stereochemistry) get_spiro_atoms() (in module orthonym.perception.rings) get_spiro_iupac_locants() (in module orthonym.rules.spiro) get_spiro_numbering() (in module orthonym.rules.spiro) get_spiro_ring_sizes() (in module orthonym.rules.spiro) get_spiro_substituents() (in module orthonym.rules.spiro) get_stereocenters() (in module orthonym.perception.stereo) get_stereodescriptor_string() (in module orthonym.perception.stereo) get_steroid_numbering() (in module orthonym.data.natural_products) get_substituent_name() (in module orthonym.rules.cycloalkanes) get_substituent_prefix_form() (in module orthonym.assembly.substituent_prefix_forms) get_substituents() (in module orthonym.perception.chains) (in module orthonym.rules.ortho_fused) get_substituted_fused_het_prefix() (in module orthonym.data.fused_heterocycles) get_suffix() (in module orthonym.rules) (in module orthonym.rules.seniority) get_suffix_multiplier_prefix() (in module orthonym.assembly.naming_utils) get_sulfanyl_prefix() (in module orthonym.assembly.substituent_prefix_forms) get_sulfinyl_prefix() (in module orthonym.assembly.substituent_prefix_forms) get_sulfonyl_prefix() (in module orthonym.assembly.substituent_prefix_forms) get_sulfur_prefix() (in module orthonym.rules.sulfur) get_supported_ring_sizes() (in module orthonym.data.hw_stems) get_systematic_acylate() (in module orthonym.data.trivial_acids) get_tricyclo_numbering() (in module orthonym.rules.tricyclo) get_undefined_stereocenters() (in module orthonym.perception.stereo) get_unsaturated_stem() (in module orthonym.data.hw_stems) get_unverified_retained_name() (in module orthonym.data) get_validation_stats() (orthonym.namer.Orthonym method) (orthonym.validation.opsin_grammar.OpsinGrammar method) (orthonym.validation.OpsinGrammar method) get_xanthine_info() (in module orthonym.data.xanthine_derivatives) get_xanthine_n_positions() (in module orthonym.data.xanthine_derivatives) get_xanthine_name() (in module orthonym.data.xanthine_derivatives) glycosyl_substituent_prefix() (in module orthonym.data.sugar_names)

H

handle_duplicate_edge_fusion() (in module orthonym.rules.fusion_descriptors) handler (orthonym.assembly.coverage_scoring.CandidateName attribute) (orthonym.assembly.handlers.InnerDispatchEntry attribute) (orthonym.assembly.inner_dispatch.InnerDispatchEntry attribute) (orthonym.assembly.inner_dispatch.InnerDispatchResult attribute) (orthonym.routing.ClassDispatchEntry attribute) (orthonym.routing.ClassDispatchResult attribute) (orthonym.routing.dispatch_table.ClassDispatchEntry attribute) (orthonym.routing.dispatch_table.ClassDispatchResult attribute) handler_id (orthonym.assembly.candidate_pool.HandlerPolicy attribute) (orthonym.assembly.composer.HandlerResult attribute) (orthonym.assembly.handlers.InnerDispatchEntry attribute) (orthonym.assembly.inner_dispatch.InnerDispatchEntry attribute) (orthonym.assembly.inner_dispatch.InnerDispatchResult attribute) HandlerPolicy (class in orthonym.assembly.candidate_pool) HandlerResult (class in orthonym.assembly.composer) hapticity_n (orthonym.perception.metals.LigandGroup attribute) has_aromatic_chalcogen_bridge() (in module orthonym.rules.bridged_fused) has_aromatic_mancude_bridge() (in module orthonym.rules.bridged_fused) has_covalent_metal_carbon_bond() (in module orthonym.perception.metals) has_functional_group() (in module orthonym.perception.functional_groups) has_isotopes() (in module orthonym.rules.isotopes) has_ortho_fused_pair() (in module orthonym.perception.mancude) has_retained_name() (in module orthonym.data) has_stereochemistry() (in module orthonym.perception.stereo) has_structural_hyphen() (in module orthonym.assembly.naming_utils) has_unverifiable_atoms() (in module orthonym.validation.reconstruct)

heavy_atoms (orthonym.validation.name_morphemes.ArityEstimate attribute) het_count_neg (orthonym.rules.fused_ring_selection.ComponentRank attribute) het_locants_stub (orthonym.rules.fused_ring_selection.ComponentRank attribute) het_type_locants_stub (orthonym.rules.fused_ring_selection.ComponentRank attribute) het_variety_neg (orthonym.rules.fused_ring_selection.ComponentRank attribute) hetero_per_atom (orthonym.rules.vonbaeyer_universal.RingAnalysis attribute) hetero_prefix (orthonym.rules.vonbaeyer_universal.RingAnalysis attribute) HETEROCHALCOGEN_ABA (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) heterocycle_atom_to_locant (orthonym.namer.MolecularFeatures attribute) heterocycle_info (orthonym.namer.MolecularFeatures attribute) heterocycle_substituents (orthonym.namer.MolecularFeatures attribute) HETEROIMINE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) HETERONE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) HOMONUCLEAR_PNICTOGEN_CHAIN (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) hydrazonamide_name_to_hydrazonamido_prefix() (in module orthonym.assembly.substituent_naming) hydrazonoyl_amido_prefix_from_branch() (in module orthonym.assembly.substituent_naming) hydro (orthonym.rules.bridged_fused_pin.BridgedParent attribute) HYDRO (orthonym.validation.binding_spine.BindingKind attribute) HYDRO_FUSED_PEROXOL (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) hydro_state() (in module orthonym.rules.bridged_fused_pin.hydro) hydro_text() (in module orthonym.rules.bridged_fused_pin.hydro) HydroState (class in orthonym.rules.bridged_fused_pin.hydro)

I

identical_parent_units() (in module orthonym.rules.pin_vocabulary) identical_prefixes_cited_apart (class in orthonym.assembly.composition_primitives) identical_prefixes_grouped() (in module orthonym.assembly.composition_primitives) identify_bridges() (in module orthonym.rules.bridged_fused) identify_fused_core() (in module orthonym.rules.bridged_fused) identify_fused_rings() (in module orthonym.rules.ortho_fused) identify_fused_system() (in module orthonym.rules.polycyclics) identify_fusion_edges() (in module orthonym.rules.fusion_descriptors) identify_main_bridgeheads() (in module orthonym.rules.polycyclic_bridged) identify_parent_and_child() (in module orthonym.rules.fusion_descriptors) identify_polycyclic() (in module orthonym.rules.polycyclics) identify_ring_system() (in module orthonym.rules.ring_substituents) identify_xanthine() (in module orthonym.data.xanthine_derivatives) ih_sets (orthonym.rules.bridged_fused_pin.hydro.HydroState attribute) ih_text() (in module orthonym.rules.bridged_fused_pin.hydro) imidamide_name_to_imidamido_prefix() (in module orthonym.assembly.substituent_naming) imidoyl_amido_prefix_from_branch() (in module orthonym.assembly.substituent_naming) in_class (orthonym.assembly.substituent_enumerator.FreeValencePrefix attribute) in_pin_promotion() (in module orthonym.rules.pin_vocabulary) inchikey_of() (in module orthonym.perception.molcache) indicated_h (orthonym.assembly.handlers.NameTreeNode attribute) (orthonym.assembly.name_tree.NameTreeNode attribute) (orthonym.validation.reconstruct.NameFacts attribute) indicated_hydrogen (orthonym.rules.bridged_fused_pin.BridgedParent attribute) inject_stereo_from_locant_map() (in module orthonym.rules.stereochemistry) inject_stereo_reanchored_rt_gated() (in module orthonym.rules.stereochemistry) InnerDispatchEntry (class in orthonym.assembly.handlers) (class in orthonym.assembly.inner_dispatch) InnerDispatchResult (class in orthonym.assembly.inner_dispatch) INORGANIC_ACID (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) INOSITOL (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) input_inchikey (orthonym.validation.atom_coverage.CoverageResult attribute) (orthonym.validation.CoverageResult attribute) input_invariants() (in module orthonym.perception.structure_conservation) input_stereo_undefined() (in module orthonym.perception.stereo) integrate_universal_prefixes() (in module orthonym.assembly.handlers._enrichment) invoke() (orthonym.validation.opsin_server.PersistentOpsin method) ion_sites (orthonym.namer.MolecularFeatures attribute) is_alkaloid() (in module orthonym.perception.natural_products) is_aromatic (orthonym.namer.MolecularFeatures attribute) is_aromatic_ring() (in module orthonym.perception.rings) is_benzene (orthonym.namer.MolecularFeatures attribute) is_benzene_ring() (in module orthonym.rules.benzene) is_bicyclo_system() (in module orthonym.rules.bicyclo) is_bluebook_discarded_name() (in module orthonym.rules.parent_ranking) is_branched_polyspiro() (in module orthonym.rules.spiro) is_bridged_fused() (in module orthonym.rules.bridged_fused) is_carbocyclic_reference() (in module orthonym.data.partial_saturation_refs) is_chiral() (in module orthonym.perception.stereo) is_chiral_inositol() (in module orthonym.rules.inositols) is_coarse_node() (in module orthonym.assembly.name_tree) is_complete (orthonym.validation.atom_coverage.CoverageResult attribute) (orthonym.validation.CoverageResult attribute) is_complex_substituent() (in module orthonym.assembly.naming_utils) is_cyclic (orthonym.namer.MolecularFeatures attribute) is_cyclophane() (in module orthonym.rules.phane) is_dependent (orthonym.rules.polycyclic.BridgeInfo attribute) is_dichalcogen_bridge_attach() (in module orthonym.assembly.substituent_enumerator) is_dispiroter() (in module orthonym.rules.spiro) is_enabled() (in module orthonym.jvm_budget) (in module orthonym.metrics.candidate_ledger) is_failure_name() (in module orthonym.errors) is_fully_saturated() (in module orthonym.rules.partial_saturation) is_fused_aromatic_system() (in module orthonym.rules.fused_rings) (in module orthonym.rules.polycyclics) is_fused_bicyclic() (in module orthonym.rules.fused_rings) is_fused_heterocycle() (in module orthonym.data.fused_heterocycles) is_fused_heterocyclic_system() (in module orthonym.rules.fused_rings) is_heterocyclic() (in module orthonym.perception.rings) is_hidden_amide() (in module orthonym.rules.pseudoketones) is_higher_polycyclo() (in module orthonym.rules.polycyclic_von_baeyer) is_in_ring() (in module orthonym.perception.rings) is_incumbent (orthonym.rules.parent_ranking.ParentCandidate attribute) is_inositol_skeleton() (in module orthonym.rules.inositols)

is_lactone() (in module orthonym.rules.esters) is_lambda_hydride_phosphorus() (in module orthonym.perception.lambda_hydride) is_lambda_multiring_spiro() (in module orthonym.rules.spiro) is_mancude (orthonym.rules.vonbaeyer_universal.RingAnalysis attribute) is_mancude_monocyclic_hydrocarbon() (in module orthonym.rules.cycloalkanes) is_mancude_ring_system() (in module orthonym.perception.mancude) is_metal_element() (in module orthonym.perception.metals) is_mixed_spiro_fused() (in module orthonym.rules.spiro) is_monocyclic_lactam() (in module orthonym.rules.lactams) is_monocyclic_lactone() (in module orthonym.rules.lactones) is_multimetal (orthonym.perception.metals.MetalComplex attribute) is_n_substituted_amino_acid() (in module orthonym.rules.amino_acids) is_named_ring (orthonym.assembly.resolvers.ParentInfo attribute) is_only_one_substitutable_position() (in module orthonym.assembly.naming_utils) is_pentacyclo_or_higher() (in module orthonym.rules.polycyclic_bridged) is_peptide() (in module orthonym.rules.amino_acids) is_peri_condensed() (in module orthonym.rules.polycyclics) is_phenol_benzene (orthonym.assembly.coverage_scoring.CandidateName attribute) is_pin (orthonym.assembly.offer_pool.Offer attribute) is_pin_denied() (in module orthonym.data.pin_policy) is_pin_form (orthonym.rules.bridged_fused_pin.BridgedParent attribute) (orthonym.rules.bridged_fused_pin.prefixes.BridgePrefix attribute) is_polycyclic_aromatic() (in module orthonym.data.polycyclic_data) is_polycyclic_system() (in module orthonym.rules.polycyclic) is_polyfunctional (orthonym.namer.MolecularFeatures attribute) is_principal_group_on_chain() (in module orthonym.rules.parent_selection) is_principal_group_on_ring() (in module orthonym.rules.parent_selection) is_refusal_sentinel() (in module orthonym.errors) is_retained_bicyclo() (in module orthonym.data.bicyclo_systems) is_retained_name_compound() (in module orthonym.data.retained_names) is_retained_tricyclo() (in module orthonym.rules.tricyclo) is_ring_attached_amide() (in module orthonym.rules.amides) is_ring_attached_nitrile() (in module orthonym.rules.nitriles) is_ring_parent_name() (in module orthonym.assembly.composition_primitives) is_ring_substituent() (in module orthonym.perception.chains) is_salt() (in module orthonym.rules.salts) is_saturated_ring() (in module orthonym.perception.rings) is_secondary (orthonym.rules.polycyclic.BridgeInfo attribute) is_seven_plus_ring_assembly() (in module orthonym.rules.phane) is_simple_cation() (in module orthonym.data.cation_words) is_simple_unbranched_organyl() (in module orthonym.rules.substituent_purity) is_spiro_named_components() (in module orthonym.rules.spiro) is_spiro_system() (in module orthonym.rules.spiro) is_spiro_vonbaeyer() (in module orthonym.rules.spiro) is_spirobi() (in module orthonym.rules.spiro) is_spiroter() (in module orthonym.rules.spiro) is_standard_amino_acid() (in module orthonym.data.amino_acids) is_steroid() (in module orthonym.perception.natural_products) is_substituted_substituent() (in module orthonym.assembly.naming_utils) is_suffix_group() (in module orthonym.rules.seniority) is_supported_ring_size() (in module orthonym.data.hw_stems) is_terminal (orthonym.assembly.resolvers.SuffixInfo attribute) is_tetracyclo_system() (in module orthonym.rules.polycyclic_bridged) is_tetrahydronaphthalene() (in module orthonym.rules.partial_saturation) is_top_level_naming() (in module orthonym.assembly.fragment_naming) is_tricyclo_system() (in module orthonym.rules.polycyclic_bridged) (in module orthonym.rules.tricyclo) is_tuned() (in module orthonym.runtime_tuning) is_unbranched_polyspiro_different() (in module orthonym.rules.spiro) is_xanthine_derivative() (in module orthonym.data.xanthine_derivatives) is_zwitterion() (in module orthonym.rules.salts) isolated_naming_session() (in module orthonym.assembly.fragment_naming) isotope_label_on_atoms() (in module orthonym.assembly.locant_omission) isotope_labelled_original_scope() (in module orthonym.assembly.locant_omission) isotope_parent_positional_scope() (in module orthonym.assembly.locant_omission) isotopes (orthonym.validation.reconstruct.NameFacts attribute) isotopic_naming_scope() (in module orthonym.assembly.locant_omission) italicized_prefix_is_bare() (in module orthonym.assembly.naming_utils) iupac_p_section (orthonym.data.group_split_rules.SplitRule attribute) (orthonym.data.triviality_controller_seed.SeedEntry attribute) iupac_section (orthonym.assembly.handlers.InnerDispatchEntry attribute) (orthonym.assembly.inner_dispatch.InnerDispatchEntry attribute) (orthonym.routing.ClassDispatchEntry attribute) (orthonym.routing.dispatch_table.ClassDispatchEntry attribute) iupac_section_cite (orthonym.assembly.handlers.NameTreeNode attribute) (orthonym.assembly.name_tree.NameTreeNode attribute)

J

jar_dir() (in module orthonym.jars) JarSpec (class in orthonym.jars) JarUnavailable java_cmd() (in module orthonym.jvm_flags)

JVM_CORE_HYGIENE_FLAGS (in module orthonym.jvm_flags) JVM_HYGIENE_FLAGS (in module orthonym.jvm_flags) JVM_PERF_FLAGS (in module orthonym.jvm_flags) jvm_slots() (in module orthonym.jvm_budget)

K

KETENE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) key (orthonym.data.resonance_templates.ResonanceChainTemplate attribute) (orthonym.rules.parent_ranking.ParentCandidate attribute) kind (orthonym.assembly.group_splitting.SplitEvent attribute) (orthonym.assembly.retained_substitution.ControllerEvent attribute) (orthonym.jars.JarSpec attribute) (orthonym.rules.p44_scorer.ParentCandidate attribute) (orthonym.rules.parent_ranking.ParentCandidate attribute) (orthonym.validation.binding_spine.SpineBinding attribute)

L

l3_locant_omitted_for_parent_atoms() (in module orthonym.assembly.locant_omission) l3_monosubstituted_locant_omitted() (in module orthonym.assembly.locant_omission) l3_one_kind_of_substitutable_h() (in module orthonym.assembly.locant_omission) l4_no_isomer_by_relocation() (in module orthonym.assembly.locant_omission) l5_uniform_complete() (in module orthonym.assembly.locant_omission) l6_all_substitutable_h_share_one_locant() (in module orthonym.assembly.locant_omission) l6_chain_parent_one_substitutable_atom() (in module orthonym.assembly.locant_omission) l6_ring_parent_one_substitutable_atom() (in module orthonym.assembly.locant_omission) LAMBDA5_PHOSPHANIMINE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) LAMBDA_SULFANE_IMINE_OXIDE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) last_repair_class() (orthonym.validation.opsin_grammar.OpsinGrammar method) (orthonym.validation.OpsinGrammar method) last_t4_was_final_floor() (in module orthonym.assembly.t4_coverage) last_t4_was_floor_substitute() (in module orthonym.assembly.t4_coverage) leaked_naming_state() (in module orthonym.wallclock) least_senior_six_ring_heteroatom() (in module orthonym.data.hw_stems) LedgerEntry (class in orthonym.metrics.candidate_ledger) legacy_role_coerced (orthonym.validation.binding_spine.BindingSpine attribute) legality (orthonym.rules.polycyclic.PolycyclicDescriptor attribute) length (orthonym.rules.polycyclic.BridgeInfo attribute) (orthonym.rules.polycyclic_bridged.BridgeInfo attribute) lexicon_cache_key() (in module orthonym.validation.name_morphemes) lexicon_entries() (in module orthonym.validation.name_morphemes) lexicon_size() (in module orthonym.validation.name_morphemes) lexicon_sources() (in module orthonym.validation.name_morphemes) ligand_atom_indices (orthonym.perception.metals.LigandGroup attribute) ligand_canonical_smiles (orthonym.perception.metals.LigandGroup attribute) ligand_groups (orthonym.perception.metals.MetalComplex attribute) ligand_smarts_key (orthonym.perception.metals.LigandGroup attribute) LigandGroup (class in orthonym.perception.metals)

linear_acyl_amido_prefix() (in module orthonym.assembly.substituent_naming) LINEAR_PHANE (orthonym.rules.ring_selection.RingSystemType attribute) linear_phane_scope_guard() (in module orthonym.rules.phane) LIPID (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) list_reference_names() (in module orthonym.data.partial_saturation_refs) load_cache() (in module orthonym.validation) (in module orthonym.validation.pubchem_validator) load_seed_table() (in module orthonym.data.triviality_controller_seed) load_split_rules() (in module orthonym.data.group_split_rules) loc_key() (in module orthonym.rules.bridged_fused_pin.numbering) locant (orthonym.assembly.substituent_enumerator.SubstituentInfo attribute) locant_context (orthonym.data.triviality_controller_seed.SeedEntry attribute) locant_high (orthonym.rules.polycyclic.BridgeInfo attribute) locant_low (orthonym.rules.polycyclic.BridgeInfo attribute) locant_score (orthonym.assembly.per_substring_scoring.NodeScores attribute) locant_sort_key() (in module orthonym.assembly.name_comparison) (in module orthonym.assembly.naming_utils) locant_tuple() (in module orthonym.rules.bridged_fused_pin.numbering) locants (orthonym.assembly.composer.NameFragment attribute) (orthonym.assembly.group_splitting.SplitComponent attribute) (orthonym.assembly.handlers.NameTreeNode attribute) (orthonym.assembly.name_tree.NameTreeNode attribute) (orthonym.assembly.resolvers.SuffixInfo attribute) locants_are_forced() (in module orthonym.assembly.locant_omission) located_map_completes_substituent_stereo() (in module orthonym.assembly.substituent_naming) locus_override_rule_id (orthonym.data.triviality_controller_seed.SeedEntry attribute) log_confidence() (in module orthonym.assembly.coverage_scoring) looks_like_ionic_name() (in module orthonym.perception.structure_conservation) lookup_exact_acid_name() (in module orthonym.rules.inorganic_acids) lookup_name_pubchem() (in module orthonym.validation) (in module orthonym.validation.pubchem_validator) lookup_sugar() (in module orthonym.data.sugar_names)

M

main() (in module orthonym.__main__) (in module orthonym.cli) (in module orthonym.jvm_budget) main_bridge (orthonym.rules.polycyclic_bridged.PolycyclicInfo attribute) main_ring (orthonym.rules.polycyclic_bridged.PolycyclicInfo attribute) mancude_double (orthonym.rules.bridged_fused_pin.hydro.HydroState attribute) mancude_fused_core() (in module orthonym.perception.mancude) match_fused_heterocycle_core() (in module orthonym.data.fused_heterocycles) match_polycyclic_core() (in module orthonym.data.polycyclic_data) match_token_atoms_in_mol() (in module orthonym.rules.parent_correctness) matched_entry (orthonym.assembly.inner_dispatch.InnerDispatchResult attribute) Matcher (class in orthonym.metrics.coverage_metrics) matches() (orthonym.data.resonance_templates.ResonanceChainTemplate method) MAX_BRIDGE_ATOMS (in module orthonym.rules.bridged_fused_pin.selection) MAX_CAGE_ATOMS (in module orthonym.rules.vonbaeyer_universal) MAX_FRAGMENT_ATOMS (in module orthonym.rules.terminal_fragment) MAX_INDICATED_H (in module orthonym.rules.bridged_fused_pin.hydro) max_matching_size() (in module orthonym.perception.mancude) MAX_SYSTEM_ATOMS (in module orthonym.rules.bridged_fused_pin.selection) maybe_tune_from_env() (in module orthonym.runtime_tuning) MemoMismatch METACYCLOPHANE (orthonym.rules.phane.PhaneTopology attribute) metal_atom_idx (orthonym.perception.metals.LigandGroup attribute) (orthonym.perception.metals.MetallacycleInfo attribute) metal_atom_indices (orthonym.perception.metals.MetalComplex attribute) MetalComplex (class in orthonym.perception.metals) MetallacycleInfo (class in orthonym.perception.metals) method (orthonym.assembly.coverage_audit.CoverageVerdict attribute) (orthonym.validation.atom_coverage.CoverageResult attribute) (orthonym.validation.CoverageResult attribute) MISMATCH (orthonym.validation.reconstruct.Verdict attribute) MIXED_SIGN_ZWITTERION (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) module orthonym orthonym.__main__ orthonym.assembly orthonym.assembly.candidate_pool orthonym.assembly.composer orthonym.assembly.composition_primitives orthonym.assembly.composition_tier orthonym.assembly.coverage_audit orthonym.assembly.coverage_scoring orthonym.assembly.coverage_utils orthonym.assembly.fragment_naming orthonym.assembly.general_engine orthonym.assembly.general_fusion orthonym.assembly.group_splitting orthonym.assembly.handlers orthonym.assembly.handlers._enrichment orthonym.assembly.handlers._handler_shared orthonym.assembly.handlers.acid_halide orthonym.assembly.handlers.amide orthonym.assembly.handlers.amine orthonym.assembly.handlers.anhydride orthonym.assembly.handlers.azine orthonym.assembly.handlers.boronic_acid orthonym.assembly.handlers.carbamate orthonym.assembly.handlers.carbamic_acid orthonym.assembly.handlers.chalcogen_ester orthonym.assembly.handlers.chalcogen_oxide orthonym.assembly.handlers.cyanamide orthonym.assembly.handlers.diamide orthonym.assembly.handlers.ester_family orthonym.assembly.handlers.general_acyclic orthonym.assembly.handlers.guanidine orthonym.assembly.handlers.hydrazone orthonym.assembly.handlers.hydroxamic_acid orthonym.assembly.handlers.hydroximic_acid orthonym.assembly.handlers.hydroxylamine orthonym.assembly.handlers.imidate orthonym.assembly.handlers.imidoyl_thioyl_halide orthonym.assembly.handlers.imine orthonym.assembly.handlers.ion_dispatch orthonym.assembly.handlers.isocyanate orthonym.assembly.handlers.isothiocyanate orthonym.assembly.handlers.lactam orthonym.assembly.handlers.lactone orthonym.assembly.handlers.n_oxide orthonym.assembly.handlers.n_substituted_sulfonamide orthonym.assembly.handlers.nitrate_ester orthonym.assembly.handlers.nitrile_oxide orthonym.assembly.handlers.nitrite_ester orthonym.assembly.handlers.noncarbon_ester orthonym.assembly.handlers.organometallic orthonym.assembly.handlers.oxime orthonym.assembly.handlers.partial_sat orthonym.assembly.handlers.phosphate_ester orthonym.assembly.handlers.phosphine orthonym.assembly.handlers.phosphine_oxide orthonym.assembly.handlers.phosphinic_acid orthonym.assembly.handlers.phosphonic_acid orthonym.assembly.handlers.pnictogen_inate_ester orthonym.assembly.handlers.pnictogen_oxoacid orthonym.assembly.handlers.polycyclic orthonym.assembly.handlers.ring_assembly orthonym.assembly.handlers.ring_ester orthonym.assembly.handlers.ring_nitrile orthonym.assembly.handlers.simple_molecule orthonym.assembly.handlers.sulfate_ester orthonym.assembly.handlers.sulfone orthonym.assembly.handlers.sulfonimidic_n_hydroxy orthonym.assembly.handlers.sulfonyl_halide orthonym.assembly.handlers.sulfoxide orthonym.assembly.handlers.thiocyanate orthonym.assembly.handlers.thioether orthonym.assembly.handlers.thiourea orthonym.assembly.handlers.tier_a_ring orthonym.assembly.handlers.urea orthonym.assembly.inner_dispatch orthonym.assembly.locant_omission orthonym.assembly.memo orthonym.assembly.name_comparison orthonym.assembly.name_tree orthonym.assembly.name_tree_builder orthonym.assembly.name_tree_to_string orthonym.assembly.naming_utils orthonym.assembly.nested_memo orthonym.assembly.offer_pool orthonym.assembly.per_substring_scoring orthonym.assembly.resolvers orthonym.assembly.retained_substitution orthonym.assembly.substituent_enumerator orthonym.assembly.substituent_naming orthonym.assembly.substituent_prefix_forms orthonym.assembly.t4_coverage orthonym.assembly.universal_substituent orthonym.cli orthonym.data orthonym.data.amino_acids orthonym.data.bicyclo_systems orthonym.data.bluebook_not_names orthonym.data.cation_words orthonym.data.chain_names orthonym.data.coordination_retained orthonym.data.fused_heterocycles orthonym.data.fusion_components orthonym.data.group_split_rules orthonym.data.hw_heteroatoms orthonym.data.hw_stems orthonym.data.ion_retained_names orthonym.data.natural_products orthonym.data.opsin_imports orthonym.data.opsin_imports.amino_acids_opsin orthonym.data.opsin_imports.aryl_groups orthonym.data.opsin_imports.carbohydrates_opsin orthonym.data.opsin_imports.carboxylic_acids_opsin orthonym.data.opsin_imports.cyclic_groups orthonym.data.opsin_imports.functional_terms orthonym.data.opsin_imports.fusion_components_opsin orthonym.data.opsin_imports.natural_products_opsin orthonym.data.opsin_imports.simple_groups orthonym.data.opsin_imports.substituent_names_opsin orthonym.data.opsin_imports.suffix_rules orthonym.data.opsin_imports.word_rules orthonym.data.organometallics orthonym.data.partial_saturation_refs orthonym.data.pin_policy orthonym.data.polycyclic_data orthonym.data.resonance_templates orthonym.data.retained_names orthonym.data.sugar_names orthonym.data.trivial_acids orthonym.data.triviality_controller_seed orthonym.data.xanthine_derivatives orthonym.decomposition orthonym.decomposition.bond_cleavage orthonym.decomposition.engine orthonym.decomposition.fragment_assembly orthonym.decomposition.fragment_capping orthonym.decomposition.fragment_ranker orthonym.decomposition.weave orthonym.diagnostics orthonym.errors orthonym.jars orthonym.jvm_bridge orthonym.jvm_budget orthonym.jvm_flags orthonym.metrics orthonym.metrics.abstention orthonym.metrics.breadth orthonym.metrics.candidate_ledger orthonym.metrics.coverage_metrics orthonym.metrics.provenance orthonym.namer orthonym.perception.automorphisms orthonym.perception.centres_bridge orthonym.perception.chains orthonym.perception.functional_groups orthonym.perception.ions orthonym.perception.lambda_hydride orthonym.perception.lipids orthonym.perception.mancude orthonym.perception.metals orthonym.perception.molcache orthonym.perception.natural_products orthonym.perception.rings orthonym.perception.smarts_cache orthonym.perception.stereo orthonym.perception.structure_conservation orthonym.routing orthonym.routing.dispatch_table orthonym.routing.dispatcher orthonym.rules orthonym.rules.acid_ester_anion orthonym.rules.acid_halides orthonym.rules.added_carbon_parent orthonym.rules.adducts orthonym.rules.amides orthonym.rules.amino_acids orthonym.rules.anhydrides orthonym.rules.benzene orthonym.rules.bicyclo orthonym.rules.bridged_fused orthonym.rules.bridged_fused_pin orthonym.rules.bridged_fused_pin.hydro orthonym.rules.bridged_fused_pin.numbering orthonym.rules.bridged_fused_pin.prefixes orthonym.rules.bridged_fused_pin.selection orthonym.rules.catenated_hydrides orthonym.rules.charged_router orthonym.rules.conjugate_controller orthonym.rules.cycloalkanes orthonym.rules.esters orthonym.rules.functional_replacement orthonym.rules.fused_ring_selection orthonym.rules.fused_rings orthonym.rules.fusion_descriptors orthonym.rules.fusion_numbering orthonym.rules.fusion_orientation orthonym.rules.greek_stereo_descriptors orthonym.rules.heterocycles orthonym.rules.inorganic_acids orthonym.rules.inositols orthonym.rules.ions orthonym.rules.isotopes orthonym.rules.ketenes orthonym.rules.lactams orthonym.rules.lactones orthonym.rules.lambda_convention orthonym.rules.lipids orthonym.rules.locant_validation orthonym.rules.locants orthonym.rules.mononuclear_hydrides orthonym.rules.multiplicative orthonym.rules.natural_products orthonym.rules.nitramide orthonym.rules.nitriles orthonym.rules.nucleosides orthonym.rules.oligosaccharides orthonym.rules.organometallics orthonym.rules.ortho_fused orthonym.rules.p44_scorer orthonym.rules.parent_correctness orthonym.rules.parent_ranking orthonym.rules.parent_selection orthonym.rules.partial_saturation orthonym.rules.peptides orthonym.rules.phane orthonym.rules.phosphorus orthonym.rules.pin_vocabulary orthonym.rules.polyazane orthonym.rules.polychalcogen orthonym.rules.polycyclic orthonym.rules.polycyclic_bridged orthonym.rules.polycyclic_von_baeyer orthonym.rules.polycyclics orthonym.rules.polyfunctional orthonym.rules.polyol_polyester orthonym.rules.pseudoketones orthonym.rules.purine orthonym.rules.purine_oxo orthonym.rules.radicals orthonym.rules.ring_assemblies orthonym.rules.ring_chalcogen_oxide orthonym.rules.ring_replacement orthonym.rules.ring_selection orthonym.rules.ring_substituents orthonym.rules.ring_unsaturation orthonym.rules.salts orthonym.rules.seniority orthonym.rules.skeletal_replacement orthonym.rules.spiro orthonym.rules.stereochemistry orthonym.rules.steroid_stereo orthonym.rules.substituent_purity orthonym.rules.sulfonamides orthonym.rules.sulfur orthonym.rules.sulfur_oxoacid orthonym.rules.terminal_fragment orthonym.rules.terminal_ring orthonym.rules.thioimides orthonym.rules.tricyclo orthonym.rules.vonbaeyer_universal orthonym.runtime_tuning orthonym.validation orthonym.validation.atom_coverage orthonym.validation.binding_spine orthonym.validation.coverage_gate orthonym.validation.dual_validator orthonym.validation.e1_certificate orthonym.validation.format_validator orthonym.validation.name_morphemes orthonym.validation.opsin_grammar orthonym.validation.opsin_roundtrip orthonym.validation.opsin_server orthonym.validation.proof_ledger orthonym.validation.protonation_identity orthonym.validation.pubchem_validator orthonym.validation.radical_identity orthonym.validation.reconstruct orthonym.wallclock

mol (orthonym.namer.MolecularFeatures attribute) (orthonym.rules.phane.PhaneStructure attribute) MolCacheMismatchError MolecularFeatures (class in orthonym.namer) MOLECULE (orthonym.metrics.candidate_ledger.Scope attribute) molecule_components() (in module orthonym.metrics.breadth) molecule_principal_group_and_fgs() (in module orthonym.rules.benzene) monocycle_numbering() (in module orthonym.rules.terminal_ring) MONOCYCLIC (orthonym.rules.phane.SkeletonClass attribute) (orthonym.rules.ring_selection.RingSystemType attribute) MONONUCLEAR_HYDRIDE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) MONONUCLEAR_HYDRIDE_ADDED_CARBON (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) mononuclear_parent_locant_required() (in module orthonym.assembly.locant_omission) MULTI_COMPONENT_NEUTRAL (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) MULTIPLICATIVE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) multiplicative_candidate() (in module orthonym.rules.pin_vocabulary) multiplicative_pin_expected() (in module orthonym.rules.pin_vocabulary) multiplicative_prefix (orthonym.assembly.handlers.NameTreeNode attribute) (orthonym.assembly.name_tree.NameTreeNode attribute) multiplied_component() (in module orthonym.assembly.naming_utils) multiplier_needs_hyphen() (in module orthonym.assembly.naming_utils) must_fail_closed (orthonym.assembly.substituent_enumerator.FreeValencePrefix property)

N

n_double (orthonym.rules.bridged_fused_pin.hydro.HydroState attribute) (orthonym.rules.bridged_fused_pin.selection.Split attribute) n_substituents (orthonym.namer.MolecularFeatures attribute) (orthonym.rules.amides.RingAmideParts attribute) n_substituted_acyl_amido_prefix() (in module orthonym.assembly.substituent_naming) n_substituted_sulfonamide_name() (in module orthonym.rules.sulfonamides) nacyl_float_refusing() (in module orthonym.decomposition.engine) name (orthonym.assembly.composer.ComplexRingResult attribute) (orthonym.assembly.composer.HandlerResult attribute) (orthonym.assembly.coverage_scoring.CandidateName attribute) (orthonym.assembly.general_engine.GeneralEngineResult attribute) (orthonym.assembly.handlers.NamingResult attribute) (orthonym.assembly.name_tree.NamingResult attribute) (orthonym.assembly.offer_pool.Offer attribute) (orthonym.assembly.universal_substituent.UniversalResult attribute) (orthonym.metrics.candidate_ledger.LedgerEntry attribute) (orthonym.metrics.coverage_metrics.RowResult attribute) (orthonym.rules.bridged_fused_pin.prefixes.BridgePrefix attribute) (orthonym.rules.polycyclics.PartialSatName attribute) (orthonym.rules.terminal_fragment.TerminalFragmentName attribute) (orthonym.rules.terminal_ring.TerminalRingName attribute) name() (orthonym.namer.Orthonym method) (orthonym.Orthonym method) name_acid_ester_anion() (in module orthonym.rules.acid_ester_anion) name_acid_halide() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.acid_halide) (in module orthonym.rules.acid_halides) name_acyclic_polyol_polyester() (in module orthonym.rules.polyol_polyester) name_acyl_prefix_substituent() (in module orthonym.rules.phosphorus) name_acyl_radical() (in module orthonym.rules.radicals) name_acyloxy_phosphonic_acid() (in module orthonym.rules.phosphorus) name_added_carbon_parent() (in module orthonym.rules.added_carbon_parent) name_added_h_fused_carbocycle_suffix() (in module orthonym.rules.partial_saturation) name_adduct() (in module orthonym.rules.adducts) name_aldonate_ester() (in module orthonym.data.sugar_names) name_alkoxide_anion() (in module orthonym.rules.ions) name_alkyl_radical() (in module orthonym.rules.radicals) name_amide() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.amide) (in module orthonym.rules.amides) name_amine() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.amine) name_aminium_cation() (in module orthonym.rules.ions) name_amino_acid() (in module orthonym.rules.amino_acids) name_amino_deoxy_open_sugar() (in module orthonym.data.sugar_names) name_anhydride() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.anhydride) (in module orthonym.rules.anhydrides) name_anion() (in module orthonym.rules.ions) name_arsinic_acid() (in module orthonym.assembly.handlers.pnictogen_oxoacid) (in module orthonym.rules.phosphorus) name_arsinous_acid() (in module orthonym.assembly.handlers.pnictogen_oxoacid) (in module orthonym.rules.phosphorus) name_arsonic_acid() (in module orthonym.assembly.handlers.pnictogen_oxoacid) (in module orthonym.rules.phosphorus) name_arsonous_acid() (in module orthonym.assembly.handlers.pnictogen_oxoacid) (in module orthonym.rules.phosphorus) name_aryl_radical() (in module orthonym.rules.radicals) name_azine() (in module orthonym.assembly.handlers.azine) name_azinic_derivative() (in module orthonym.rules.inorganic_acids) name_benzene_derivative() (in module orthonym.rules.benzene) name_bicyclo_system() (in module orthonym.rules.bicyclo) name_borane_amine() (in module orthonym.rules.inorganic_acids) name_boronic_acid() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.boronic_acid) name_branched_oligosaccharide() (in module orthonym.rules.oligosaccharides) name_branched_polyspiro() (in module orthonym.rules.spiro) name_bridged_fused_pin() (in module orthonym.rules.bridged_fused) name_bridged_fused_system() (in module orthonym.rules.bridged_fused) name_c_glycosyl_aglycone() (in module orthonym.data.sugar_names) name_c_substituted_sugar() (in module orthonym.data.sugar_names) name_carbamate() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.carbamate) name_carbamic_acid() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.carbamic_acid) name_carbenium_cation() (in module orthonym.rules.ions) name_carbonic_class_derivative() (in module orthonym.rules.inorganic_acids) name_carbonic_frn_family() (in module orthonym.rules.inorganic_acids) name_carbonic_monoester_acyl_halide() (in module orthonym.rules.acid_halides) name_carboxylate_anion() (in module orthonym.rules.ions) name_carries_non_pin_part() (in module orthonym.metrics.provenance) name_catenated_hydride() (in module orthonym.rules.catenated_hydrides) name_cation() (in module orthonym.rules.ions) name_chain_diamide() (in module orthonym.rules.amides) name_chain_diamide_handler() (in module orthonym.assembly.handlers.diamide) name_chalcogen_chain() (in module orthonym.rules.polychalcogen) name_chalcogen_ester() (in module orthonym.assembly.handlers.chalcogen_ester) name_chalcogen_oxide_substitutive() (in module orthonym.rules.sulfur) name_charged_spiro_system() (in module orthonym.rules.spiro) name_compound() (in module orthonym) (in module orthonym.namer) name_cyanamide() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.cyanamide) name_cyclic_oxo_compound() (in module orthonym.rules.partial_saturation) name_cyclic_polyester() (in module orthonym.rules.lactones) name_cyclophane() (in module orthonym.rules.phane) name_dicarboxylic_diester() (in module orthonym.rules.esters) name_dinuclear_hydride() (in module orthonym.rules.mononuclear_hydrides) name_disaccharide() (in module orthonym.rules.oligosaccharides) name_dispiroter() (in module orthonym.rules.spiro) name_divalent_radical() (in module orthonym.rules.radicals) name_ester() (in module orthonym.rules.esters) name_ester_as_prefix() (in module orthonym.rules.esters) name_ester_family() (in module orthonym.assembly.handlers.ester_family) name_fragment_recursively() (in module orthonym.assembly.fragment_naming) name_free_homonuclear_group14_hydride() (in module orthonym.rules.multiplicative) name_free_sugar() (in module orthonym.data.sugar_names) name_free_sugar_decorated_prefix() (in module orthonym.data.sugar_names) name_fused_heterocycle() (in module orthonym.rules.fused_rings) name_fused_lactone_system() (in module orthonym.rules.ortho_fused) name_fusion_parent() (in module orthonym.assembly.general_fusion) name_general() (in module orthonym.assembly.general_engine) name_general_acyclic() (in module orthonym.assembly.handlers.general_acyclic) name_general_chain() (in module orthonym.assembly.general_engine) name_general_monocycle() (in module orthonym.assembly.general_engine) name_general_ring() (in module orthonym.assembly.general_engine) name_general_spiro() (in module orthonym.assembly.general_engine) name_glycosyl_halide() (in module orthonym.data.sugar_names) name_glycosylamine() (in module orthonym.data.sugar_names) name_glycosyloxy_aglycone() (in module orthonym.data.sugar_names) name_glycosyloxy_yl_parent() (in module orthonym.data.sugar_names) name_guanidine() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.guanidine) name_heteroatom_radical() (in module orthonym.rules.radicals) name_heterochalcogen_aba() (in module orthonym.rules.catenated_hydrides) name_heterocycle() (in module orthonym.rules.heterocycles) name_higher_polycyclo() (in module orthonym.rules.polycyclic_von_baeyer) name_homonuclear_pnictogen_chain() (in module orthonym.rules.catenated_hydrides) name_hydrazinecarboxamide() (in module orthonym.rules.inorganic_acids) name_hydrazone() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.hydrazone) name_hydro_fused_chalcogen_suffix() (in module orthonym.rules.partial_saturation) name_hydro_mancude_fused_carbocycle() (in module orthonym.rules.partial_saturation) name_hydrogenated_fused_carbocycle() (in module orthonym.rules.partial_saturation) name_hydroxamic_acid() (in module orthonym.assembly.handlers.hydroxamic_acid) name_hydroximic_acid() (in module orthonym.assembly.handlers.hydroximic_acid) name_hydroxylamine() (in module orthonym.assembly.handlers.hydroxylamine) name_imidate() (in module orthonym.assembly.handlers.imidate) name_imidoyl_thioyl_halide() (in module orthonym.assembly.handlers.imidoyl_thioyl_halide) (in module orthonym.rules.acid_halides) name_imine() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.imine) name_independent_esters() (in module orthonym.rules.esters) name_inorganic_acid() (in module orthonym.rules.inorganic_acids) name_inositol() (in module orthonym.rules.inositols) name_ion_dispatch() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.ion_dispatch) name_iso_x_cyanate() (in module orthonym.assembly.handlers._handler_shared) name_isocyanate() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.isocyanate) name_isothiocyanate() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.isothiocyanate) name_ketene() (in module orthonym.rules.ketenes) name_lactam() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.lactam) name_lactam_ring() (in module orthonym.rules.lactams) name_lactone() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.lactone) name_lactone_ring() (in module orthonym.rules.lactones) name_lambda_multiring_spiro() (in module orthonym.rules.spiro) name_lambda_sulfane_imine_oxide() (in module orthonym.rules.mononuclear_hydrides) name_linear_oligosaccharide() (in module orthonym.rules.oligosaccharides) name_lipid() (in module orthonym.rules.lipids) name_mixed_ring_prefix() (in module orthonym.rules.ring_assemblies) name_mixed_spiro_fused() (in module orthonym.rules.spiro) name_monocyclic_lactam() (in module orthonym.rules.lactams) name_monocyclic_lactone() (in module orthonym.rules.lactones) name_mononuclear_hydride() (in module orthonym.rules.mononuclear_hydrides) name_mononuclear_hydride_added_carbon() (in module orthonym.rules.mononuclear_hydrides) name_monosaccharide_systematic() (in module orthonym.data.sugar_names) name_multiplicative() (in module orthonym.rules.multiplicative) name_n_oxide() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.n_oxide) name_n_substituted_sulfonamide() (in module orthonym.assembly.handlers.n_substituted_sulfonamide) name_natural_product() (in module orthonym.rules.natural_products) name_natural_product_with_substituents() (in module orthonym.rules.natural_products) name_nitrate_ester() (in module orthonym.assembly.handlers.nitrate_ester) name_nitrile() (in module orthonym.rules.nitriles) name_nitrile_oxide() (in module orthonym.assembly.handlers.nitrile_oxide) name_nitrite_ester() (in module orthonym.assembly.handlers.nitrite_ester) name_noncarbon_ester() (in module orthonym.rules.esters) name_noncarbon_ester_handler() (in module orthonym.assembly.handlers.noncarbon_ester) name_nonreducing_oligosaccharide() (in module orthonym.rules.oligosaccharides) name_nucleoside() (in module orthonym.rules.nucleosides) name_organometallic() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.organometallic) name_ortho_fused_bicyclic() (in module orthonym.rules.fused_rings) name_ortho_fused_system() (in module orthonym.rules.ortho_fused) name_oxime() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.oxime) name_oxime_o_sulfate_anion() (in module orthonym.rules.acid_ester_anion) name_oxo_purine() (in module orthonym.rules.purine) name_oxyl_radical() (in module orthonym.rules.radicals) name_p_frn_ester() (in module orthonym.rules.inorganic_acids) name_p_oxoacid_chalcogen_frn() (in module orthonym.rules.inorganic_acids) name_p_oxoacid_frn() (in module orthonym.rules.inorganic_acids)

name_p_oxoacid_halide_amide() (in module orthonym.rules.inorganic_acids) name_partial_sat() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.partial_sat) name_partially_saturated_carbocycle() (in module orthonym.rules.polycyclics) name_partially_saturated_carbocycle_with_locants() (in module orthonym.rules.polycyclics) name_partially_saturated_monocyclic_heterocycle() (in module orthonym.rules.heterocycles) name_peptide() (in module orthonym.rules.peptides) name_phenolate_anion() (in module orthonym.rules.ions) name_phosphane_carboxylic_acid() (in module orthonym.rules.phosphorus) name_phosphanyl_substituent() (in module orthonym.rules.phosphorus) name_phosphate_ester() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.phosphate_ester) (in module orthonym.rules.phosphorus) name_phosphate_ester_anion() (in module orthonym.rules.phosphorus) name_phosphine() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.phosphine) (in module orthonym.rules.phosphorus) name_phosphine_oxide() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.phosphine_oxide) (in module orthonym.rules.phosphorus) name_phosphinic_acid() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.phosphinic_acid) (in module orthonym.rules.phosphorus) name_phosphinous_acid() (in module orthonym.assembly.handlers.pnictogen_oxoacid) (in module orthonym.rules.phosphorus) name_phosphoanhydride_oxy_substituent() (in module orthonym.rules.phosphorus) name_phosphonic_acid() (in module orthonym.assembly.handlers.phosphonic_acid) (in module orthonym.rules.phosphorus) name_phosphonous_acid() (in module orthonym.assembly.handlers.pnictogen_oxoacid) (in module orthonym.rules.phosphorus) name_phosphoxane_oxy_substituent() (in module orthonym.rules.phosphorus) name_pipeline_only() (in module orthonym.namer) name_pnictogen_inate_ester() (in module orthonym.assembly.handlers.pnictogen_inate_ester) name_polyacid_anion() (in module orthonym.rules.inorganic_acids) name_polyacid_derivative() (in module orthonym.rules.inorganic_acids) name_polyacid_polyester() (in module orthonym.rules.esters) name_polyazane() (in module orthonym.rules.polyazane) name_polycyclic() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.polycyclic) (in module orthonym.rules.polycyclics) name_polycyclic_complete() (in module orthonym.rules.polycyclic) name_polycyclic_with_heteroatoms() (in module orthonym.rules.polycyclic) name_polycyclo_system() (in module orthonym.rules.tricyclo) name_polycyclo_with_functional_groups() (in module orthonym.rules.tricyclo) name_polyfunctional() (in module orthonym.rules.polyfunctional) name_polyfunctional_diester_free_hydroxy() (in module orthonym.rules.esters) name_polyfunctional_ester_via_acid() (in module orthonym.rules.esters) name_polyol_polyester() (in module orthonym.rules.esters) name_polysulfoxide_sulfone() (in module orthonym.rules.polychalcogen) name_prefix_order_fallback() (in module orthonym.assembly.t4_coverage) name_pseudoketone() (in module orthonym.rules.pseudoketones) name_purine_26_dione() (in module orthonym.rules.purine_oxo) name_purine_substituent() (in module orthonym.rules.purine) name_quaternary_aminium() (in module orthonym.rules.ions) name_r_group() (in module orthonym.assembly.handlers._handler_shared) name_radical() (in module orthonym.rules.radicals) name_ring_assembly() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.ring_assembly) (in module orthonym.rules.ring_assemblies) name_ring_assembly_prefix() (in module orthonym.rules.ring_assemblies) name_ring_chalcogen_oxide() (in module orthonym.rules.ring_chalcogen_oxide) name_ring_ester() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.ring_ester) name_ring_ketone_with_added_indicated_h() (in module orthonym.rules.partial_saturation) name_ring_nitrile() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.ring_nitrile) name_ring_system_substituent() (in module orthonym.rules.ring_substituents) name_salt() (in module orthonym.rules.salts) name_saturated_fused_bicyclic() (in module orthonym.rules.fused_rings) name_scope_depth() (in module orthonym.assembly.fragment_naming) name_selenone() (in module orthonym.assembly.handlers.chalcogen_oxide) name_selenoxide() (in module orthonym.assembly.handlers.chalcogen_oxide) name_silicate_ester() (in module orthonym.rules.inorganic_acids) name_silicic_acid_frn() (in module orthonym.rules.inorganic_acids) name_simple_molecule() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.simple_molecule) name_spiro_named_components() (in module orthonym.rules.spiro) name_spiro_system() (in module orthonym.rules.spiro) name_spiro_vonbaeyer() (in module orthonym.rules.spiro) name_spirobi() (in module orthonym.rules.spiro) name_spiroter() (in module orthonym.rules.spiro) name_stibinic_acid() (in module orthonym.assembly.handlers.pnictogen_oxoacid) (in module orthonym.rules.phosphorus) name_stibinous_acid() (in module orthonym.assembly.handlers.pnictogen_oxoacid) (in module orthonym.rules.phosphorus) name_stibonic_acid() (in module orthonym.assembly.handlers.pnictogen_oxoacid) (in module orthonym.rules.phosphorus) name_stibonous_acid() (in module orthonym.assembly.handlers.pnictogen_oxoacid) (in module orthonym.rules.phosphorus) name_substituent() (in module orthonym.assembly.substituent_enumerator) name_substituent_for_ordering() (in module orthonym.assembly.substituent_enumerator) name_substituent_fragment() (in module orthonym.assembly.substituent_naming) name_substituted_benzene() (in module orthonym.rules.benzene) name_substituted_fused_aromatic() (in module orthonym.rules.polycyclics) name_substituted_heterocycle() (in module orthonym.rules.heterocycles) name_substituted_nitramide() (in module orthonym.rules.nitramide) name_substituted_polycyclic() (in module orthonym.rules.polycyclics) name_substituted_purine() (in module orthonym.rules.purine) name_sugar_ester() (in module orthonym.data.sugar_names) name_sugar_o_methyl() (in module orthonym.data.sugar_names) name_sulfate_ester() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.sulfate_ester) (in module orthonym.rules.sulfur_oxoacid) name_sulfate_ester_anion() (in module orthonym.rules.acid_ester_anion) name_sulfide() (in module orthonym.rules.sulfur) name_sulfone() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.sulfone) (in module orthonym.rules.sulfur) name_sulfonic_acid() (in module orthonym.rules.sulfur) name_sulfonimidic_n_hydroxy() (in module orthonym.assembly.handlers.sulfonimidic_n_hydroxy) name_sulfonyl_halide() (in module orthonym.assembly.handlers.sulfonyl_halide) (in module orthonym.rules.sulfur) name_sulfoxide() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.sulfoxide) (in module orthonym.rules.sulfur) name_sulfur_oxoacid_acyl_for_amino() (in module orthonym.rules.sulfur_oxoacid) name_sulfur_oxoacid_oxy_substituent() (in module orthonym.rules.sulfur_oxoacid) name_symmetric_multiplicative_diacid_diester() (in module orthonym.rules.esters) name_t4_complete() (in module orthonym.assembly.t4_coverage) name_t4_complete_candidate() (in module orthonym.assembly.t4_coverage) name_tellurone() (in module orthonym.assembly.handlers.chalcogen_oxide) name_telluroxide() (in module orthonym.assembly.handlers.chalcogen_oxide) name_thiocyanate() (in module orthonym.assembly.handlers.thiocyanate) name_thioether() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.thioether) name_thioimide() (in module orthonym.rules.thioimides) name_thiol() (in module orthonym.rules.sulfur) name_thiourea() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.thiourea) name_tier_a_ring() (in module orthonym.assembly.handlers.tier_a_ring) name_tiered() (orthonym.namer.Orthonym method) (orthonym.Orthonym method) name_to_opsin_smiles() (orthonym.assembly.retained_substitution.OpsinOracle method) name_to_smiles() (orthonym.assembly.retained_substitution.OpsinOracle method) name_tree_to_string() (in module orthonym.assembly.handlers) (in module orthonym.assembly.name_tree_to_string) name_tricyclo_system() (in module orthonym.rules.tricyclo) name_trivalent_radical() (in module orthonym.rules.radicals) name_unbranched_polyspiro_different() (in module orthonym.rules.spiro) name_universal_substituent_prefix() (in module orthonym.assembly.universal_substituent) name_universal_substitutive() (in module orthonym.assembly.universal_substituent) name_urea() (in module orthonym.assembly.handlers) (in module orthonym.assembly.handlers.urea) name_with_confidence() (orthonym.namer.Orthonym method) (orthonym.Orthonym method) name_with_tree() (in module orthonym) (in module orthonym.namer) (orthonym.namer.Orthonym method) (orthonym.Orthonym method) name_ylidene_substituent() (in module orthonym.assembly.substituent_enumerator) name_ylidyne_substituent() (in module orthonym.assembly.substituent_enumerator) name_zwitterion() (in module orthonym.rules.salts) NameFacts (class in orthonym.validation.reconstruct) NameFragment (class in orthonym.assembly.composer) NameTreeNode (class in orthonym) (class in orthonym.assembly.handlers) (class in orthonym.assembly.name_tree) NameTreeSerializerError naming_pass_cap() (in module orthonym.assembly.fragment_naming) naming_passes() (in module orthonym.assembly.fragment_naming) NamingResult (class in orthonym) (class in orthonym.assembly.handlers) (class in orthonym.assembly.name_tree) NATURAL_PRODUCT (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) needs_brackets() (in module orthonym.assembly.naming_utils) needs_p1634_marks() (in module orthonym.assembly.naming_utils) needs_recursive_naming() (in module orthonym.assembly.substituent_naming) needs_stereo_injection() (in module orthonym.rules.stereochemistry) net_charge (orthonym.validation.reconstruct.NameFacts attribute) net_formal_charge() (in module orthonym.perception.structure_conservation) NITRAMIDE_SUBSTITUTED (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) no_disub_hydroxylamine_core() (in module orthonym.assembly.handlers.hydroxylamine) NO_PARENT (orthonym.metrics.abstention.AbstentionCode attribute) no_verified_pin() (in module orthonym.errors) node_cycle (orthonym.rules.phane.PhaneStructure attribute) node_scores (orthonym.assembly.coverage_scoring.CandidateName attribute) NodeScores (class in orthonym.assembly.per_substring_scoring) non_pin_vocabulary() (in module orthonym.rules.pin_vocabulary) non_principal_groups (orthonym.namer.MolecularFeatures attribute) nonstandard_bonding_number() (in module orthonym.rules.lambda_convention) note_touched() (in module orthonym.metrics.provenance) notes (orthonym.data.group_split_rules.SplitRule attribute) (orthonym.data.triviality_controller_seed.SeedEntry attribute) NUCLEOSIDE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) nuclide_symbol() (in module orthonym.rules.isotopes) number_bicyclic_system() (in module orthonym.rules.ortho_fused) number_heterocycle_ring() (in module orthonym.rules.heterocycles) Numbering (class in orthonym.rules.bridged_fused_pin.numbering) numbering (orthonym.rules.polycyclic.PolycyclicDescriptor attribute) (orthonym.rules.terminal_fragment.TerminalFragmentName attribute) (orthonym.rules.terminal_ring.TerminalRingName attribute) numbering_held_by_drawn_alternation() (in module orthonym.data.fused_heterocycles) numberings() (in module orthonym.rules.bridged_fused_pin.numbering) numerical_term() (in module orthonym.data.chain_names)

O

Offer (class in orthonym.assembly.offer_pool) ok (orthonym.validation.binding_spine.SpineProof attribute) (orthonym.validation.e1_certificate.E1Verdict attribute) opens_with_replacement_prefix() (in module orthonym.assembly.naming_utils) opsin_atom_locant_map() (in module orthonym.validation.opsin_roundtrip) opsin_available() (in module orthonym.jvm_bridge) opsin_extended_smiles() (in module orthonym.jvm_bridge) opsin_grammar_suggest_fix() (in module orthonym.validation) (in module orthonym.validation.opsin_grammar) opsin_grammar_validate() (in module orthonym.validation) (in module orthonym.validation.opsin_grammar) opsin_label_for_gate_outcome() (in module orthonym.metrics.provenance) opsin_parse() (in module orthonym.validation) (in module orthonym.validation.opsin_roundtrip) opsin_parse_both_versions() (in module orthonym.validation.opsin_roundtrip) opsin_parsed (orthonym.metrics.coverage_metrics.RowResult attribute) (orthonym.validation.dual_validator.DualResult attribute) (orthonym.validation.DualResult attribute) opsin_reference_mol() (in module orthonym.rules.parent_correctness) opsin_roundtrip_check() (in module orthonym.validation) (in module orthonym.validation.opsin_roundtrip) opsin_rt (orthonym.validation.dual_validator.DualResult attribute) (orthonym.validation.DualResult attribute) opsin_rt_verified_at (orthonym.data.group_split_rules.SplitRule attribute) (orthonym.data.triviality_controller_seed.SeedEntry attribute) opsin_smiles (orthonym.validation.dual_validator.DualResult attribute) (orthonym.validation.DualResult attribute) opsin_stdout() (in module orthonym.jvm_bridge) OpsinGrammar (class in orthonym.validation) (class in orthonym.validation.opsin_grammar) OpsinOracle (class in orthonym.assembly.retained_substitution) OptionalNamingCapExceeded ORGANOMETALLIC (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) organyl_prefix_name() (in module orthonym.rules.substituent_purity) orient_benzene() (in module orthonym.rules.benzene) orient_chain() (in module orthonym.rules.locants) orient_cycloalkane() (in module orthonym.rules.cycloalkanes) orient_cycloalkene() (in module orthonym.rules.cycloalkanes) orient_heterocycle() (in module orthonym.rules.heterocycles) orient_heterocycle_with_substituents() (in module orthonym.rules.heterocycles) orient_stub (orthonym.rules.fused_ring_selection.ComponentRank attribute) oriented_heterocycle (orthonym.namer.MolecularFeatures attribute) oriented_ring (orthonym.namer.MolecularFeatures attribute) ORTHOCYCLOPHANE (orthonym.rules.phane.PhaneTopology attribute) orthonym module Orthonym (class in orthonym) (class in orthonym.namer) orthonym.__main__ module orthonym.assembly module orthonym.assembly.candidate_pool module orthonym.assembly.composer module orthonym.assembly.composition_primitives module orthonym.assembly.composition_tier module orthonym.assembly.coverage_audit module orthonym.assembly.coverage_scoring module orthonym.assembly.coverage_utils module orthonym.assembly.fragment_naming module orthonym.assembly.general_engine module orthonym.assembly.general_fusion module orthonym.assembly.group_splitting module orthonym.assembly.handlers module orthonym.assembly.handlers._enrichment module orthonym.assembly.handlers._handler_shared module orthonym.assembly.handlers.acid_halide module orthonym.assembly.handlers.amide module orthonym.assembly.handlers.amine module orthonym.assembly.handlers.anhydride module orthonym.assembly.handlers.azine module orthonym.assembly.handlers.boronic_acid module orthonym.assembly.handlers.carbamate module orthonym.assembly.handlers.carbamic_acid module orthonym.assembly.handlers.chalcogen_ester module orthonym.assembly.handlers.chalcogen_oxide module orthonym.assembly.handlers.cyanamide module orthonym.assembly.handlers.diamide module orthonym.assembly.handlers.ester_family module orthonym.assembly.handlers.general_acyclic module orthonym.assembly.handlers.guanidine module orthonym.assembly.handlers.hydrazone module orthonym.assembly.handlers.hydroxamic_acid module orthonym.assembly.handlers.hydroximic_acid module orthonym.assembly.handlers.hydroxylamine module orthonym.assembly.handlers.imidate module orthonym.assembly.handlers.imidoyl_thioyl_halide module orthonym.assembly.handlers.imine module orthonym.assembly.handlers.ion_dispatch module orthonym.assembly.handlers.isocyanate module orthonym.assembly.handlers.isothiocyanate module orthonym.assembly.handlers.lactam module orthonym.assembly.handlers.lactone module orthonym.assembly.handlers.n_oxide module orthonym.assembly.handlers.n_substituted_sulfonamide module orthonym.assembly.handlers.nitrate_ester module orthonym.assembly.handlers.nitrile_oxide module orthonym.assembly.handlers.nitrite_ester module orthonym.assembly.handlers.noncarbon_ester module orthonym.assembly.handlers.organometallic module orthonym.assembly.handlers.oxime module orthonym.assembly.handlers.partial_sat module orthonym.assembly.handlers.phosphate_ester module orthonym.assembly.handlers.phosphine module orthonym.assembly.handlers.phosphine_oxide module orthonym.assembly.handlers.phosphinic_acid module orthonym.assembly.handlers.phosphonic_acid module orthonym.assembly.handlers.pnictogen_inate_ester module orthonym.assembly.handlers.pnictogen_oxoacid module orthonym.assembly.handlers.polycyclic module orthonym.assembly.handlers.ring_assembly module orthonym.assembly.handlers.ring_ester module orthonym.assembly.handlers.ring_nitrile module orthonym.assembly.handlers.simple_molecule module orthonym.assembly.handlers.sulfate_ester module orthonym.assembly.handlers.sulfone module orthonym.assembly.handlers.sulfonimidic_n_hydroxy module orthonym.assembly.handlers.sulfonyl_halide module orthonym.assembly.handlers.sulfoxide module orthonym.assembly.handlers.thiocyanate module orthonym.assembly.handlers.thioether module orthonym.assembly.handlers.thiourea module orthonym.assembly.handlers.tier_a_ring module orthonym.assembly.handlers.urea module orthonym.assembly.inner_dispatch module orthonym.assembly.locant_omission module orthonym.assembly.memo module orthonym.assembly.name_comparison module orthonym.assembly.name_tree module orthonym.assembly.name_tree_builder module orthonym.assembly.name_tree_to_string module orthonym.assembly.naming_utils module orthonym.assembly.nested_memo module orthonym.assembly.offer_pool module orthonym.assembly.per_substring_scoring module orthonym.assembly.resolvers module orthonym.assembly.retained_substitution module orthonym.assembly.substituent_enumerator module orthonym.assembly.substituent_naming module orthonym.assembly.substituent_prefix_forms module orthonym.assembly.t4_coverage module orthonym.assembly.universal_substituent module orthonym.cli module orthonym.data module orthonym.data.amino_acids module orthonym.data.bicyclo_systems module orthonym.data.bluebook_not_names module orthonym.data.cation_words module orthonym.data.chain_names module orthonym.data.coordination_retained module orthonym.data.fused_heterocycles module orthonym.data.fusion_components module orthonym.data.group_split_rules module orthonym.data.hw_heteroatoms module orthonym.data.hw_stems module orthonym.data.ion_retained_names module orthonym.data.natural_products module orthonym.data.opsin_imports module orthonym.data.opsin_imports.amino_acids_opsin module orthonym.data.opsin_imports.aryl_groups module orthonym.data.opsin_imports.carbohydrates_opsin module orthonym.data.opsin_imports.carboxylic_acids_opsin module orthonym.data.opsin_imports.cyclic_groups module orthonym.data.opsin_imports.functional_terms module orthonym.data.opsin_imports.fusion_components_opsin module orthonym.data.opsin_imports.natural_products_opsin module orthonym.data.opsin_imports.simple_groups module orthonym.data.opsin_imports.substituent_names_opsin module orthonym.data.opsin_imports.suffix_rules module orthonym.data.opsin_imports.word_rules module orthonym.data.organometallics module orthonym.data.partial_saturation_refs module orthonym.data.pin_policy module orthonym.data.polycyclic_data module orthonym.data.resonance_templates module orthonym.data.retained_names module orthonym.data.sugar_names module orthonym.data.trivial_acids module

orthonym.data.triviality_controller_seed module orthonym.data.xanthine_derivatives module orthonym.decomposition module orthonym.decomposition.bond_cleavage module orthonym.decomposition.engine module orthonym.decomposition.fragment_assembly module orthonym.decomposition.fragment_capping module orthonym.decomposition.fragment_ranker module orthonym.decomposition.weave module orthonym.diagnostics module orthonym.errors module orthonym.jars module orthonym.jvm_bridge module orthonym.jvm_budget module orthonym.jvm_flags module orthonym.metrics module orthonym.metrics.abstention module orthonym.metrics.breadth module orthonym.metrics.candidate_ledger module orthonym.metrics.coverage_metrics module orthonym.metrics.provenance module orthonym.namer module orthonym.perception.automorphisms module orthonym.perception.centres_bridge module orthonym.perception.chains module orthonym.perception.functional_groups module orthonym.perception.ions module orthonym.perception.lambda_hydride module orthonym.perception.lipids module orthonym.perception.mancude module orthonym.perception.metals module orthonym.perception.molcache module orthonym.perception.natural_products module orthonym.perception.rings module orthonym.perception.smarts_cache module orthonym.perception.stereo module orthonym.perception.structure_conservation module orthonym.routing module orthonym.routing.dispatch_table module orthonym.routing.dispatcher module orthonym.rules module orthonym.rules.acid_ester_anion module orthonym.rules.acid_halides module orthonym.rules.added_carbon_parent module orthonym.rules.adducts module orthonym.rules.amides module orthonym.rules.amino_acids module orthonym.rules.anhydrides module orthonym.rules.benzene module orthonym.rules.bicyclo module orthonym.rules.bridged_fused module orthonym.rules.bridged_fused_pin module orthonym.rules.bridged_fused_pin.hydro module orthonym.rules.bridged_fused_pin.numbering module orthonym.rules.bridged_fused_pin.prefixes module orthonym.rules.bridged_fused_pin.selection module orthonym.rules.catenated_hydrides module orthonym.rules.charged_router module orthonym.rules.conjugate_controller module orthonym.rules.cycloalkanes module orthonym.rules.esters module orthonym.rules.functional_replacement module orthonym.rules.fused_ring_selection module orthonym.rules.fused_rings module orthonym.rules.fusion_descriptors module orthonym.rules.fusion_numbering module orthonym.rules.fusion_orientation module orthonym.rules.greek_stereo_descriptors module orthonym.rules.heterocycles module orthonym.rules.inorganic_acids module orthonym.rules.inositols module orthonym.rules.ions module orthonym.rules.isotopes module orthonym.rules.ketenes module orthonym.rules.lactams module orthonym.rules.lactones module orthonym.rules.lambda_convention module orthonym.rules.lipids module orthonym.rules.locant_validation module orthonym.rules.locants module orthonym.rules.mononuclear_hydrides module orthonym.rules.multiplicative module orthonym.rules.natural_products module orthonym.rules.nitramide module orthonym.rules.nitriles module orthonym.rules.nucleosides module orthonym.rules.oligosaccharides module orthonym.rules.organometallics module orthonym.rules.ortho_fused module orthonym.rules.p44_scorer module orthonym.rules.parent_correctness module orthonym.rules.parent_ranking module orthonym.rules.parent_selection module orthonym.rules.partial_saturation module orthonym.rules.peptides module orthonym.rules.phane module orthonym.rules.phosphorus module orthonym.rules.pin_vocabulary module orthonym.rules.polyazane module orthonym.rules.polychalcogen module orthonym.rules.polycyclic module orthonym.rules.polycyclic_bridged module orthonym.rules.polycyclic_von_baeyer module orthonym.rules.polycyclics module orthonym.rules.polyfunctional module orthonym.rules.polyol_polyester module orthonym.rules.pseudoketones module orthonym.rules.purine module orthonym.rules.purine_oxo module orthonym.rules.radicals module orthonym.rules.ring_assemblies module orthonym.rules.ring_chalcogen_oxide module orthonym.rules.ring_replacement module orthonym.rules.ring_selection module orthonym.rules.ring_substituents module orthonym.rules.ring_unsaturation module orthonym.rules.salts module orthonym.rules.seniority module orthonym.rules.skeletal_replacement module orthonym.rules.spiro module orthonym.rules.stereochemistry module orthonym.rules.steroid_stereo module orthonym.rules.substituent_purity module orthonym.rules.sulfonamides module orthonym.rules.sulfur module orthonym.rules.sulfur_oxoacid module orthonym.rules.terminal_fragment module orthonym.rules.terminal_ring module orthonym.rules.thioimides module orthonym.rules.tricyclo module orthonym.rules.vonbaeyer_universal module orthonym.runtime_tuning module orthonym.validation module orthonym.validation.atom_coverage module orthonym.validation.binding_spine module orthonym.validation.coverage_gate module orthonym.validation.dual_validator module orthonym.validation.e1_certificate module orthonym.validation.format_validator module orthonym.validation.name_morphemes module orthonym.validation.opsin_grammar module orthonym.validation.opsin_roundtrip module orthonym.validation.opsin_server module orthonym.validation.proof_ledger module orthonym.validation.protonation_identity module orthonym.validation.pubchem_validator module orthonym.validation.radical_identity module orthonym.validation.reconstruct module orthonym.wallclock module OrthonymLimitError, [1] OTHER (orthonym.metrics.abstention.AbstentionCode attribute) overflow (orthonym.rules.pin_vocabulary.PromotionProbe attribute) own_hang_budgets() (in module orthonym.assembly.fragment_naming) oxamoyl_branch_name() (in module orthonym.assembly.substituent_naming) oxo_ene_valence_illegal() (in module orthonym.perception.structure_conservation) oxo_prefix_parent_numberings() (in module orthonym.rules.partial_saturation)

P

p_section_cite (orthonym.assembly.group_splitting.SplitEvent attribute) (orthonym.assembly.retained_substitution.ControllerEvent attribute) PARACYCLOPHANE (orthonym.rules.phane.PhaneTopology attribute) parent (orthonym.rules.bridged_fused_pin.selection.Split attribute) PARENT (orthonym.validation.binding_spine.BindingKind attribute) parent_atom_indices (orthonym.assembly.coverage_scoring.CandidateName attribute) parent_atoms (orthonym.assembly.composer.HandlerResult attribute) (orthonym.rules.parent_selection.ParentSelectionResult attribute) parent_covered_atoms() (in module orthonym.assembly.composition_tier) parent_kind (orthonym.validation.reconstruct.NameFacts attribute) parent_label (orthonym.assembly.resolvers.ParentInfo attribute) parent_length (orthonym.validation.reconstruct.NameFacts attribute) parent_name (orthonym.rules.phane.Amplificant attribute) parent_pcg_count (orthonym.assembly.coverage_scoring.CandidateName attribute) parent_pool_size (orthonym.rules.parent_selection.ParentSelectionResult attribute) parent_scope_has_positional_isotope() (in module orthonym.assembly.locant_omission) parent_score (orthonym.assembly.per_substring_scoring.NodeScores attribute) parent_selection_result (orthonym.namer.MolecularFeatures attribute) parent_stem (orthonym.assembly.handlers.NameTreeNode attribute) (orthonym.assembly.name_tree.NameTreeNode attribute) parent_to_prefix() (in module orthonym.assembly.substituent_naming) parent_type (orthonym.assembly.resolvers.ParentInfo attribute) (orthonym.rules.parent_selection.ParentSelectionResult attribute) parent_word() (orthonym.rules.amides.RingAmideParts method) ParentCandidate (class in orthonym.rules.p44_scorer) (class in orthonym.rules.parent_ranking) ParentCorrectnessScorer (class in orthonym.rules.parent_correctness) parenthesization_hint (orthonym.assembly.handlers.NameTreeNode attribute) (orthonym.assembly.name_tree.NameTreeNode attribute) ParentInfo (class in orthonym.assembly.resolvers) ParentSelectionResult (class in orthonym.rules.parent_selection) PARITY (orthonym.metrics.coverage_metrics.Matcher attribute) parity (orthonym.metrics.coverage_metrics.RowResult attribute) parity_match() (in module orthonym.metrics.coverage_metrics) parse_centres_labels() (in module orthonym.perception.centres_bridge) parse_ester_fragments() (in module orthonym.rules.esters) parse_lambda_locant() (in module orthonym.assembly.name_comparison) parse_monocycle_replacement_name() (in module orthonym.rules.terminal_ring) parse_refusal_codes() (in module orthonym.metrics.breadth) parse_salt_fragments() (in module orthonym.perception.ions) parse_status() (orthonym.assembly.retained_substitution.OpsinOracle method) parse_suppressed_candidates() (in module orthonym.metrics.breadth) parse_von_baeyer_descriptor() (in module orthonym.rules.vonbaeyer_universal) parsed_heavy_atoms (orthonym.validation.atom_coverage.CoverageResult attribute) (orthonym.validation.CoverageResult attribute) parsed_inchikey (orthonym.validation.atom_coverage.CoverageResult attribute) (orthonym.validation.CoverageResult attribute) parsed_smiles (orthonym.validation.atom_coverage.CoverageResult attribute) (orthonym.validation.CoverageResult attribute) partial_sat_sp3_substituent_drop() (in module orthonym.perception.structure_conservation) PartialSatName (class in orthonym.rules.polycyclics) peek_abstention() (in module orthonym.metrics.abstention) PEPTIDE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) per_atom (orthonym.rules.ring_replacement.ReplacementPrefix attribute) PerfBudgetExceeded PerNodeScorer (class in orthonym.assembly.per_substring_scoring) PersistentOpsin (class in orthonym.validation.opsin_server) pg_count (orthonym.rules.p44_scorer.ParentCandidate attribute) PhaneStructure (class in orthonym.rules.phane) PhaneTopology (class in orthonym.rules.phane) PIN_ALLOW (in module orthonym.data.pin_policy) PIN_DENY (in module orthonym.data.pin_policy) PIN_DENY_HC (in module orthonym.data.pin_policy) pin_heteroaryl_substituent_name() (in module orthonym.rules.ring_substituents) pin_promotion_active() (in module orthonym.rules.pin_vocabulary) pin_promotion_var (in module orthonym.assembly.memo) PIN_VERIFIED (in module orthonym.assembly.offer_pool) PNICTOGEN_CARBOXYLIC_ACID (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute)

POLY_ANION (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) POLYAZANE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) POLYCHALCOGEN_OXIDE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) polycyclic_core_numbering() (in module orthonym.rules.ring_substituents) polycyclic_name (orthonym.namer.MolecularFeatures attribute) polycyclic_substituents (orthonym.namer.MolecularFeatures attribute) PolycyclicDescriptor (class in orthonym.rules.polycyclic) PolycyclicInfo (class in orthonym.rules.polycyclic_bridged) polyfunctional_substituent_located() (in module orthonym.assembly.substituent_naming) pool_candidates() (in module orthonym.rules.p44_scorer) pop_non_pin_log() (in module orthonym.metrics.provenance) pop_pool() (in module orthonym.assembly.candidate_pool) pop_sandbox() (in module orthonym.assembly.memo) pop_scope() (in module orthonym.assembly.memo) pop_touched_log() (in module orthonym.metrics.provenance) position_locants (orthonym.perception.lipids.BackboneMatch attribute) predicate (orthonym.assembly.handlers.InnerDispatchEntry attribute) (orthonym.assembly.inner_dispatch.InnerDispatchEntry attribute) (orthonym.routing.ClassDispatchEntry attribute) (orthonym.routing.dispatch_table.ClassDispatchEntry attribute) prefix (orthonym.assembly.substituent_enumerator.FreeValencePrefix attribute) (orthonym.rules.ring_replacement.ReplacementPrefix attribute) PREFIX (orthonym.validation.binding_spine.BindingKind attribute) prefix_citation_sort_key() (in module orthonym.assembly.naming_utils) prefix_form (orthonym.assembly.group_splitting.SplitComponent attribute) prefix_locant_order_key() (in module orthonym.assembly.composition_primitives) prefix_order_fallback (orthonym.assembly.universal_substituent.UniversalResult attribute) prefixes (orthonym.assembly.handlers.NameTreeNode attribute) (orthonym.assembly.name_tree.NameTreeNode attribute) prefixes_apart_var (in module orthonym.assembly.memo) principal_chain (orthonym.namer.MolecularFeatures attribute) principal_group (orthonym.namer.MolecularFeatures attribute) (orthonym.validation.reconstruct.NameFacts attribute) principal_group_atoms (orthonym.namer.MolecularFeatures attribute) principal_group_required (orthonym.data.triviality_controller_seed.SeedEntry attribute) principal_group_ring_atoms() (in module orthonym.rules.benzene) principal_ring (orthonym.namer.MolecularFeatures attribute) principal_ring_system (orthonym.rules.parent_selection.ParentSelectionResult attribute) principal_suffix() (in module orthonym.rules.bridged_fused_pin) priority (orthonym.assembly.candidate_pool.HandlerPolicy attribute) (orthonym.assembly.composer.NameFragment attribute) (orthonym.assembly.handlers.InnerDispatchEntry attribute) (orthonym.assembly.inner_dispatch.InnerDispatchEntry attribute) (orthonym.routing.ClassDispatchEntry attribute) (orthonym.routing.dispatch_table.ClassDispatchEntry attribute) process_cache_stats() (in module orthonym.assembly.memo) PRODUCED (orthonym.metrics.candidate_ledger.Stage attribute) promote_at_pin_tier() (in module orthonym.rules.pin_vocabulary) promotion_could_change() (in module orthonym.rules.pin_vocabulary) promotion_site_probe() (in module orthonym.rules.pin_vocabulary) PromotionProbe (class in orthonym.rules.pin_vocabulary) protonation_site_verdict() (in module orthonym.validation.protonation_identity) PSEUDOKETONE_HETERO (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) pubchem_inchi (orthonym.validation.dual_validator.DualResult attribute) (orthonym.validation.DualResult attribute) pubchem_resolved (orthonym.validation.dual_validator.DualResult attribute) (orthonym.validation.DualResult attribute) pubchem_rt (orthonym.validation.dual_validator.DualResult attribute) (orthonym.validation.DualResult attribute) pure_cache_or_compute() (in module orthonym.assembly.memo) push_non_pin_log() (in module orthonym.metrics.provenance) push_pool() (in module orthonym.assembly.candidate_pool) push_sandbox() (in module orthonym.assembly.memo) push_scope() (in module orthonym.assembly.memo) push_touched_log() (in module orthonym.metrics.provenance)

R

RADICAL (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) radical_identity_verdict() (in module orthonym.validation.radical_identity) radical_profile() (in module orthonym.validation.radical_identity) radical_sites (orthonym.namer.MolecularFeatures attribute) rank (orthonym.rules.parent_ranking.ParentCandidate attribute) rank_fragments() (in module orthonym.decomposition.fragment_ranker) rank_offers() (in module orthonym.assembly.offer_pool) rank_parent_candidates() (in module orthonym.rules.parent_ranking) read_ledger() (in module orthonym.metrics.candidate_ledger) rearm_hang_budgets() (in module orthonym.assembly.fragment_naming) reason (orthonym.validation.e1_certificate.E1Verdict attribute) (orthonym.validation.reconstruct.ReconResult attribute) reasoning (orthonym.rules.parent_selection.ParentSelectionResult attribute) recognize_sugar_skeleton() (in module orthonym.data.sugar_names) reconcile_multiplier_count() (in module orthonym.rules.locant_validation) ReconResult (class in orthonym.validation.reconstruct) reconstruct_and_verify() (in module orthonym.validation.reconstruct) reconstruct_von_baeyer_skeleton() (in module orthonym.rules.vonbaeyer_universal) reconstructed_smiles (orthonym.validation.reconstruct.ReconResult attribute) record_abstention() (in module orthonym.metrics.abstention) record_amine_cation_prefix() (in module orthonym.assembly.substituent_naming) record_beyond_pin_caps() (in module orthonym.rules.vonbaeyer_universal) record_candidate() (in module orthonym.metrics.candidate_ledger) record_derived_non_pin_fragment() (in module orthonym.metrics.provenance) record_gate_outcome() (in module orthonym.metrics.provenance) record_general_ring_prefix() (in module orthonym.metrics.provenance) record_if_non_pin_amino_acid_name() (in module orthonym.data.amino_acids) record_non_pin_fragment() (in module orthonym.metrics.provenance) record_non_pin_label() (in module orthonym.metrics.provenance) record_pin_promotion_rerun() (in module orthonym.metrics.provenance) record_polyacid_monoester_non_pin() (in module orthonym.rules.esters) record_prefix_from_acid_status() (in module orthonym.assembly.substituent_naming) record_source() (in module orthonym.metrics.provenance) record_spine() (in module orthonym.validation.proof_ledger) record_stereo_unexpressed() (in module orthonym.metrics.provenance) record_suffix_free_prefix_name() (in module orthonym.metrics.provenance) record_suppression() (in module orthonym.metrics.abstention) record_uncertified_pin_name() (in module orthonym.metrics.provenance) refusal_structure() (in module orthonym.metrics.breadth) register_retained_name() (in module orthonym.data) render_ring_unsaturation() (in module orthonym.rules.ring_unsaturation) renest_group_and_ancestors() (in module orthonym.assembly.naming_utils) REPLACEMENT (orthonym.validation.binding_spine.BindingKind attribute) ReplacementPrefix (class in orthonym.rules.ring_replacement) replacements (orthonym.validation.reconstruct.NameFacts attribute) require_all() (in module orthonym.jars) requires_added_carbon_suffix() (in module orthonym.rules.added_carbon_parent) reset_dispatch_stats() (in module orthonym.routing) (in module orthonym.routing.dispatcher) (orthonym.namer.Orthonym method) (orthonym.routing.ClassFirstRouter method) (orthonym.routing.dispatcher.ClassFirstRouter method) reset_inner_dispatch_stats() (in module orthonym.assembly.inner_dispatch) reset_naming_state() (in module orthonym.wallclock) reset_t4_floor_substitute() (in module orthonym.assembly.t4_coverage) reset_verify_mismatches() (in module orthonym.assembly.memo) residual (orthonym.rules.bridged_fused_pin.selection.Split attribute) residual_refusal_code() (in module orthonym.metrics.breadth) resolve_gate_outcome() (in module orthonym.metrics.provenance)

resolve_parent() (in module orthonym.assembly.resolvers) resolve_suffix() (in module orthonym.assembly.resolvers) resolve_suffix_prefix_collision() (in module orthonym.assembly.composition_primitives) resolves_via (orthonym.data.group_split_rules.SplitComponent attribute) ResonanceChainTemplate (class in orthonym.data.resonance_templates) restore_provenance() (in module orthonym.metrics.provenance) result (orthonym.assembly.inner_dispatch.InnerDispatchResult attribute) result_obj (orthonym.assembly.offer_pool.Offer attribute) retained (orthonym.rules.amides.RingAmideParts attribute) RETAINED_NAME (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) retained_pin_carboxylic_acid() (in module orthonym.data.trivial_acids) retained_pin_name (orthonym.data.triviality_controller_seed.SeedEntry attribute) retained_von_baeyer_parent() (in module orthonym.rules.polycyclic) retrieve_confidence() (in module orthonym.assembly.coverage_scoring) ring_amide_parts() (in module orthonym.rules.amides) ring_anchored_pg_atoms() (in module orthonym.assembly.composer) RING_ASSEMBLY (orthonym.rules.ring_selection.RingSystemType attribute) ring_assembly_info (orthonym.namer.MolecularFeatures attribute) ring_atom_fg_prefixes() (in module orthonym.rules.ring_substituents) ring_atom_indices (orthonym.perception.metals.MetallacycleInfo attribute) ring_atoms (orthonym.assembly.composer.ComplexRingResult attribute) ring_atoms_ordered (orthonym.rules.phane.Amplificant attribute) RING_CHALCOGEN_OXIDE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) ring_count (orthonym.rules.polycyclic.PolycyclicDescriptor attribute) (orthonym.rules.polycyclic_bridged.PolycyclicInfo attribute) ring_count_neg (orthonym.rules.fused_ring_selection.ComponentRank attribute) ring_double_bond_locant() (in module orthonym.rules.cycloalkanes) ring_double_bond_locants (orthonym.namer.MolecularFeatures attribute) ring_double_bonds (orthonym.namer.MolecularFeatures attribute) ring_hydride (orthonym.rules.amides.RingAmideParts attribute) ring_info (orthonym.assembly.coverage_scoring.CandidateName attribute) ring_principal_suffix_atoms() (in module orthonym.rules.heterocycles) ring_sizes_neg (orthonym.rules.fused_ring_selection.ComponentRank attribute) ring_skeleton_key() (in module orthonym.data.fused_heterocycles) ring_substituents (orthonym.namer.MolecularFeatures attribute) ring_substituents_as_groups (orthonym.namer.MolecularFeatures attribute) ring_system() (in module orthonym.rules.bridged_fused_pin.selection) ring_system_score() (in module orthonym.rules.ring_selection) ring_systems (orthonym.namer.MolecularFeatures attribute) ring_systems() (in module orthonym.metrics.breadth) (in module orthonym.rules.bridged_fused_pin.selection) ring_type (orthonym.namer.MolecularFeatures attribute) ring_unsaturation() (in module orthonym.rules.bridged_fused_pin.selection) RingAmideParts (class in orthonym.rules.amides) RingAnalysis (class in orthonym.rules.vonbaeyer_universal) RingSystemType (class in orthonym.rules.ring_selection) RingUnsaturation (class in orthonym.rules.ring_unsaturation) role (orthonym.assembly.general_engine.TokenBinding attribute) (orthonym.assembly.group_splitting.SplitComponent attribute) (orthonym.data.group_split_rules.SplitComponent attribute) roots (orthonym.validation.binding_spine.BindingSpine attribute) route_charged() (in module orthonym.rules.charged_router) row_attribution() (in module orthonym.metrics.breadth) RowClassification (class in orthonym.metrics.coverage_metrics) RowResult (class in orthonym.metrics.coverage_metrics) rt_oracle_result (orthonym.assembly.group_splitting.SplitEvent attribute) (orthonym.assembly.retained_substitution.ControllerEvent attribute) rt_safe() (orthonym.assembly.retained_substitution.OpsinOracle method) RT_VALID (orthonym.metrics.coverage_metrics.RowClassification attribute)

S

S1_PARENT_SKELETONS (in module orthonym.rules.bridged_fused_pin.selection) SALT (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) saturated (orthonym.rules.bridged_fused_pin.hydro.HydroState attribute) save_cache() (in module orthonym.validation) (in module orthonym.validation.pubchem_validator) Scope (class in orthonym.metrics.candidate_ledger) scope (orthonym.metrics.candidate_ledger.LedgerEntry attribute) scope_forces_locants() (in module orthonym.assembly.locant_omission) scope_has_isotopic_modification() (in module orthonym.assembly.locant_omission) score() (orthonym.rules.parent_correctness.ParentCorrectnessScorer static method) score_fragment_seniority() (in module orthonym.decomposition.fragment_ranker) score_orientation() (in module orthonym.rules.fusion_orientation) score_orientation_general() (in module orthonym.rules.fusion_orientation) score_tree() (orthonym.assembly.per_substring_scoring.PerNodeScorer static method) secondary_bridges (orthonym.rules.polycyclic_bridged.PolycyclicInfo attribute) seed_entry_name (orthonym.assembly.retained_substitution.ControllerEvent attribute) SeedEntry (class in orthonym.data.triviality_controller_seed) select_base_component() (in module orthonym.rules.fused_ring_selection) select_best_candidate() (in module orthonym.assembly.coverage_scoring) select_ligand_naming() (in module orthonym.rules.organometallics) select_lowest_locant_match() (in module orthonym.data.fused_heterocycles) select_offer() (in module orthonym.assembly.offer_pool) select_parent() (in module orthonym.rules.parent_selection) select_parent_unified() (in module orthonym.rules.p44_scorer) select_principal_ring_system() (in module orthonym.rules.ring_selection) select_ring_or_chain_parent() (in module orthonym.rules.cycloalkanes) select_rt_passing() (in module orthonym.assembly.offer_pool) senior_het_neg (orthonym.rules.fused_ring_selection.ComponentRank attribute) senior_ring_system (orthonym.namer.MolecularFeatures attribute) set_reference_name() (in module orthonym.rules.parent_correctness) severity (orthonym.validation.binding_spine.Finding attribute) sha256 (orthonym.jars.JarSpec attribute) should_omit_locant_one() (in module orthonym.assembly.naming_utils) side_effect_inventory (orthonym.assembly.handlers.InnerDispatchEntry attribute) (orthonym.assembly.inner_dispatch.InnerDispatchEntry attribute) (orthonym.routing.ClassDispatchEntry attribute) (orthonym.routing.dispatch_table.ClassDispatchEntry attribute) side_get() (in module orthonym.assembly.memo) side_put() (in module orthonym.assembly.memo) simple_multiplier_word() (in module orthonym.assembly.naming_utils) site (orthonym.metrics.candidate_ledger.LedgerEntry attribute) sites (orthonym.perception.lipids.BackboneMatch attribute) (orthonym.rules.pin_vocabulary.PromotionProbe attribute) SKELETAL_REPLACEMENT (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) skeleton_automorphisms() (in module orthonym.perception.automorphisms) skeleton_class (orthonym.rules.phane.PhaneStructure attribute) SkeletonClass (class in orthonym.rules.phane) slot_dir() (in module orthonym.jvm_budget) smiles (orthonym.metrics.coverage_metrics.RowResult attribute) (orthonym.namer.MolecularFeatures attribute) sort_heteroatoms_by_priority() (in module orthonym.data.hw_heteroatoms) source (orthonym.assembly.offer_pool.Offer attribute) species_type (orthonym.namer.MolecularFeatures attribute) speculative_fragment_naming() (in module orthonym.assembly.fragment_naming) spelled_offring_atoms (orthonym.rules.polycyclics.PartialSatName attribute) spend_analysis_call() (in module orthonym.assembly.fragment_naming) spend_fragment_work() (in module orthonym.assembly.fragment_naming) spend_perf_work() (in module orthonym.assembly.fragment_naming) SpineBinding (class in orthonym.validation.binding_spine) SpineProof (class in orthonym.validation.binding_spine) SPIRO (orthonym.rules.phane.SkeletonClass attribute) (orthonym.rules.ring_selection.RingSystemType attribute) SpiroSystem (class in orthonym.rules.vonbaeyer_universal) Split (class in orthonym.rules.bridged_fused_pin.selection) split_components() (in module orthonym.rules.adducts)

split_composite_fg() (in module orthonym.assembly.group_splitting) SplitComponent (class in orthonym.assembly.group_splitting) (class in orthonym.data.group_split_rules) SplitEvent (class in orthonym.assembly.group_splitting) SplitRule (class in orthonym.data.group_split_rules) Stage (class in orthonym.metrics.candidate_ledger) stage (orthonym.metrics.candidate_ledger.LedgerEntry attribute) start_bh (orthonym.rules.polycyclic.BridgeInfo attribute) (orthonym.rules.polycyclic_bridged.BridgeInfo attribute) start_naming_session() (in module orthonym.assembly.fragment_naming) starts_with_locant() (in module orthonym.assembly.naming_utils) STAT_KEYS (orthonym.routing.ClassFirstRouter attribute) (orthonym.routing.dispatcher.ClassFirstRouter attribute) (orthonym.validation.opsin_grammar.OpsinGrammar attribute) (orthonym.validation.OpsinGrammar attribute) stats (orthonym.validation.binding_spine.SpineProof attribute) status() (in module orthonym.jvm_budget) stereo (orthonym.assembly.handlers.NameTreeNode attribute) (orthonym.assembly.name_tree.NameTreeNode attribute) stereo_atom_to_locant (orthonym.assembly.general_engine.GeneralEngineResult attribute) (orthonym.validation.binding_spine.BindingSpine attribute) stereo_in_key (orthonym.data.triviality_controller_seed.SeedEntry attribute) stereocenters (orthonym.namer.MolecularFeatures attribute) store_confidence() (in module orthonym.assembly.coverage_scoring) StoutClass (class in orthonym.routing) (class in orthonym.routing.dispatch_table) STRICT (orthonym.metrics.coverage_metrics.Matcher attribute) strict (orthonym.metrics.coverage_metrics.RowResult attribute) strict_match() (in module orthonym.metrics.coverage_metrics) strict_mode() (in module orthonym.diagnostics) strip_alphanumerical_noise() (in module orthonym.assembly.naming_utils) strip_isotopes() (in module orthonym.rules.isotopes) strip_italicized_structural_prefix() (in module orthonym.assembly.naming_utils) strip_jvm_noise() (in module orthonym.jvm_flags) strip_stereo() (in module orthonym.rules.stereochemistry) strip_stereo_blocks() (in module orthonym.rules.stereochemistry) substituent_rings (orthonym.rules.parent_selection.ParentSelectionResult attribute) substituent_score (orthonym.assembly.per_substring_scoring.NodeScores attribute) SubstituentInfo (class in orthonym.assembly.substituent_enumerator) substituents (orthonym.namer.MolecularFeatures attribute) (orthonym.validation.reconstruct.NameFacts attribute) substituents_included (orthonym.assembly.composer.ComplexRingResult attribute) substitutable_h_count() (in module orthonym.assembly.locant_omission) substitutable_positions() (in module orthonym.assembly.locant_omission) substitution_type (orthonym.assembly.retained_substitution.ControllerEvent attribute) (orthonym.data.triviality_controller_seed.SeedEntry attribute) SubstitutionType (class in orthonym.data.triviality_controller_seed) subtree_atoms() (orthonym.validation.binding_spine.SpineBinding method) suffix (orthonym.assembly.handlers.NameTreeNode attribute) (orthonym.assembly.name_tree.NameTreeNode attribute) (orthonym.rules.amides.RingAmideParts attribute) SUFFIX (orthonym.validation.binding_spine.BindingKind attribute) suffix_nitrogen_hydrogens_are_caps() (in module orthonym.assembly.locant_omission) suffix_takes_derived_multiplier() (in module orthonym.assembly.naming_utils) SuffixInfo (class in orthonym.assembly.resolvers) sugar_to_glycoside_class_name() (in module orthonym.data.sugar_names) sugar_to_glycosyl_prefix() (in module orthonym.data.sugar_names) sugar_to_glycosyloxy_prefix() (in module orthonym.data.sugar_names) suggest_fix() (orthonym.validation.opsin_grammar.OpsinGrammar method) (orthonym.validation.OpsinGrammar method) SULFINE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) sulfino_hydrazonoyl_amido_prefix_from_branch() (in module orthonym.assembly.substituent_naming) sulfonamido_prefix_from_n_branch() (in module orthonym.assembly.substituent_naming) SUPERSEDED (orthonym.metrics.candidate_ledger.Stage attribute) SUPPRESSED (orthonym.metrics.candidate_ledger.Stage attribute) system_type (orthonym.rules.polycyclic_bridged.PolycyclicInfo attribute)

T

terminal_basis_available() (in module orthonym.metrics.breadth) terminal_fragment_name() (in module orthonym.rules.terminal_fragment) TERMINAL_RING_ASSEMBLY_SITE (in module orthonym.assembly.general_engine) terminal_ring_name() (in module orthonym.rules.terminal_ring) TERMINAL_RING_PARENT_SITE (in module orthonym.assembly.general_engine) terminal_site() (in module orthonym.metrics.breadth) terminal_stage() (in module orthonym.metrics.breadth) TerminalFragmentName (class in orthonym.rules.terminal_fragment) TerminalRingName (class in orthonym.rules.terminal_ring) text (orthonym.assembly.composer.NameFragment attribute) (orthonym.assembly.resolvers.SuffixInfo attribute) text() (orthonym.rules.bridged_fused_pin.BridgedParent method) text_without_locants (orthonym.assembly.composer.NameFragment attribute) THIOIMIDE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) tier (orthonym.assembly.candidate_pool.HandlerPolicy attribute) (orthonym.assembly.offer_pool.Offer attribute) (orthonym.routing.ClassDispatchEntry attribute) (orthonym.routing.ClassDispatchResult attribute) (orthonym.routing.dispatch_table.ClassDispatchEntry attribute) (orthonym.routing.dispatch_table.ClassDispatchResult attribute) token (orthonym.assembly.general_engine.TokenBinding attribute) (orthonym.validation.binding_spine.SpineBinding attribute) token_arity() (in module orthonym.validation.name_morphemes)

TokenBinding (class in orthonym.assembly.general_engine) total_atoms (orthonym.rules.polycyclic.PolycyclicDescriptor attribute) (orthonym.rules.vonbaeyer_universal.RingAnalysis attribute) total_charge (orthonym.namer.MolecularFeatures attribute) total_heavy_atoms (orthonym.assembly.composer.HandlerResult attribute) (orthonym.validation.atom_coverage.CoverageResult attribute) (orthonym.validation.CoverageResult attribute) total_slots() (in module orthonym.jvm_budget) tree (orthonym.assembly.coverage_scoring.CandidateName attribute) (orthonym.assembly.handlers.NamingResult attribute) (orthonym.assembly.name_tree.NamingResult attribute) triple_bonds (orthonym.namer.MolecularFeatures attribute) triple_locants (orthonym.rules.ring_unsaturation.RingUnsaturation attribute) triple_pairs (orthonym.rules.ring_unsaturation.RingUnsaturation attribute) try_decompose() (in module orthonym.decomposition) (in module orthonym.decomposition.engine) try_skeletal_replacement_name() (in module orthonym.rules.skeletal_replacement) try_weave() (in module orthonym.decomposition.weave) tune_batch_process() (in module orthonym.runtime_tuning) TYPE_1 (orthonym.data.triviality_controller_seed.SubstitutionType attribute) TYPE_2A (orthonym.data.triviality_controller_seed.SubstitutionType attribute) TYPE_2B (orthonym.data.triviality_controller_seed.SubstitutionType attribute) TYPE_2C (orthonym.data.triviality_controller_seed.SubstitutionType attribute) TYPE_3 (orthonym.data.triviality_controller_seed.SubstitutionType attribute)

U

unbranched_alkylidene_name() (in module orthonym.assembly.naming_utils) unclaimed_atom_indices (orthonym.validation.atom_coverage.CoverageResult attribute) (orthonym.validation.CoverageResult attribute) unclaimed_atoms (orthonym.validation.atom_coverage.CoverageResult attribute) (orthonym.validation.CoverageResult attribute) uncovered_fragments() (in module orthonym.assembly.composition_tier) unexpressed (orthonym.rules.ring_replacement.ReplacementPrefix attribute) UNIT_TERMS (in module orthonym.data.chain_names) UniversalCage (class in orthonym.rules.vonbaeyer_universal) UniversalResult (class in orthonym.assembly.universal_substituent) unmeasured_confidence() (in module orthonym.assembly.coverage_scoring)

UnnameableSubstituentError UNPARSEABLE (orthonym.metrics.coverage_metrics.RowClassification attribute) unsaturated (orthonym.rules.bridged_fused_pin.selection.Split attribute) unsaturation (orthonym.rules.vonbaeyer_universal.RingAnalysis attribute) unsaturation_locants (orthonym.assembly.handlers.NameTreeNode attribute) (orthonym.assembly.name_tree.NameTreeNode attribute) unsaturations (orthonym.validation.reconstruct.NameFacts attribute) unsupported_element_branch() (in module orthonym.errors) unsupported_ring_system() (in module orthonym.errors) url (orthonym.jars.JarSpec attribute) uronic_free_acid_name() (in module orthonym.data.sugar_names) uronic_glycoside_head() (in module orthonym.data.sugar_names)

V

validate() (orthonym.validation.opsin_grammar.OpsinGrammar method) (orthonym.validation.OpsinGrammar method) validate_atom_coverage() (in module orthonym.validation) (in module orthonym.validation.atom_coverage) validate_batch() (in module orthonym.validation.dual_validator) validate_binding_proof() (in module orthonym.namer) validate_compound() (in module orthonym.validation) (in module orthonym.validation.dual_validator) validate_name_format() (in module orthonym.validation) (in module orthonym.validation.format_validator) validate_stereo_locants() (in module orthonym.rules.locant_validation) validate_suffix_locants() (in module orthonym.rules.locant_validation) vb_lambda_for_atom() (in module orthonym.rules.ring_replacement)

Verdict (class in orthonym.validation.reconstruct) verdict (orthonym.validation.reconstruct.ReconResult attribute) verify_atom_coverage() (in module orthonym.validation.e1_certificate) verify_certificate() (in module orthonym.validation.e1_certificate) verify_mismatch_count() (in module orthonym.assembly.memo) verify_or_none() (in module orthonym.validation.reconstruct) verify_spine() (in module orthonym.validation.binding_spine) version (orthonym.jars.JarSpec attribute) VON_BAEYER (orthonym.rules.phane.SkeletonClass attribute) (orthonym.rules.ring_selection.RingSystemType attribute) von_baeyer_ring_count() (in module orthonym.rules.polycyclic) vonbaeyer_cage_has_aromaticity() (in module orthonym.rules.polycyclic) VonBaeyerAnalyzer (class in orthonym.rules.polycyclic)

W

walk() (orthonym.validation.binding_spine.BindingSpine method) (orthonym.validation.binding_spine.SpineBinding method)

wall_clock_limit (class in orthonym.wallclock) WallClockTimeout weave_is_verified() (in module orthonym.decomposition.weave)

Y

YLIDE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute)

Z

ZWITTERION (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute)