Index

A

A_CHAIN_ENDS (in module orthonym.assembly.book_prefixes) a_chain_licensed() (in module orthonym.assembly.book_prefixes) 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) accepted_charge_forms() (in module orthonym.perception.charge_shift) accommodate() (in module orthonym.rules.bridged_fused_pin.hydro) 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) acid_split_outcome() (in module orthonym.metrics.provenance) active (orthonym.rules.pin_vocabulary.PromotionProbe attribute) ACYCLIC (orthonym.rules.phane.SkeletonClass attribute) acyclic_branch_on_nitrogen() (in module orthonym.rules.n_branch) acyclic_n_parent() (in module orthonym.assembly.capped_name) 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_derivation() (in module orthonym.assembly.book_prefixes) acyl_group_prefix() (in module orthonym.assembly.book_prefixes) acyl_prefix_for() (in module orthonym.rules.functional_replacement) acyl_prefix_from_branch() (in module orthonym.assembly.substituent_naming) acyl_prefix_text() (in module orthonym.assembly.acyl_prefix) acyl_side_atoms() (in module orthonym.assembly.book_prefixes) acylated_ring_nitrogen() (in module orthonym.assembly.strict_ring_prefix) acylhydrazide (orthonym.assembly.hetero_group_prefixes.GroupShape attribute) 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) added (orthonym.rules.ring_hydrogen.RingHydrogen attribute) added_ih_groups() (in module orthonym.validation.spelling.indicated_hydrogen) added_text() (in module orthonym.rules.ring_hydrogen) adj (orthonym.rules.bridged_fused_pin.hydro.HydroState attribute) admit_core() (orthonym.assembly.strict_ring_prefix.StrictRingPolicy method) admitted_metal_atom_name() (in module orthonym.rules.metal_atoms) 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) alphanumerical_order_check() (in module orthonym.validation.spelling.checks_marks) alt_het_tuple (orthonym.rules.fused_ring_selection.ComponentRank attribute) ambient_naming_state() (in module orthonym.assembly.nested_memo) ambiguity_messages() (in module orthonym.validation.opsin_ambiguity) AMBIGUITY_WARNING (in module orthonym.validation.opsin_ambiguity) amide_n_substituent_block() (in module orthonym.decomposition.amide_n_substituents) amide_type (orthonym.namer.MolecularFeatures attribute) amide_with_c_locant() (in module orthonym.decomposition.amide_c_locant) amido_n_has_substituent() (in module orthonym.rules.inorganic_acids) amine_parent_ok() (in module orthonym.assembly.strict_ring_prefix) amine_parent_tie() (in module orthonym.perception.chains) amine_promotion() (in module orthonym.rules.n_branch) amine_ring_parent_check() (in module orthonym.validation.spelling.checks_amine_parent) AMINO_ACID (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) AMMINE_COMPONENT_NAMES (in module orthonym.rules.metal_atoms) ammine_component_names() (in module orthonym.rules.metal_atoms) Amplificant (class in orthonym.rules.phane) amplificants (orthonym.rules.phane.PhaneStructure attribute) analyse() (in module orthonym.validation.spelling.indicated_hydrogen) 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) anhydride_acids_round_trip() (in module orthonym.validation.anhydride_acids) ANHYDRIDE_ACIDS_RULE (in module orthonym.validation.anhydride_acids) anilino_for_branches() (in module orthonym.rules.anilino_nitrogen)

anilino_preferred_prefix() (in module orthonym.rules.ring_substituents) anilino_prefix_check() (in module orthonym.validation.spelling.checks_prefixes) anilino_prefix_from_aniline_name() (in module orthonym.rules.ring_substituents) anilino_prefix_from_n_branch() (in module orthonym.rules.ring_substituents) anion (orthonym.validation.thioperoxol_twin.ThioperoxolTwin attribute) anion_equals_another_secondary_amine() (in module orthonym.rules.amine_anion_symmetry) ANION_PARENT_NAME (in module orthonym.rules.porphyrin) 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) append_missing() (in module orthonym.metrics.provenance) append_relative_stereo_offer() (in module orthonym.rules.relative_stereo) 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) arm_is_acyl() (in module orthonym.rules.amine_anion_label) aromatic_view() (in module orthonym.rules.monocycle_forms) aromatic_with_exocyclic_double_bond() (in module orthonym.assembly.strict_ring_prefix) as_dict() (orthonym.errors.OrthonymLimitError method) as_prefix (orthonym.validation.spelling.linear_phane.LinearPhaneVerdict attribute) assemble_fragment_name() (in module orthonym.decomposition.fragment_assembly) 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) assembly_admits_macrocycle() (in module orthonym.rules.metal_macrocycles) assembly_component_enclosure_check() (in module orthonym.validation.spelling.checks_marks) ASSEMBLY_HEAD (in module orthonym.validation.spelling.checks_assembly) assembly_indicated_hydrogen_check() (in module orthonym.validation.spelling.checks_hydrogen) assign_stereochemistry() (in module orthonym.perception.stereo) at_pin_tier() (in module orthonym.rules.pin_vocabulary) atom (orthonym.assembly.universal_halane.HalaneUnit attribute) (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.assembly.hetero_group_prefixes.GroupPart attribute) (orthonym.rules.bridged_fused_pin.fusion_components.Component attribute) (orthonym.rules.p44_scorer.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_of() (in module orthonym.perception.molcache) attach (orthonym.assembly.hetero_group_prefixes.GroupPart attribute) 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) azide_atoms() (in module orthonym.perception.charge_shift) AZINIC_DERIVATIVE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) azolium_demote_name() (in module orthonym.rules.azolium_cations) azolium_hydron_centres() (in module orthonym.rules.azolium_cations) azolium_hydron_site_name() (in module orthonym.rules.azolium_cations) azolium_zwitterion_name() (in module orthonym.rules.azolium_cations)

B

backbone_atom_to_locant (orthonym.perception.lipids.BackboneMatch attribute) BackboneMatch (class in orthonym.perception.lipids) bare_hydrogen_groups() (in module orthonym.validation.twin_spellings) bare_letter_allowed() (in module orthonym.rules.isotope_letters) bare_oxophosphanyl_oxy_prefix() (in module orthonym.rules.phosphorus) bare_ring_assembly_info() (in module orthonym.assembly.ring_assembly_fragment) base (orthonym.rules.bridged_fused_pin.BridgedParent attribute) base_form() (in module orthonym.rules.bridged_fused_pin.fusion_components) 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) BB_PARENTS (in module orthonym.rules.bridged_fused_pin.parent_table) beats() (in module orthonym.assembly.form_choice) 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) benzo_hw_name() (in module orthonym.rules.halogen_ring_fusion) benzo_name() (in module orthonym.rules.bridged_fused_pin.fusion_components) benzo_numberings() (in module orthonym.rules.bridged_fused_pin.fusion_components) best() (orthonym.assembly.candidate_pool.CandidatePool method) BEST_EFFORT_MAX_CAGE_ATOMS (in module orthonym.rules.vonbaeyer_universal) BEST_EFFORT_MAX_UNION_RINGS (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) bis_before_simple_component_check() (in module orthonym.validation.spelling.checks_marks) blank() (in module orthonym.failure_mode) blocks() (in module orthonym.validation.spelling.indicated_hydrogen) bond (orthonym.data.group_split_rules.SplitComponent attribute) bond_ids (orthonym.validation.binding_spine.SpineBinding attribute) bond_loc() (in module orthonym.validation.spelling.models) bond_orders (orthonym.data.resonance_templates.ResonanceChainTemplate attribute) bonds (orthonym.assembly.ring_ylidene_stereo.RingYlidene attribute) bonds_of() (in module orthonym.perception.molcache) book_forms_enabled() (in module orthonym.assembly.book_prefixes) book_forms_fired (orthonym.assembly.universal_substituent.UniversalResult attribute) book_forms_kinds (orthonym.assembly.universal_substituent.UniversalResult attribute) book_forms_minus() (in module orthonym.assembly.book_prefixes) book_forms_var (in module orthonym.assembly.memo) bound_checks (orthonym.rules.main_ring_paths.RingGraph attribute) bound_cuts (orthonym.rules.main_ring_paths.RingGraph attribute)

bound_is_useless() (orthonym.rules.main_ring_paths.RingGraph method) BOUND_MIN_CHECKS (in module orthonym.rules.main_ring_paths) bracket_depths() (in module orthonym.assembly.naming_utils) branch_carriers() (in module orthonym.rules.monocycle_forms) BRANCH_FALLBACK (in module orthonym.assembly.substituent_naming) 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_prefix_words() (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) bridging_group_reaches() (in module orthonym.rules.parent_selection) 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_fused() (in module orthonym.rules.bridged_fused_pin) build_fused_substituent() (in module orthonym.rules.bridged_fused_pin) build_hw_name() (in module orthonym.rules.heterocycles) build_imidic_ester_name() (in module orthonym.assembly.handlers.imidic_ester) 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_substituent() (in module orthonym.rules.bridged_fused_pin) build_systematic_fusion_name() (in module orthonym.rules.fusion_descriptors) builder_declining_on_error() (in module orthonym.rules.bridged_fused) built() (in module orthonym.assembly.prefix_derivation) BUILTIN_CHECK_MODULES (in module orthonym.validation.pin_spelling) butan_2_yl_check() (in module orthonym.validation.spelling.checks_prefixes)

C

cache_key() (in module orthonym.validation.read_back_policy) 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) caches() (in module orthonym.perception.molcache) cage_atoms (orthonym.rules.vonbaeyer_universal.RingAnalysis attribute) cage_caps() (in module orthonym.rules.vonbaeyer_universal) cage_core_ok() (in module orthonym.assembly.strict_ring_prefix) 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) canonical_smiles_keeping_the_reading() (in module orthonym.perception.lone_pair_reading) capped_probe_ctx (in module orthonym.rules.centre_ligands) carbohydrate_core() (in module orthonym.assembly.strict_ring_prefix) 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) carried() (in module orthonym.assembly.prefix_derivation) (in module orthonym.metrics.producer_trail) carries_capped_locants() (in module orthonym.assembly.capped_name) carries_hydro_prefix() (in module orthonym.assembly.naming_utils) carveout_outcome() (in module orthonym.metrics.provenance) cascade_locant() (in module orthonym.rules.locants) CASCADE_REFUSAL (in module orthonym.errors) CascadeRefusal (class in orthonym.errors) catalogue_benzo_name() (in module orthonym.rules.fusion_descriptors) 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) cationic_parent_centres() (in module orthonym.assembly.form_choice) centre_ligand_prefixes() (in module orthonym.rules.centre_ligands) centre_name() (in module orthonym.rules.centre_ligands) 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_methyl_check() (in module orthonym.validation.spelling.checks_prefixes) chain_parent_prefix_seniority() (in module orthonym.perception.chains) chain_prefix_positions() (in module orthonym.assembly.chain_prefix_positions) chain_stem_ending() (in module orthonym.assembly.capped_name) chain_symmetry_key() (in module orthonym.perception.chains) chain_vector() (in module orthonym.data.resonance_templates) CHALCOGEN_CHAIN (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) CHALCOGEN_HEAD (in module orthonym.assembly.book_prefixes) 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_drawings() (in module orthonym.perception.charge_shift) charge_dropped() (in module orthonym.perception.structure_conservation) charge_placements() (in module orthonym.perception.charge_shift) charge_places() (in module orthonym.perception.charge_shift) charge_shift_forms() (in module orthonym.perception.charge_shift) charged (orthonym.assembly.hetero_group_prefixes.GroupShape attribute) charged_core() (in module orthonym.assembly.strict_ring_prefix) charges (orthonym.data.resonance_templates.ResonanceChainTemplate attribute) check_pin_spelling() (in module orthonym.validation.pin_spelling) children (orthonym.validation.binding_spine.SpineBinding attribute) (orthonym.validation.spelling.lexer.Encl 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_key() (in module orthonym.rules.bridged_fused_pin.prefixes) citation_order (orthonym.rules.bridged_fused_pin.numbering.Numbering attribute) cite_n_substituent_stereo() (in module orthonym.assembly.n_substituent_stereo) cite_organyl_in_composed_prefix() (in module orthonym.assembly.substituent_enumerator) cite_where_it_belongs() (in module orthonym.rules.isotope_induced) cited_locants() (in module orthonym.assembly.identical_prefixes) cites_a_locant() (in module orthonym.rules.ion_locants) cites_locant (orthonym.rules.terminal_ring.TerminalRingName attribute) cites_locant() (orthonym.rules.fused_forms.FusedForm method) (orthonym.rules.monocycle_forms.MonocycleForm method) 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_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_held() (in module orthonym.assembly.default_tier_offer) 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) clear_withdrawn_names() (in module orthonym.rules.relative_stereo) cleave_and_cap() (in module orthonym.decomposition) (in module orthonym.decomposition.fragment_capping) close() (orthonym.validation.opsin_server.PersistentOpsin method) close_trail() (in module orthonym.metrics.producer_trail) 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_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_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) (orthonym.data.metal_scope.MetalScope attribute) complete_stereo() (in module orthonym.rules.isotope_induced) ComplexRingResult (class in orthonym.assembly.composer) Component (class in orthonym.rules.bridged_fused_pin.fusion_components) COMPONENT_CACHE_MAX (in module orthonym.rules.main_ring_paths) component_sort_key() (in module orthonym.rules.adducts) component_substituent_locants() (in module orthonym.rules.spiro_carbocycle) ComponentRank (class in orthonym.rules.fused_ring_selection) components (orthonym.data.group_split_rules.SplitRule attribute) components_outside() (orthonym.rules.main_ring_paths.RingGraph method) compose_group() (in module orthonym.assembly.hetero_group_prefixes) compose_last_resort() (in module orthonym.rules.isotope_scopes) compose_scopes() (in module orthonym.rules.isotope_scopes) composed_alkoxy_prefix() (in module orthonym.assembly.substituent_enumerator) composed_chalcogen_group_prefix() (in module orthonym.assembly.substituent_enumerator) composed_group() (in module orthonym.assembly.n_unit_prefix) 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) compound_prefix_enclosure_check() (in module orthonym.validation.spelling.checks_marks) compulsory_prefix_smarts (orthonym.data.triviality_controller_seed.SeedEntry attribute) 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) content (orthonym.validation.spelling.lexer.Encl attribute) CONTRACTED (in module orthonym.rules.bridged_fused_pin.fusion_components) ControllerEvent (class in orthonym.assembly.retained_substitution) convert_pair_blocks() (in module orthonym.rules.relative_stereo) core_atoms (orthonym.perception.lipids.BackboneMatch attribute) core_automorphisms() (in module orthonym.assembly.strict_ring_prefix) core_numberings() (in module orthonym.data.fused_heterocycles) (in module orthonym.rules.porphyrin) count (orthonym.assembly.composer.NameFragment attribute) (orthonym.assembly.group_splitting.SplitComponent attribute) (orthonym.assembly.resolvers.SuffixInfo attribute) (orthonym.validation.thioperoxol_twin.ThioperoxolTwin attribute) count_assembly_texts() (in module orthonym.validation.spelling.checks_assembly) count_defined_stereo_elements() (in module orthonym.rules.stereochemistry) count_defined_stereo_in_fragment() (in module orthonym.rules.stereochemistry) 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_triple_bonds() (in module orthonym.perception.rings) count_rings_at_least() (in module orthonym.perception.mancude) count_stereocenters() (in module orthonym.perception.stereo) counted (orthonym.validation.spelling.lexer.Encl property) COVER_CAP (in module orthonym.rules.isotope_scopes) 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

decline_reason() (in module orthonym.rules.porphyrin) DECOMPOSITION_PRE_GENERAL (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) decorate_induced() (in module orthonym.rules.isotope_induced) decorate_isotope_stereo() (in module orthonym.rules.isotope_induced) decorate_isotopic_name() (in module orthonym.rules.isotopes) decorate_passes() (in module orthonym.rules.isotope_passes) decorated_ring_substituent_name() (in module orthonym.rules.ring_substituents) DEFAULT_ATOM_WORK_BUDGET (in module orthonym.assembly.universal_substituent) default_tier_engine() (in module orthonym.assembly.default_tier_offer) default_tier_name_scope() (in module orthonym.assembly.default_tier_offer) default_tier_row_for() (in module orthonym.assembly.default_tier_offer) defers (orthonym.assembly.substituent_enumerator.FreeValencePrefix property) denotable_atoms() (in module orthonym.rules.isotope_letters) depth (orthonym.metrics.candidate_ledger.LedgerEntry attribute) derivation (orthonym.rules.bridged_fused_pin.derived_parents.DerivedParent attribute) derivation_of() (in module orthonym.assembly.prefix_derivation) DERIVED_PARENTS (in module orthonym.rules.bridged_fused_pin.derived_parents) DerivedParent (class in orthonym.rules.bridged_fused_pin.derived_parents) 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_locants_fit_their_unit() (in module orthonym.validation.spelling.checks_placement) descriptor_spans() (in module orthonym.rules.isotope_induced) (in module orthonym.validation.twin_spellings) 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) (orthonym.validation.pin_spelling.SpellingFailure 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_hydro_ring_assembly() (in module orthonym.rules.ring_assemblies) 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_simple_cis_trans() (in module orthonym.rules.stereochemistry) diazene_is_senior_parent() (in module orthonym.validation.spelling.polyazane_parent) 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) distinct_classes() (in module orthonym.rules.isotope_letters) 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) drawings (orthonym.assembly.metal_offer.MetalOffer attribute) dropped_centres_invisible_to_inchi() (in module orthonym.perception.lone_pair_reading) dropped_forms_var (in module orthonym.assembly.memo) DualResult (class in orthonym.validation) (class in orthonym.validation.dual_validator)

E

E1Verdict (class in orthonym.validation.e1_certificate) ears() (in module orthonym.rules.bridged_fused_pin.selection) edge_position_to_letter() (in module orthonym.rules.fusion_descriptors) ELEMENT_LOCANT (in module orthonym.validation.spelling.models) 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) embedded_name() (in module orthonym.validation.thioperoxol_twin) 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_one_carbon_iminide() (in module orthonym.rules.iminide_one_carbon) 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_ring_cation_azanide() (in module orthonym.rules.charged_router) emit_ring_poly_cation_ium() (in module orthonym.rules.ions) 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) enc (orthonym.validation.spelling.lexer.Tok attribute) (orthonym.validation.spelling.units.Pref attribute) Encl (class in orthonym.validation.spelling.lexer) encl (orthonym.validation.spelling.lexer.Unit attribute) enclose_if_compound() (in module orthonym.assembly.naming_utils) enclose_second_prefix() (in module orthonym.assembly.prefix_marks)

enclosed (orthonym.assembly.prefix_derivation.PrefixDerivation attribute) enclosed_anion_suffix_check() (in module orthonym.validation.spelling.checks_thioperoxol) enclosing_closer() (in module orthonym.assembly.naming_utils) enclosing_marks_check() (in module orthonym.validation.spelling.checks_marks) enclosing_opener() (in module orthonym.assembly.naming_utils) enclosures() (in module orthonym.validation.spelling.lexer) encoding (orthonym.assembly.group_splitting.SplitEvent attribute) (orthonym.data.group_split_rules.SplitRule attribute) end (orthonym.validation.spelling.lexer.Encl attribute) end_bh (orthonym.rules.polycyclic.BridgeInfo attribute) (orthonym.rules.polycyclic_bridged.BridgeInfo attribute) end_naming_session() (in module orthonym.assembly.fragment_naming) ending (orthonym.assembly.universal_halane.HalaneUnit attribute) endings (orthonym.validation.spelling.units.Parsed attribute) ends_in_bridge_prefix() (in module orthonym.rules.bridged_fused_pin.prefixes) engine_orders_with_mancude() (in module orthonym.assembly.engine_prefix_ordering) engine_prefix_ordering() (in module orthonym.assembly.engine_prefix_ordering) enter_name_scope() (in module orthonym.assembly.fragment_naming) enumerate_metal_ligand_groups() (in module orthonym.perception.metals) enumerate_paths() (in module orthonym.rules.main_ring_paths) 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) exit_name_scope() (in module orthonym.assembly.fragment_naming) exocyclic_atom_indices (orthonym.perception.metals.MetallacycleInfo attribute) exocyclic_double_atoms() (in module orthonym.rules.ring_hydrogen) exocyclic_double_bonds_to_aromatic() (in module orthonym.perception.charge_shift) exocyclic_substituent_name() (in module orthonym.rules.polycyclics) express_junior_anionic_chalcogens() (in module orthonym.rules.ions) expressed (orthonym.validation.spelling.linear_phane.LinearPhaneVerdict attribute) extended_smiles_or_unavailable() (in module orthonym.validation.opsin_roundtrip) 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) failure_mode_scope() (in module orthonym.failure_mode) family (orthonym.perception.lipids.BackboneMatch attribute) 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_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_pair() (in module orthonym.rules.diacylhydrazides) 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) first (orthonym.rules.bridged_fused_pin.prefixes.BridgePrefix attribute) FLOOD_ATOMS_PER_UNIT (in module orthonym.rules.main_ring_paths) FORCED_LOCANT_REASON (in module orthonym.validation.opsin_ambiguity) forced_locant_reason() (in module orthonym.assembly.locant_omission) forced_locant_scope() (in module orthonym.assembly.locant_omission) form_result_rank() (in module orthonym.assembly.metal_offer) 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_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_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) format_suffix_with_locants() (in module orthonym.assembly.naming_utils) forms_enabled() (in module orthonym.assembly.book_prefixes) 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_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 (orthonym.rules.bridged_fused_pin.hydro.HydroState attribute) FREE_HOMONUCLEAR_G14_HYDRIDE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) free_valence (orthonym.assembly.substituent_enumerator.FreeValencePrefix attribute) free_valence_added (orthonym.rules.fused_forms.FusedForm 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) fresh_scope() (in module orthonym.assembly.memo) from_token_bindings() (orthonym.validation.binding_spine.BindingSpine class method) front_ih_groups() (in module orthonym.validation.spelling.indicated_hydrogen) functional_group_classes() (in module orthonym.assembly.strict_ring_prefix) functional_groups (orthonym.namer.MolecularFeatures attribute) FUSED (orthonym.rules.ring_selection.RingSystemType attribute) fused_lambda_entries() (in module orthonym.rules.lambda_convention) fused_lambda_prefix() (in module orthonym.rules.lambda_convention) fused_parent() (in module orthonym.rules.bridged_fused_pin.parents) fused_ring_atom_drop() (in module orthonym.perception.structure_conservation) fused_rings() (in module orthonym.rules.bridged_fused_pin.selection) fused_split() (in module orthonym.rules.bridged_fused_pin.selection) fused_system_form() (in module orthonym.rules.fused_forms) fused_system_ketone_form() (in module orthonym.rules.fused_forms) FusedForm (class in orthonym.rules.fused_forms) FusedKetoneForm (class in orthonym.rules.fused_forms) FusedParent (class in orthonym.rules.bridged_fused_pin.parents) fusion (orthonym.rules.bridged_fused_pin.hydro.HydroState attribute) FUSION (orthonym.validation.binding_spine.BindingKind attribute) fusion_nomenclature_applies() (in module orthonym.rules.polycyclic) fusion_pin_class() (in module orthonym.perception.mancude) fv_has_hydrogen (orthonym.rules.monocycle_forms.MonocycleForm attribute) fv_hydro_locant (orthonym.rules.monocycle_forms.MonocycleForm attribute)

G

gate_candidate() (in module orthonym.gate_retry) gate_nonsuffix_nacyl_float() (in module orthonym.decomposition.engine) GATE_OUTCOME_ACID_SPLIT_PREFIX (in module orthonym.metrics.provenance) GATE_OUTCOME_AMBIGUOUS_SUPPRESSED (in module orthonym.metrics.provenance) 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_TWIN_PREFIX (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) general_tier_engine() (in module orthonym.assembly.default_tier_offer) general_tier_twin_round_trip() (in module orthonym.validation.twin_spellings) 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_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) geometry_labels() (in module orthonym.perception.lone_pair_reading) 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_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_anoate_name() (in module orthonym.data.chain_names) get_aromatic_reference() (in module orthonym.data.partial_saturation_refs) get_benzene_ring() (in module orthonym.rules.benzene) get_benzene_substituents() (in module orthonym.rules.benzene) 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_bridge_lengths() (in module orthonym.rules.bicyclo) get_bridge_prefix() (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_carotene_parent_name() (in module orthonym.data.natural_products) get_cation_name() (in module orthonym.data.ion_retained_names) get_cation_word() (in module orthonym.data.cation_words) 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_component_by_pattern() (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_stereo() (in module orthonym.perception.stereo) get_enoate_name() (in module orthonym.data.chain_names) get_fg_prefix_form() (in module orthonym.rules.polyfunctional) get_functional_group_locants() (in module orthonym.rules.locants) 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_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_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_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_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_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_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_substituent_name() (in module orthonym.rules.ring_substituents) get_ring_substituents() (in module orthonym.rules.cycloalkanes) get_ring_systems() (in module orthonym.perception.rings) get_ring_triple_bonds() (in module orthonym.rules.cycloalkanes) 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_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_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) 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_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_name() (in module orthonym.data.xanthine_derivatives) GIVEN_CHAIN_GROUPS (in module orthonym.perception.chains) glycosyl_substituent_prefix() (in module orthonym.data.sugar_names) grid_orientations() (in module orthonym.rules.fusion_orientation) GROUP_1 (in module orthonym.data.metal_scope) group_identical_prefixes() (in module orthonym.assembly.identical_prefixes) group_shape() (in module orthonym.assembly.hetero_group_prefixes) group_shape_ok() (in module orthonym.rules.oxoacid_group_prefix) GroupPart (class in orthonym.assembly.hetero_group_prefixes) groups (orthonym.rules.ring_hydrogen.RingHydrogen attribute) GroupShape (class in orthonym.assembly.hetero_group_prefixes) guanidine_parent_matches() (in module orthonym.rules.seniority)

H

halane_parent() (in module orthonym.assembly.universal_halane) HALANE_STEM (in module orthonym.assembly.universal_halane) halane_unit() (in module orthonym.assembly.universal_halane) HalaneUnit (class in orthonym.assembly.universal_halane) halido_twin() (in module orthonym.validation.halido_twin) 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) handles() (in module orthonym.input_mol) hang_budget_trips() (in module orthonym.assembly.fragment_naming) hapticity_n (orthonym.perception.metals.LigandGroup attribute) HAPTO_DESCRIPTOR (in module orthonym.validation.halido_twin) has_aromatic_chalcogen_bridge() (in module orthonym.rules.bridged_fused) has_aromatic_mancude_bridge() (in module orthonym.rules.bridged_fused) has_bridged_fused_reading() (in module orthonym.rules.bridged_fused_pin) has_complete_scope() (in module orthonym.data.metal_scope) has_covalent_metal_carbon_bond() (in module orthonym.perception.metals) has_halane_candidate() (in module orthonym.assembly.universal_halane) has_isotopes() (in module orthonym.rules.isotopes) has_mechanism() (in module orthonym.data.metal_scope) has_ortho_fused_pair() (in module orthonym.perception.mancude) has_replacement_chain() (in module orthonym.rules.oxoacid_group_prefix) has_retained_name() (in module orthonym.data) has_structural_hyphen() (in module orthonym.assembly.naming_utils) has_unchecked_parent_numbering() (in module orthonym.rules.bridged_fused_pin) has_unverifiable_atoms() (in module orthonym.validation.reconstruct) has_valence() (in module orthonym.data.metal_scope) heavy_atoms (orthonym.validation.name_morphemes.ArityEstimate attribute) heavy_label_on_delocalized_atoms() (in module orthonym.rules.isotopes) held_names() (in module orthonym.assembly.default_tier_offer) 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_component_name() (in module orthonym.rules.bridged_fused_pin.hetero_fusion) hetero_ligand_prefix() (in module orthonym.rules.heterone_ligands)

hetero_mono_name() (in module orthonym.rules.bridged_fused_pin.fusion_components) hetero_mono_stem() (in module orthonym.rules.bridged_fused_pin.fusion_components) hetero_per_atom (orthonym.rules.vonbaeyer_universal.RingAnalysis attribute) hetero_prefix (orthonym.rules.vonbaeyer_universal.RingAnalysis attribute) HETERO_ROOT_VALENCE (in module orthonym.assembly.book_prefixes) hetero_roots_composable() (in module orthonym.assembly.book_prefixes) 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) heteromonocycle_parent_with_hydrogen() (in module orthonym.rules.heterocycles) heteromonocycle_ring_hydrogen() (in module orthonym.rules.heterocycles) HETERONE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) heterone_prefix_check() (in module orthonym.validation.spelling.checks_heterone) hold_withdrawn() (in module orthonym.assembly.default_tier_offer) holds_amine_or_senior_group() (in module orthonym.rules.n_branch) holds_pseudoasymmetric_block() (in module orthonym.rules.relative_stereo) HOMONUCLEAR_PNICTOGEN_CHAIN (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) host (orthonym.assembly.hetero_group_prefixes.GroupPart attribute) HW_ORDER (in module orthonym.rules.bridged_fused_pin.fusion_components) hydrazine_is_senior_parent() (in module orthonym.validation.spelling.polyazane_parent) hydrazine_parent_check() (in module orthonym.validation.spelling.checks_parent) hydrazine_substituents() (in module orthonym.assembly.hetero_group_prefixes) hydrazinyl_check() (in module orthonym.validation.spelling.checks_prefixes) hydrazonamide_name_to_hydrazonamido_prefix() (in module orthonym.assembly.substituent_naming) hydrazonoyl_amido_prefix_from_branch() (in module orthonym.assembly.substituent_naming) HYDRIDE_ION (in module orthonym.rules.metal_atoms) hydro (orthonym.rules.bridged_fused_pin.BridgedParent attribute) (orthonym.rules.ring_hydrogen.RingHydrogen attribute) HYDRO (orthonym.validation.binding_spine.BindingKind attribute) hydro (orthonym.validation.spelling.units.Parsed attribute) hydro_assembly_withheld() (in module orthonym.rules.ring_assemblies) HYDRO_FUSED_PEROXOL (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) hydro_ring_cation_name() (in module orthonym.rules.ring_cation_hydro) hydro_ring_zwitterion_name() (in module orthonym.rules.ring_cation_hydro) hydro_state() (in module orthonym.rules.bridged_fused_pin.hydro) hydro_text() (in module orthonym.rules.bridged_fused_pin.hydro) (in module orthonym.rules.ring_hydrogen) hydron_site_parent() (in module orthonym.rules.ring_cation_hydro) hydron_sites() (in module orthonym.perception.charge_shift) HydroState (class in orthonym.rules.bridged_fused_pin.hydro) hydroxy_is_principal() (in module orthonym.rules.benzene_prefix_forms) hypervalent_core() (in module orthonym.assembly.strict_ring_prefix) hyphen_after_enclosure_check() (in module orthonym.validation.spelling.checks_marks)

I

identical_parent_units() (in module orthonym.rules.pin_vocabulary) identical_prefixes_check() (in module orthonym.validation.spelling.checks_identical_prefixes) 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_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 (orthonym.validation.spelling.units.Parsed attribute) 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) iminyl_word_check() (in module orthonym.validation.spelling.checks_prefixes) implied_group_hydrogens() (in module orthonym.rules.isotope_licence) in_class (orthonym.assembly.substituent_enumerator.FreeValencePrefix attribute) in_fragment_recursion() (in module orthonym.assembly.fragment_naming) in_one_amidine_group() (in module orthonym.rules.isotope_compare) in_pin_promotion() (in module orthonym.rules.pin_vocabulary) inchikey_of() (in module orthonym.perception.molcache) indicated (orthonym.rules.ring_hydrogen.RingHydrogen attribute) 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) indicated_hydrogen_check() (in module orthonym.validation.spelling.checks_hydrogen) indicated_text() (in module orthonym.rules.ring_hydrogen) induced_centres() (in module orthonym.rules.isotope_induced) 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) innermost_name_input() (in module orthonym.assembly.fragment_naming) INORGANIC_ACID (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) inorganic_anion_word() (in module orthonym.rules.metal_atoms) INOSITOL (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) input_allows_radicals() (in module orthonym.validation.read_back_policy) 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) int_locs() (in module orthonym.validation.spelling.models) interior_pin_name() (in module orthonym.rules.fused_interior) INTERIOR_PIN_PARENTS (in module orthonym.data.fused_interior_pins) internal (orthonym.assembly.hetero_group_prefixes.GroupShape attribute) InvalidInputError invoke() (orthonym.validation.opsin_server.PersistentOpsin method) ion_sites (orthonym.namer.MolecularFeatures attribute) ionic (orthonym.assembly.universal_halane.HalaneUnit attribute) is_acyl_prefix() (in module orthonym.assembly.acyl_prefix) is_alkyl_attachment() (in module orthonym.assembly.retained_c2_chain) 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_biconnected_ring_system() (in module orthonym.rules.vonbaeyer_universal) is_bicyclo_system() (in module orthonym.rules.bicyclo) is_bonded_metal_name_without_pin() (in module orthonym.rules.metal_labels) is_branched_polyspiro() (in module orthonym.rules.spiro) is_bridged_fused() (in module orthonym.rules.bridged_fused) is_callers_own_call() (in module orthonym.failure_mode) is_carbanion_salt_of_group_3_12_metal() (in module orthonym.rules.metal_labels) is_cascade_refusal() (in module orthonym.errors) 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_complete_metal() (in module orthonym.data.metal_scope) 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_enclosed() (in module orthonym.assembly.naming_utils) is_fusable_system() (in module orthonym.rules.fused_forms) is_fused_bicyclic() (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_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_linear_phane_name() (in module orthonym.validation.spelling.linear_phane) is_macrocycle_complex_name_without_pin() (in module orthonym.rules.metal_labels) 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_atom_or_ion_name_without_pin() (in module orthonym.rules.metal_labels) is_metal_element() (in module orthonym.perception.metals) is_metal_name_without_pin() (in module orthonym.rules.metal_labels) 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_named_metal() (in module orthonym.data.metal_scope) is_named_ring (orthonym.assembly.resolvers.ParentInfo attribute) is_offered() (in module orthonym.assembly.default_tier_offer) is_one_component_name() (in module orthonym.rules.bridged_fused_pin.fusion_components) is_only_one_substitutable_position() (in module orthonym.assembly.naming_utils) is_oxoacid_centre() (in module orthonym.rules.oxoacid_group_prefix) is_oxoacid_linker() (in module orthonym.rules.oxoacid_group_prefix) is_peptide() (in module orthonym.rules.amino_acids) 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_pin_parent_name() (in module orthonym.rules.bridged_fused_pin.parents) is_poly_anhydride_name() (in module orthonym.validation.anhydride_acids) 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_pseudoketone_oxo() (in module orthonym.assembly.composer) is_pyrrole_type() (in module orthonym.rules.pyrrole_type) is_refusal_sentinel() (in module orthonym.errors) is_retained_amino_acid_name() (in module orthonym.data.amino_acids) is_retained_bicyclo() (in module orthonym.data.bicyclo_systems) 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_saturated_chain_carbon() (in module orthonym.rules.n_branch) 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_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_substituted_contracted_alkoxy() (in module orthonym.assembly.naming_utils) is_substituted_substituent() (in module orthonym.assembly.naming_utils) is_suspended() (in module orthonym.assembly.ring_ylidene_stereo) is_terminal (orthonym.assembly.resolvers.SuffixInfo attribute) 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) isolated_naming_session() (in module orthonym.assembly.fragment_naming) isolated_provenance (class in orthonym.metrics.provenance) 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) isotope_retained_c2_unit_scope() (in module orthonym.assembly.locant_omission) isotopes (orthonym.validation.reconstruct.NameFacts attribute) isotopic_naming_scope() (in module orthonym.assembly.locant_omission) ISOTOPIC_STEREO_LOCANTS (in module orthonym.assembly.locant_omission) ital (orthonym.validation.spelling.units.Pref attribute) 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) join() (orthonym.rules.fused_forms.FusedKetoneForm method)

joins_identical_hetero_ring_systems() (in module orthonym.rules.bridged_fused) joins_identical_ring_systems() (in module orthonym.rules.ring_assembly_screen) 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

kekule_ring_double() (in module orthonym.validation.spelling.indicated_hydrogen) kept_forms_var (in module orthonym.assembly.memo) kept_stereo() (in module orthonym.perception.charge_shift) KETENE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) key (orthonym.data.resonance_templates.ResonanceChainTemplate attribute) (orthonym.validation.spelling.units.Pref attribute) key_sees_bond() (in module orthonym.assembly.ring_ylidene_stereo) key_visible_ring_ylidene_bonds() (in module orthonym.assembly.ring_ylidene_stereo) keyless (orthonym.assembly.metal_offer.MetalOffer attribute) kind (orthonym.assembly.group_splitting.SplitEvent attribute) (orthonym.assembly.hetero_group_prefixes.GroupShape attribute) (orthonym.assembly.retained_substitution.ControllerEvent attribute) (orthonym.jars.JarSpec attribute) (orthonym.rules.bridged_fused_pin.fusion_components.Component attribute) (orthonym.rules.fused_forms.FusedForm attribute) (orthonym.rules.monocycle_forms.MonocycleForm attribute) (orthonym.rules.p44_scorer.ParentCandidate attribute) (orthonym.validation.binding_spine.SpineBinding attribute) (orthonym.validation.spelling.lexer.Encl attribute) (orthonym.validation.spelling.lexer.Tok attribute) (orthonym.validation.spelling.units.Pref attribute)

known_non_pin() (in module orthonym.rules.fused_pin_offer)

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) lacks_hydrogen() (in module orthonym.rules.bridged_fused_pin.hydro) lam (orthonym.assembly.universal_halane.HalaneUnit attribute) LAMBDA5_PHOSPHANIMINE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) lambda_hetero_prefix() (in module orthonym.rules.cage_lambda) LAMBDA_SULFANE_IMINE_OXIDE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) last_resort_active() (in module orthonym.validation.thioperoxol_twin) last_resort_scope() (in module orthonym.validation.thioperoxol_twin) LAST_STATS (in module orthonym.rules.isotope_scopes) last_t4_was_final_floor() (in module orthonym.assembly.t4_coverage) last_t4_was_floor_substitute() (in module orthonym.assembly.t4_coverage) LATE_KINDS (in module orthonym.assembly.hetero_group_prefixes) 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_reading() (in module orthonym.validation.read_back_policy) 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) letter_ranks() (in module orthonym.rules.isotope_letters) letters() (in module orthonym.validation.spelling.lexer) LEVEL_MIN_RINGS (in module orthonym.rules.main_ring_paths) LEVEL_PRUNE_MAX_FREE (in module orthonym.rules.main_ring_paths) lexicon_cache_key() (in module orthonym.validation.name_morphemes) lexicon_entries() (in module orthonym.validation.name_morphemes) lexicon_sources() (in module orthonym.validation.name_morphemes) licensed() (in module orthonym.rules.isotope_licence) licensed_ambiguity() (in module orthonym.validation.opsin_ambiguity) 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) limit_of() (in module orthonym.failure_mode) linear_acyl_amido_prefix() (in module orthonym.assembly.substituent_naming) LINEAR_PHANE (orthonym.rules.ring_selection.RingSystemType attribute) linear_phane_pin_check() (in module orthonym.validation.spelling.checks_phane)

linear_phane_pin_expected() (in module orthonym.validation.spelling.linear_phane) linear_phane_scope_guard() (in module orthonym.rules.phane) LinearPhaneVerdict (class in orthonym.validation.spelling.linear_phane) LIPID (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) 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.hetero_group_prefixes.GroupPart attribute) (orthonym.assembly.substituent_enumerator.SubstituentInfo attribute) locant_citation_check() (in module orthonym.validation.spelling.checks_locants) locant_context (orthonym.data.triviality_controller_seed.SeedEntry attribute) locant_high (orthonym.rules.polycyclic.BridgeInfo attribute) locant_key() (in module orthonym.rules.fused_forms) locant_low (orthonym.rules.polycyclic.BridgeInfo attribute) locant_omission_check() (in module orthonym.validation.spelling.checks_locants) locant_roles() (in module orthonym.assembly.form_choice) 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) locanted_prefix_block() (in module orthonym.rules.locanted_prefixes) 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) (orthonym.rules.bridged_fused_pin.derived_parents.DerivedParent attribute) locants_are_forced() (in module orthonym.assembly.locant_omission) locate_stereo_blocks() (in module orthonym.rules.stereochemistry) located_map_completes_substituent_stereo() (in module orthonym.assembly.substituent_naming) locs (orthonym.validation.spelling.lexer.Tok attribute) (orthonym.validation.spelling.units.Pref attribute) locus_override_rule_id (orthonym.data.triviality_controller_seed.SeedEntry attribute) log_confidence() (in module orthonym.assembly.coverage_scoring) logger (in module orthonym.failure_mode) lone_pair_centres() (in module orthonym.perception.lone_pair_reading) longest_bridge() (in module orthonym.rules.main_ring_paths) looks_like_ionic_name() (in module orthonym.perception.structure_conservation) lookup() (in module orthonym.metrics.producer_trail) 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) lower_locants() (in module orthonym.assembly.form_choice)

M

macrocycle_anion_name() (in module orthonym.rules.metal_macrocycles) macrocycle_component_names() (in module orthonym.rules.metal_macrocycles) macrocycle_ion_fragments() (in module orthonym.rules.metal_macrocycles) 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) make_metal_offer_scope() (in module orthonym.assembly.metal_offer) mancude_double (orthonym.rules.bridged_fused_pin.hydro.HydroState attribute) mancude_fused_core() (in module orthonym.perception.mancude) mark_decorated_assembly() (in module orthonym.rules.nested_assembly) mask (orthonym.rules.main_ring_paths.RingGraph attribute) 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) matching_close() (in module orthonym.assembly.naming_utils) MAX_ADDED_H (in module orthonym.rules.bridged_fused_pin.hydro) MAX_BRIDGES (in module orthonym.rules.bridged_fused_pin.selection) MAX_CAGE_ATOMS (in module orthonym.rules.vonbaeyer_universal) MAX_COMPETITOR_BRANCH_ATOMS (in module orthonym.rules.bridged_fused_pin.selection) MAX_CONFIGURATIONS (in module orthonym.perception.charge_shift) MAX_FRAGMENT_ATOMS (in module orthonym.rules.terminal_fragment) MAX_FUSED_RING_SIZE (in module orthonym.rules.bridged_fused_pin.selection) MAX_INDICATED_H (in module orthonym.rules.bridged_fused_pin.hydro) max_matching() (in module orthonym.validation.spelling.indicated_hydrogen) max_matching_size() (in module orthonym.perception.mancude) MAX_PI_NODES (in module orthonym.perception.charge_shift) MAX_RINGS (in module orthonym.rules.bridged_fused_pin.poly_fusion) MAX_SUFFIX_COUNT (in module orthonym.rules.bridged_fused_pin) MAX_SYSTEM_ATOMS (in module orthonym.rules.bridged_fused_pin.selection) maybe_tune_from_env() (in module orthonym.runtime_tuning) mechanical_forms() (in module orthonym.assembly.book_prefixes) mechanisms (orthonym.data.metal_scope.MetalScope attribute) MemoMismatch merge_n_block_into_name() (in module orthonym.assembly.identical_prefixes) merge_stereodescriptors() (in module orthonym.rules.stereochemistry) METACYCLOPHANE (orthonym.rules.phane.PhaneTopology attribute) METAL_ATOM (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) metal_atom_idx (orthonym.perception.metals.LigandGroup attribute) (orthonym.perception.metals.MetallacycleInfo attribute) metal_atom_indices (orthonym.perception.metals.MetalComplex attribute) metal_atom_name() (in module orthonym.rules.metal_atoms) metal_connected_spelling_and_order() (in module orthonym.assembly.metal_offer) METAL_DATIVE_SPLIT_RUN (in module orthonym.assembly.metal_offer) metal_dative_split_spelling_and_order() (in module orthonym.assembly.metal_offer) metal_disconnected_spelling_and_order() (in module orthonym.assembly.metal_offer) metal_offer_for() (in module orthonym.assembly.metal_offer) METAL_OFFER_OWNED (in module orthonym.assembly.metal_offer) METAL_REWRITE_RULE (in module orthonym.assembly.metal_offer) METAL_REWRITE_RUN (in module orthonym.assembly.metal_offer) metal_rewrite_spelling_and_order() (in module orthonym.assembly.metal_offer) MetalComplex (class in orthonym.perception.metals) MetallacycleInfo (class in orthonym.perception.metals) MetalOffer (class in orthonym.assembly.metal_offer) METALS (in module orthonym.perception.charge_shift) MetalScope (class in orthonym.data.metal_scope) method (orthonym.assembly.coverage_audit.CoverageVerdict attribute) (orthonym.validation.atom_coverage.CoverageResult attribute) (orthonym.validation.CoverageResult attribute) methyl_group_name() (in module orthonym.assembly.book_prefixes) METHYL_HEADS (in module orthonym.assembly.book_prefixes) methyl_prefix_has_no_locant() (in module orthonym.validation.spelling.checks_ring_prefix) MISMATCH (orthonym.validation.reconstruct.Verdict attribute) MIXED_SIGN_ZWITTERION (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) MOBILE_N_CATION (in module orthonym.perception.charge_shift) mode (orthonym.assembly.ring_ylidene_stereo.RingYlidene attribute) module orthonym orthonym.__main__ orthonym.assembly orthonym.assembly.acyl_amido_polyacid orthonym.assembly.acyl_prefix orthonym.assembly.book_prefixes orthonym.assembly.budget_rescue orthonym.assembly.candidate_pool orthonym.assembly.capped_name orthonym.assembly.chain_prefix_positions orthonym.assembly.composer orthonym.assembly.composition_primitives orthonym.assembly.coverage_audit orthonym.assembly.coverage_scoring orthonym.assembly.default_tier_offer orthonym.assembly.engine_prefix_ordering orthonym.assembly.form_choice orthonym.assembly.fragment_naming orthonym.assembly.general_engine orthonym.assembly.general_fusion orthonym.assembly.group_splitting orthonym.assembly.handlers 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.diacylhydrazide 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.imidic_ester 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.prefix_claims 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.hetero_group_prefixes orthonym.assembly.identical_prefixes orthonym.assembly.inner_dispatch orthonym.assembly.locant_omission orthonym.assembly.memo orthonym.assembly.metal_offer orthonym.assembly.n_branch_prefixes orthonym.assembly.n_substituent_stereo orthonym.assembly.n_unit_prefix 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.prefix_derivation orthonym.assembly.prefix_marks orthonym.assembly.radical_floor orthonym.assembly.resolvers orthonym.assembly.retained_c2_chain orthonym.assembly.retained_substitution orthonym.assembly.ring_assembly_fragment orthonym.assembly.ring_ylidene_stereo orthonym.assembly.spelling_offer orthonym.assembly.strict_ring_prefix orthonym.assembly.substituent_enumerator orthonym.assembly.substituent_naming orthonym.assembly.substituent_prefix_forms orthonym.assembly.t4_coverage orthonym.assembly.universal_halane 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.fused_interior_pins orthonym.data.fusion_components orthonym.data.group_split_rules orthonym.data.halogen_ring_parents orthonym.data.hw_heteroatoms orthonym.data.hw_stems orthonym.data.ion_retained_names orthonym.data.metal_scope orthonym.data.multipliers 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.amide_c_locant orthonym.decomposition.amide_n_substituents 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.failure_mode orthonym.gate_retry orthonym.input_mol 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.producer_trail orthonym.metrics.provenance orthonym.namer orthonym.perception.automorphisms orthonym.perception.centres_bridge orthonym.perception.centres_mancude orthonym.perception.chains orthonym.perception.charge_shift orthonym.perception.functional_groups orthonym.perception.ions orthonym.perception.lambda_hydride orthonym.perception.lipids orthonym.perception.lone_pair_reading 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.rdkit_log orthonym.routing orthonym.routing.dispatch_table orthonym.routing.dispatcher orthonym.rules orthonym.rules.acid_ester_anion orthonym.rules.acid_halides orthonym.rules.acid_salt_anions orthonym.rules.added_carbon_parent orthonym.rules.adducts orthonym.rules.amides orthonym.rules.amine_anion_label orthonym.rules.amine_anion_symmetry orthonym.rules.amino_acids orthonym.rules.anhydrides orthonym.rules.anilino_nitrogen orthonym.rules.azolium_cations orthonym.rules.benzene orthonym.rules.benzene_prefix_forms orthonym.rules.bicyclo orthonym.rules.bridged_fused orthonym.rules.bridged_fused_pin orthonym.rules.bridged_fused_pin.derived_parents orthonym.rules.bridged_fused_pin.fusion_components orthonym.rules.bridged_fused_pin.fusion_names orthonym.rules.bridged_fused_pin.hetero_fusion orthonym.rules.bridged_fused_pin.hydro orthonym.rules.bridged_fused_pin.numbering orthonym.rules.bridged_fused_pin.parent_table orthonym.rules.bridged_fused_pin.parents orthonym.rules.bridged_fused_pin.poly_fusion orthonym.rules.bridged_fused_pin.prefixes orthonym.rules.bridged_fused_pin.selection orthonym.rules.cage_lambda orthonym.rules.catenated_hydrides orthonym.rules.centre_ligands orthonym.rules.charged_router orthonym.rules.conjugate_controller orthonym.rules.cycloalkanes orthonym.rules.diacylhydrazides orthonym.rules.esters orthonym.rules.functional_replacement orthonym.rules.fused_forms orthonym.rules.fused_interior orthonym.rules.fused_pin_offer 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.halogen_ring_fusion orthonym.rules.hetero_monocycle_substituent orthonym.rules.heterocycles orthonym.rules.heterone_ligands orthonym.rules.iminide_one_carbon orthonym.rules.inorganic_acids orthonym.rules.inositols orthonym.rules.ion_locants orthonym.rules.ions orthonym.rules.isotope_compare orthonym.rules.isotope_induced orthonym.rules.isotope_letters orthonym.rules.isotope_licence orthonym.rules.isotope_passes orthonym.rules.isotope_scopes orthonym.rules.isotopes orthonym.rules.ketenes orthonym.rules.lactams orthonym.rules.lactones orthonym.rules.lambda_convention orthonym.rules.linear_phane_screen orthonym.rules.lipids orthonym.rules.locant_validation orthonym.rules.locanted_prefixes orthonym.rules.locants orthonym.rules.macrocycle_orientation orthonym.rules.main_ring_paths orthonym.rules.metal_atoms orthonym.rules.metal_labels orthonym.rules.metal_macrocycles orthonym.rules.monocycle_forms orthonym.rules.mononuclear_hydrides orthonym.rules.multiplicative orthonym.rules.multiplicative_general orthonym.rules.n_branch orthonym.rules.natural_products orthonym.rules.nested_assembly orthonym.rules.nitramide orthonym.rules.nitriles orthonym.rules.nucleosides orthonym.rules.oligosaccharides orthonym.rules.organometallics orthonym.rules.oxoacid_group_prefix orthonym.rules.p44_scorer orthonym.rules.parent_correctness 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.porphyrin orthonym.rules.pseudoketones orthonym.rules.purine orthonym.rules.purine_oxo orthonym.rules.pyrrole_type orthonym.rules.radicals orthonym.rules.relative_stereo orthonym.rules.ring_assemblies orthonym.rules.ring_assembly_screen orthonym.rules.ring_cation_hydro orthonym.rules.ring_cation_hydron orthonym.rules.ring_chalcogen_oxide orthonym.rules.ring_hydrogen orthonym.rules.ring_position_kinds orthonym.rules.ring_prefix_sequence orthonym.rules.ring_replacement orthonym.rules.ring_selection orthonym.rules.ring_substituents orthonym.rules.ring_unsaturation orthonym.rules.ring_ylidene_carrier orthonym.rules.ring_ylidene_prefix orthonym.rules.salts orthonym.rules.seniority orthonym.rules.skeletal_replacement orthonym.rules.spiro orthonym.rules.spiro_carbocycle orthonym.rules.spiro_polyspiro 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.anhydride_acids 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.halido_twin orthonym.validation.name_morphemes orthonym.validation.opsin_ambiguity orthonym.validation.opsin_grammar orthonym.validation.opsin_roundtrip orthonym.validation.opsin_server orthonym.validation.phane_read_back orthonym.validation.pin_spelling orthonym.validation.polyester_twin orthonym.validation.proof_ledger orthonym.validation.protonation_identity orthonym.validation.pubchem_validator orthonym.validation.radical_identity orthonym.validation.read_back_policy orthonym.validation.reconstruct orthonym.validation.spelling orthonym.validation.spelling.checks_amine_parent orthonym.validation.spelling.checks_assembly orthonym.validation.spelling.checks_group_count orthonym.validation.spelling.checks_heterone orthonym.validation.spelling.checks_hydrogen orthonym.validation.spelling.checks_identical_prefixes orthonym.validation.spelling.checks_locants orthonym.validation.spelling.checks_marks orthonym.validation.spelling.checks_one_carbon_parent orthonym.validation.spelling.checks_parent orthonym.validation.spelling.checks_phane orthonym.validation.spelling.checks_placement orthonym.validation.spelling.checks_prefixes orthonym.validation.spelling.checks_pseudohalide orthonym.validation.spelling.checks_ring_prefix orthonym.validation.spelling.checks_thioperoxol orthonym.validation.spelling.indicated_hydrogen orthonym.validation.spelling.lexer orthonym.validation.spelling.linear_phane orthonym.validation.spelling.models orthonym.validation.spelling.polyazane_parent orthonym.validation.spelling.units orthonym.validation.stereo_descriptors orthonym.validation.stereo_stated orthonym.validation.thioperoxol_twin orthonym.validation.twin_spellings orthonym.validation.uide_twin 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) mono_numberings() (in module orthonym.rules.bridged_fused_pin.fusion_components) monocycle_form() (in module orthonym.rules.monocycle_forms) monocycle_locant_check() (in module orthonym.validation.spelling.checks_thioperoxol) monocycle_numbering() (in module orthonym.rules.terminal_ring) MonocycleForm (class in orthonym.rules.monocycle_forms) MONOCYCLIC (orthonym.rules.phane.SkeletonClass attribute) (orthonym.rules.ring_selection.RingSystemType attribute) MONONUCLEAR_HEAD (in module orthonym.assembly.book_prefixes) 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) mult (orthonym.validation.spelling.units.Pref attribute) MULTI_COMPONENT_NEUTRAL (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) multiple_bond_endings_spellable() (in module orthonym.assembly.composition_primitives) 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) multiplicity (orthonym.validation.stereo_descriptors.StereoBlockUnits attribute) multiplied (orthonym.validation.spelling.units.Parsed attribute) multiplied_acid_word() (in module orthonym.rules.anhydrides) multiplied_component() (in module orthonym.assembly.naming_utils) multiplied_in_general_form() (in module orthonym.rules.bridged_fused_pin.prefixes) multiplier_needs_hyphen() (in module orthonym.assembly.naming_utils) multiplier_table() (in module orthonym.data.multipliers) multiplying_prefix() (in module orthonym.data.chain_names) multiplying_prefix_check() (in module orthonym.validation.spelling.checks_marks) must_fail_closed (orthonym.assembly.substituent_enumerator.FreeValencePrefix property)

N

n_aryl_parent_check() (in module orthonym.validation.spelling.checks_parent) n_branch_last_resort_prefix() (in module orthonym.assembly.n_branch_prefixes) n_double (orthonym.rules.bridged_fused_pin.hydro.HydroState attribute) (orthonym.rules.bridged_fused_pin.selection.Split attribute) n_prefix_breaks_citation_order() (in module orthonym.decomposition.fragment_assembly) n_prefix_with_a_locant_is_enclosed() (in module orthonym.validation.spelling.checks_placement) 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) n_unit_prefix() (in module orthonym.assembly.n_unit_prefix) n_yl_without_added_hydrogen() (in module orthonym.assembly.strict_ring_prefix) nacyl_float_as_acylamino() (in module orthonym.decomposition.engine) 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.fusion_components.Component attribute) (orthonym.rules.bridged_fused_pin.parents.FusedParent 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) (orthonym.validation.thioperoxol_twin.ThioperoxolTwin 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_acid_linked_branch() (in module orthonym.assembly.substituent_enumerator) 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_after_budget_trip() (in module orthonym.assembly.budget_rescue) name_aldonate_ester() (in module orthonym.data.sugar_names) 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_carbocyclic_monocycle_component() (in module orthonym.rules.spiro_carbocycle) 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_diacylhydrazide() (in module orthonym.rules.diacylhydrazides) name_diacylhydrazide_handler() (in module orthonym.assembly.handlers.diacylhydrazide) 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_carbocycle_pin() (in module orthonym.rules.bridged_fused) name_fused_heterocycle() (in module orthonym.rules.fused_rings) name_fused_with_pin_offer() (in module orthonym.rules.fused_pin_offer) 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_multiplicative() (in module orthonym.rules.multiplicative_general) 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_halane_component() (in module orthonym.assembly.universal_halane) name_halogen_benzo_system() (in module orthonym.rules.halogen_ring_fusion) 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_imidic_ester() (in module orthonym.assembly.handlers.imidic_ester) 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_neutral_ring_for_ion() (in module orthonym.rules.ion_locants) 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_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_oxoacid_functional_parent() (in module orthonym.rules.phosphorus) 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_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_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_identical_inorganic_ester() (in module orthonym.rules.esters) name_polyol_polyester() (in module orthonym.rules.esters) name_polyspiro_different_core() (in module orthonym.rules.spiro_polyspiro) name_polysulfoxide_sulfone() (in module orthonym.rules.polychalcogen) name_porphyrin_dianion() (in module orthonym.rules.porphyrin) 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_acid_salt_anion() (in module orthonym.rules.acid_salt_anions) 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_states_fewer_stereo() (in module orthonym.validation.stereo_stated) 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_heterocycle() (in module orthonym.rules.heterocycles) name_substituted_nitramide() (in module orthonym.rules.nitramide) name_substituted_polycyclic() (in module orthonym.rules.polycyclics) name_substituted_porphyrin() (in module orthonym.rules.porphyrin) 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_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_amino_substituent() (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_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_tiered_with_offer() (in module orthonym.assembly.spelling_offer) 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_unsaturated_carbocyclic_side_ring() (in module orthonym.rules.spiro_carbocycle) 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_forced_locants() (in module orthonym.gate_retry) name_with_metal_offer() (in module orthonym.assembly.metal_offer) 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) names_a_replacement_chain() (in module orthonym.rules.relative_stereo) names_the_input() (in module orthonym.assembly.universal_halane) 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) naphthalenyl_prefix() (in module orthonym.rules.ring_substituents) NATURAL_PRODUCT (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) nbr_mask (orthonym.rules.main_ring_paths.RingGraph attribute) nbrs (orthonym.rules.main_ring_paths.RingGraph attribute) needs_brackets() (in module orthonym.assembly.naming_utils) needs_locant() (in module orthonym.rules.isotope_licence) needs_p1634_marks() (in module orthonym.assembly.naming_utils) needs_stereo_injection() (in module orthonym.rules.stereochemistry) neighbors_of() (in module orthonym.perception.molcache) nested (orthonym.validation.spelling.units.Pref attribute) net_charge (orthonym.validation.reconstruct.NameFacts attribute) net_formal_charge() (in module orthonym.perception.structure_conservation) neutralized_cation() (in module orthonym.rules.ring_cation_hydro) 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) nodes (orthonym.validation.spelling.linear_phane.LinearPhaneVerdict attribute) NodeScores (class in orthonym.assembly.per_substring_scoring) non_mancude_ring_atoms() (in module orthonym.perception.centres_mancude) non_pin_label_rule_failures() (in module orthonym.metrics.provenance) non_pin_parts() (in module orthonym.assembly.form_choice) 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) normalise() (in module orthonym.validation.spelling.lexer) normalize_locant() (in module orthonym.rules.bridged_fused_pin.parents) note() (in module orthonym.metrics.producer_trail) note_amine_chain_parent() (in module orthonym.assembly.spelling_offer) note_book_form() (in module orthonym.assembly.book_prefixes) note_ps_form() (in module orthonym.rules.oxoacid_group_prefix) note_relaxed_adduct() (in module orthonym.assembly.default_tier_offer) note_touched() (in module orthonym.metrics.provenance) note_withdrawn_name() (in module orthonym.rules.relative_stereo) noted() (in module orthonym.metrics.producer_trail) notes (orthonym.data.group_split_rules.SplitRule attribute) (orthonym.data.triviality_controller_seed.SeedEntry attribute) (orthonym.validation.spelling.units.Parsed attribute) NUCLEOSIDE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) nuclide_symbol() (in module orthonym.rules.isotopes) number_heterocycle_ring() (in module orthonym.rules.heterocycles) Numbering (class in orthonym.rules.bridged_fused_pin.numbering) numbering (orthonym.rules.fused_forms.FusedForm attribute) (orthonym.rules.fused_forms.FusedKetoneForm attribute) (orthonym.rules.monocycle_forms.MonocycleForm attribute) (orthonym.rules.polycyclic.PolycyclicDescriptor attribute) (orthonym.rules.terminal_fragment.TerminalFragmentName attribute) (orthonym.rules.terminal_ring.TerminalRingName attribute) numbering_check() (in module orthonym.validation.spelling.checks_locants) numbering_dicts() (orthonym.rules.bridged_fused_pin.fusion_components.Component method) numbering_held_by_drawn_alternation() (in module orthonym.data.fused_heterocycles) numbering_key() (in module orthonym.rules.ring_hydrogen) numberings (orthonym.rules.bridged_fused_pin.fusion_components.Component attribute) (orthonym.rules.bridged_fused_pin.parents.FusedParent attribute) numberings() (in module orthonym.rules.bridged_fused_pin.numbering) numeral() (in module orthonym.rules.bridged_fused_pin.fusion_components) numerical_term() (in module orthonym.data.chain_names)

O

occurrences (orthonym.validation.spelling.linear_phane.LinearPhaneVerdict attribute) Offer (class in orthonym.assembly.offer_pool) offer_default_tier_row() (in module orthonym.assembly.default_tier_offer) ok (orthonym.validation.binding_spine.SpineProof attribute) (orthonym.validation.e1_certificate.E1Verdict attribute) olate_with_senior_neutral_group() (in module orthonym.rules.charged_router) one_carbon_amine_locant_check() (in module orthonym.validation.spelling.checks_one_carbon_parent) one_kind_of_ring_position() (in module orthonym.rules.ring_position_kinds) one_kind_of_substitutable_position() (in module orthonym.rules.ring_position_kinds) one_position_parent_enclosure_check() (in module orthonym.validation.spelling.checks_marks) only_hydrazine_is_functional() (in module orthonym.validation.spelling.polyazane_parent) open_trail() (in module orthonym.metrics.producer_trail) 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_name (orthonym.rules.bridged_fused_pin.derived_parents.DerivedParent attribute) 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_spelling() (in module orthonym.validation.twin_spellings) opsin_stdout() (in module orthonym.jvm_bridge) opsin_structure() (in module orthonym.rules.bridged_fused_pin.fusion_names) (in module orthonym.rules.bridged_fused_pin.hetero_fusion) opsin_warnings() (in module orthonym.jvm_bridge) OpsinGrammar (class in orthonym.validation) (class in orthonym.validation.opsin_grammar) OpsinOracle (class in orthonym.assembly.retained_substitution) OpsinUnavailable, [1] OptionalNamingCapExceeded order (orthonym.assembly.hetero_group_prefixes.GroupPart attribute) order_after_hydro (orthonym.validation.spelling.units.Parsed attribute) ORGANOMETALLIC (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) organometallic_charge_conserved() (in module orthonym.rules.organometallics) 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_macrocycle_for_replacement() (in module orthonym.rules.macrocycle_orientation) orient_stub (orthonym.rules.fused_ring_selection.ComponentRank attribute) oriented_heterocycle (orthonym.namer.MolecularFeatures attribute) oriented_ring (orthonym.namer.MolecularFeatures attribute) ortho_fused_pair() (in module orthonym.assembly.strict_ring_prefix) ortho_rings() (in module orthonym.rules.bridged_fused_pin.fusion_components) ORTHOCYCLOPHANE (orthonym.rules.phane.PhaneTopology attribute) orthonym module Orthonym (class in orthonym) (class in orthonym.namer) orthonym.__main__ module orthonym.assembly module orthonym.assembly.acyl_amido_polyacid module orthonym.assembly.acyl_prefix module orthonym.assembly.book_prefixes module orthonym.assembly.budget_rescue module orthonym.assembly.candidate_pool module orthonym.assembly.capped_name module orthonym.assembly.chain_prefix_positions module orthonym.assembly.composer module orthonym.assembly.composition_primitives module orthonym.assembly.coverage_audit module orthonym.assembly.coverage_scoring module orthonym.assembly.default_tier_offer module orthonym.assembly.engine_prefix_ordering module orthonym.assembly.form_choice 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._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.diacylhydrazide 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.imidic_ester 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.prefix_claims 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.hetero_group_prefixes module orthonym.assembly.identical_prefixes module orthonym.assembly.inner_dispatch module orthonym.assembly.locant_omission module orthonym.assembly.memo module orthonym.assembly.metal_offer module orthonym.assembly.n_branch_prefixes module orthonym.assembly.n_substituent_stereo module orthonym.assembly.n_unit_prefix 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.prefix_derivation module orthonym.assembly.prefix_marks module orthonym.assembly.radical_floor module orthonym.assembly.resolvers module orthonym.assembly.retained_c2_chain module orthonym.assembly.retained_substitution module orthonym.assembly.ring_assembly_fragment module orthonym.assembly.ring_ylidene_stereo module orthonym.assembly.spelling_offer module orthonym.assembly.strict_ring_prefix 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_halane 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.fused_interior_pins module orthonym.data.fusion_components module orthonym.data.group_split_rules module orthonym.data.halogen_ring_parents module orthonym.data.hw_heteroatoms module orthonym.data.hw_stems module orthonym.data.ion_retained_names module orthonym.data.metal_scope module orthonym.data.multipliers 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.amide_c_locant module orthonym.decomposition.amide_n_substituents 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.failure_mode module orthonym.gate_retry module orthonym.input_mol 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.producer_trail module orthonym.metrics.provenance module orthonym.namer module orthonym.perception.automorphisms module orthonym.perception.centres_bridge module orthonym.perception.centres_mancude module orthonym.perception.chains module

orthonym.perception.charge_shift module orthonym.perception.functional_groups module orthonym.perception.ions module orthonym.perception.lambda_hydride module orthonym.perception.lipids module orthonym.perception.lone_pair_reading 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.rdkit_log 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.acid_salt_anions module orthonym.rules.added_carbon_parent module orthonym.rules.adducts module orthonym.rules.amides module orthonym.rules.amine_anion_label module orthonym.rules.amine_anion_symmetry module orthonym.rules.amino_acids module orthonym.rules.anhydrides module orthonym.rules.anilino_nitrogen module orthonym.rules.azolium_cations module orthonym.rules.benzene module orthonym.rules.benzene_prefix_forms module orthonym.rules.bicyclo module orthonym.rules.bridged_fused module orthonym.rules.bridged_fused_pin module orthonym.rules.bridged_fused_pin.derived_parents module orthonym.rules.bridged_fused_pin.fusion_components module orthonym.rules.bridged_fused_pin.fusion_names module orthonym.rules.bridged_fused_pin.hetero_fusion module orthonym.rules.bridged_fused_pin.hydro module orthonym.rules.bridged_fused_pin.numbering module orthonym.rules.bridged_fused_pin.parent_table module orthonym.rules.bridged_fused_pin.parents module orthonym.rules.bridged_fused_pin.poly_fusion module orthonym.rules.bridged_fused_pin.prefixes module orthonym.rules.bridged_fused_pin.selection module orthonym.rules.cage_lambda module orthonym.rules.catenated_hydrides module orthonym.rules.centre_ligands module orthonym.rules.charged_router module orthonym.rules.conjugate_controller module orthonym.rules.cycloalkanes module orthonym.rules.diacylhydrazides module orthonym.rules.esters module orthonym.rules.functional_replacement module orthonym.rules.fused_forms module orthonym.rules.fused_interior module orthonym.rules.fused_pin_offer 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.halogen_ring_fusion module orthonym.rules.hetero_monocycle_substituent module orthonym.rules.heterocycles module orthonym.rules.heterone_ligands module orthonym.rules.iminide_one_carbon module orthonym.rules.inorganic_acids module orthonym.rules.inositols module orthonym.rules.ion_locants module orthonym.rules.ions module orthonym.rules.isotope_compare module orthonym.rules.isotope_induced module orthonym.rules.isotope_letters module orthonym.rules.isotope_licence module orthonym.rules.isotope_passes module orthonym.rules.isotope_scopes module orthonym.rules.isotopes module orthonym.rules.ketenes module orthonym.rules.lactams module orthonym.rules.lactones module orthonym.rules.lambda_convention module orthonym.rules.linear_phane_screen module orthonym.rules.lipids module orthonym.rules.locant_validation module orthonym.rules.locanted_prefixes module orthonym.rules.locants module orthonym.rules.macrocycle_orientation module orthonym.rules.main_ring_paths module orthonym.rules.metal_atoms module orthonym.rules.metal_labels module orthonym.rules.metal_macrocycles module orthonym.rules.monocycle_forms module orthonym.rules.mononuclear_hydrides module orthonym.rules.multiplicative module orthonym.rules.multiplicative_general module orthonym.rules.n_branch module orthonym.rules.natural_products module orthonym.rules.nested_assembly module orthonym.rules.nitramide module orthonym.rules.nitriles module orthonym.rules.nucleosides module orthonym.rules.oligosaccharides module orthonym.rules.organometallics module orthonym.rules.oxoacid_group_prefix module orthonym.rules.p44_scorer module orthonym.rules.parent_correctness 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.porphyrin module orthonym.rules.pseudoketones module orthonym.rules.purine module orthonym.rules.purine_oxo module orthonym.rules.pyrrole_type module orthonym.rules.radicals module orthonym.rules.relative_stereo module orthonym.rules.ring_assemblies module orthonym.rules.ring_assembly_screen module orthonym.rules.ring_cation_hydro module orthonym.rules.ring_cation_hydron module orthonym.rules.ring_chalcogen_oxide module orthonym.rules.ring_hydrogen module orthonym.rules.ring_position_kinds module orthonym.rules.ring_prefix_sequence module orthonym.rules.ring_replacement module orthonym.rules.ring_selection module orthonym.rules.ring_substituents module orthonym.rules.ring_unsaturation module orthonym.rules.ring_ylidene_carrier module orthonym.rules.ring_ylidene_prefix module orthonym.rules.salts module orthonym.rules.seniority module orthonym.rules.skeletal_replacement module orthonym.rules.spiro module orthonym.rules.spiro_carbocycle module orthonym.rules.spiro_polyspiro 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.anhydride_acids 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.halido_twin module orthonym.validation.name_morphemes module orthonym.validation.opsin_ambiguity module orthonym.validation.opsin_grammar module orthonym.validation.opsin_roundtrip module orthonym.validation.opsin_server module orthonym.validation.phane_read_back module orthonym.validation.pin_spelling module orthonym.validation.polyester_twin module orthonym.validation.proof_ledger module orthonym.validation.protonation_identity module orthonym.validation.pubchem_validator module orthonym.validation.radical_identity module orthonym.validation.read_back_policy module orthonym.validation.reconstruct module orthonym.validation.spelling module orthonym.validation.spelling.checks_amine_parent module orthonym.validation.spelling.checks_assembly module orthonym.validation.spelling.checks_group_count module orthonym.validation.spelling.checks_heterone module orthonym.validation.spelling.checks_hydrogen module orthonym.validation.spelling.checks_identical_prefixes module orthonym.validation.spelling.checks_locants module orthonym.validation.spelling.checks_marks module orthonym.validation.spelling.checks_one_carbon_parent module orthonym.validation.spelling.checks_parent module orthonym.validation.spelling.checks_phane module orthonym.validation.spelling.checks_placement module orthonym.validation.spelling.checks_prefixes module orthonym.validation.spelling.checks_pseudohalide module orthonym.validation.spelling.checks_ring_prefix module orthonym.validation.spelling.checks_thioperoxol module orthonym.validation.spelling.indicated_hydrogen module orthonym.validation.spelling.lexer module orthonym.validation.spelling.linear_phane module orthonym.validation.spelling.models module orthonym.validation.spelling.polyazane_parent module orthonym.validation.spelling.units module orthonym.validation.stereo_descriptors module orthonym.validation.stereo_stated module orthonym.validation.thioperoxol_twin module orthonym.validation.twin_spellings module orthonym.validation.uide_twin module orthonym.wallclock module OrthonymLimitError, [1] OTHER (orthonym.metrics.abstention.AbstentionCode attribute) outermost_name_input() (in module orthonym.assembly.fragment_naming) outermost_tier_contexts() (in module orthonym.assembly.budget_rescue) outside (orthonym.rules.main_ring_paths.RingGraph 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) oxides (orthonym.assembly.universal_halane.HalaneUnit attribute) oxo_class_ok() (in module orthonym.assembly.strict_ring_prefix) oxo_ene_valence_illegal() (in module orthonym.perception.structure_conservation) oxo_prefix_parent_numberings() (in module orthonym.rules.partial_saturation) oxoacid_group_prefix() (in module orthonym.rules.oxoacid_group_prefix) oxoacid_group_prefix_ex() (in module orthonym.rules.oxoacid_group_prefix)

P

P10 (in module orthonym.validation.spelling.models) p44_2_1_key() (in module orthonym.rules.bridged_fused_pin.selection) p45_acid_chain() (in module orthonym.perception.chains) p45_pending() (in module orthonym.perception.chains) p45_principal_chain() (in module orthonym.perception.chains) 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) (orthonym.rules.fused_forms.FusedForm attribute) (orthonym.rules.fused_forms.FusedKetoneForm attribute) (orthonym.rules.monocycle_forms.MonocycleForm attribute) PARENT (orthonym.validation.binding_spine.BindingKind attribute) parent (orthonym.validation.spelling.lexer.Encl attribute) (orthonym.validation.spelling.units.Parsed attribute) parent_atom_indices (orthonym.assembly.coverage_scoring.CandidateName attribute) parent_atoms (orthonym.assembly.composer.HandlerResult attribute) (orthonym.rules.parent_selection.ParentSelectionResult attribute) parent_cites_locant (orthonym.rules.fused_forms.FusedForm attribute) (orthonym.rules.monocycle_forms.MonocycleForm attribute) parent_group_count_check() (in module orthonym.validation.spelling.checks_group_count) parent_kind (orthonym.validation.reconstruct.NameFacts attribute) parent_label (orthonym.assembly.resolvers.ParentInfo attribute) parent_length (orthonym.validation.reconstruct.NameFacts attribute) parent_locs (orthonym.validation.spelling.units.Parsed attribute) parent_name (orthonym.rules.phane.Amplificant attribute) parent_pool_size (orthonym.rules.parent_selection.ParentSelectionResult attribute) parent_positional_scope() (in module orthonym.assembly.locant_omission) parent_prefix() (in module orthonym.rules.ring_hydrogen) parent_ring_outside() (in module orthonym.assembly.strict_ring_prefix) 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_token() (orthonym.rules.fused_forms.FusedKetoneForm method) 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) 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_BUDGET (in module orthonym.rules.isotope_scopes) 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_name() (in module orthonym.validation.spelling.units) 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 (class in orthonym.validation.spelling.units) 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) parts (orthonym.assembly.hetero_group_prefixes.GroupShape attribute) 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 perfect_matching() (in module orthonym.perception.charge_shift) peripheral_cycle() (in module orthonym.rules.bridged_fused_pin.fusion_components) periphery_numbering_ok() (in module orthonym.rules.bridged_fused_pin.fusion_components) PerNodeScorer (class in orthonym.assembly.per_substring_scoring) PersistentOpsin (class in orthonym.validation.opsin_server) pg_count (orthonym.rules.p44_scorer.ParentCandidate attribute) phane_may_be_pin() (in module orthonym.rules.linear_phane_screen) phane_name_shape() (in module orthonym.validation.phane_read_back) phane_read_back() (in module orthonym.validation.phane_read_back) PHANE_READ_BACK_RULE (in module orthonym.validation.phane_read_back) phane_reading() (in module orthonym.rules.bridged_fused_pin.selection) PhaneStructure (class in orthonym.rules.phane) PhaneTopology (class in orthonym.rules.phane) phosphate_ester_offered() (in module orthonym.rules.phosphorus) pi_atoms() (in module orthonym.perception.charge_shift) pi_capable() (in module orthonym.perception.charge_shift) pi_system() (in module orthonym.perception.charge_shift) pi_work() (in module orthonym.perception.charge_shift) PIN_ALLOW (in module orthonym.data.pin_policy) pin_ceiling_name() (in module orthonym.assembly.budget_rescue) pin_ceilings_scope() (in module orthonym.rules.vonbaeyer_universal) 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_PARENT_NAMES (in module orthonym.rules.bridged_fused_pin.parents) pin_promotion_active() (in module orthonym.rules.pin_vocabulary) pin_promotion_var (in module orthonym.assembly.memo) pin_spellings_on() (in module orthonym.validation.twin_spellings) pin_tier_ring_prefix() (in module orthonym.assembly.strict_ring_prefix)

PIN_VERIFIED (in module orthonym.assembly.offer_pool) PNICTOGEN_CARBOXYLIC_ACID (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) pnictogen_oxoacid_prefix() (in module orthonym.rules.benzene_prefix_forms) POLY_ANION (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) poly_branch() (in module orthonym.assembly.strict_ring_prefix) polyacid_acyl_amido_prefix() (in module orthonym.assembly.acyl_amido_polyacid) POLYAZANE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) polyazane_is_senior_parent() (in module orthonym.validation.spelling.polyazane_parent) POLYCHALCOGEN_OXIDE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) polycomponent_name() (in module orthonym.rules.bridged_fused_pin.poly_fusion) 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) polyester_has_free_acid() (in module orthonym.validation.polyester_twin) polyester_twin() (in module orthonym.validation.polyester_twin) 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) positions_alike_prefix() (in module orthonym.assembly.book_prefixes) predicate (orthonym.assembly.handlers.InnerDispatchEntry attribute) (orthonym.assembly.inner_dispatch.InnerDispatchEntry attribute) (orthonym.routing.ClassDispatchEntry attribute) (orthonym.routing.dispatch_table.ClassDispatchEntry attribute) Pref (class in orthonym.validation.spelling.units) prefer_clean_name() (in module orthonym.assembly.spelling_offer) prefix (orthonym.assembly.substituent_enumerator.FreeValencePrefix attribute) (orthonym.rules.ring_replacement.ReplacementPrefix attribute) PREFIX (orthonym.validation.binding_spine.BindingKind attribute) prefix() (orthonym.rules.fused_forms.FusedForm method) (orthonym.rules.monocycle_forms.MonocycleForm method) prefix_at_locant() (orthonym.rules.fused_forms.FusedForm method) (orthonym.rules.monocycle_forms.MonocycleForm method) prefix_citation_sort_key() (in module orthonym.assembly.naming_utils) prefix_form (orthonym.assembly.group_splitting.SplitComponent attribute) prefix_form() (in module orthonym.rules.bridged_fused_pin.fusion_components) prefix_locant_order_key() (in module orthonym.assembly.composition_primitives) prefix_order_fallback (orthonym.assembly.universal_substituent.UniversalResult attribute) prefix_roman_and_italic() (in module orthonym.assembly.naming_utils) PrefixDerivation (class in orthonym.assembly.prefix_derivation) prefixes (orthonym.assembly.handlers.NameTreeNode attribute) (orthonym.assembly.name_tree.NameTreeNode attribute) (orthonym.validation.spelling.units.Parsed attribute) prefixes_apart_var (in module orthonym.assembly.memo) PrefixName (class in orthonym.assembly.prefix_derivation) preselected_only (orthonym.rules.ring_replacement.ReplacementPrefix attribute) principal_chain (orthonym.namer.MolecularFeatures attribute) principal_chain_check() (in module orthonym.validation.spelling.checks_parent) principal_chain_with_ring_prefixes() (in module orthonym.perception.chains) principal_class (orthonym.validation.spelling.linear_phane.LinearPhaneVerdict attribute) principal_class_check() (in module orthonym.validation.spelling.checks_parent) principal_group (orthonym.namer.MolecularFeatures attribute) (orthonym.validation.reconstruct.NameFacts attribute) principal_group() (in module orthonym.assembly.strict_ring_prefix) principal_group_atoms (orthonym.namer.MolecularFeatures attribute) principal_group_count_check() (in module orthonym.validation.spelling.checks_parent) principal_group_in() (in module orthonym.assembly.n_unit_prefix) principal_group_in_fragment() (in module orthonym.assembly.strict_ring_prefix) 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) producer_record() (in module orthonym.metrics.provenance) 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) propan_2_yl_check() (in module orthonym.validation.spelling.checks_prefixes) protonation_site_verdict() (in module orthonym.validation.protonation_identity) ps_tier_ctx (in module orthonym.rules.oxoacid_group_prefix) pseudohalide_prefix_check() (in module orthonym.validation.spelling.checks_pseudohalide) 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) publish_tier_flags() (in module orthonym.validation.twin_spellings) 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_centres_agree() (in module orthonym.rules.isotope_compare) radical_identity_verdict() (in module orthonym.validation.radical_identity) radical_profile() (in module orthonym.validation.radical_identity) RADICAL_READING (in module orthonym.rules.isotope_compare) radical_sites (orthonym.namer.MolecularFeatures attribute) rank_fragments() (in module orthonym.decomposition.fragment_ranker) rank_key() (in module orthonym.rules.bridged_fused_pin.fusion_components) rank_offers() (in module orthonym.assembly.offer_pool) raw (orthonym.validation.spelling.units.Pref attribute) raw_reading() (in module orthonym.perception.lone_pair_reading) rdkit_flags0_affordable() (in module orthonym.perception.charge_shift) rdkit_flags8_affordable() (in module orthonym.perception.charge_shift) rdkit_logs_off() (in module orthonym.rdkit_log) rdkit_logs_on() (in module orthonym.rdkit_log) RDKIT_RESONANCE0_MAX_WORK (in module orthonym.perception.charge_shift) RDKIT_RESONANCE_MAX_CONJUGATED (in module orthonym.perception.charge_shift) read_ledger() (in module orthonym.metrics.candidate_ledger) read_n_group() (in module orthonym.assembly.n_unit_prefix) read_prefix() (in module orthonym.assembly.identical_prefixes) read_units() (in module orthonym.validation.spelling.models) reading_base_for() (in module orthonym.validation.read_back_policy) reading_for() (in module orthonym.validation.read_back_policy) reanchor_bridging_amine() (in module orthonym.rules.n_branch) 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) reconcile_prefix_claims() (in module orthonym.assembly.handlers.prefix_claims) 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_biphenyl_parent_label() (in module orthonym.rules.benzene) record_breadth_promotion() (in module orthonym.metrics.provenance) record_candidate() (in module orthonym.metrics.candidate_ledger) record_derived_non_pin_fragment() (in module orthonym.metrics.provenance) record_derived_uncertified_pin_name() (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_metal_rewrite_non_pin() (in module orthonym.assembly.metal_offer) record_non_pin_azanide() (in module orthonym.rules.amine_anion_label) 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_polyol_mixed_anion_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) record_verified_through_split() (in module orthonym.metrics.provenance) recording_scopes() (in module orthonym.assembly.memo) refusal_structure() (in module orthonym.metrics.breadth) register() (in module orthonym.validation.pin_spelling) register_retained_name() (in module orthonym.data) registered_rules() (in module orthonym.validation.pin_spelling) reject_ambiguous() (in module orthonym.validation.opsin_ambiguity) relaxed_adduct_active() (in module orthonym.assembly.default_tier_offer) relaxed_adduct_row() (in module orthonym.assembly.default_tier_offer) render_ring_unsaturation() (in module orthonym.rules.ring_unsaturation) renest_group_and_ancestors() (in module orthonym.assembly.naming_utils) renumber() (orthonym.assembly.strict_ring_prefix.StrictRingPolicy method) repl (orthonym.validation.spelling.units.Parsed attribute) REPL_ELEMENT (in module orthonym.validation.spelling.units) 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() (in module orthonym.failure_mode) 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_producer_record() (in module orthonym.metrics.provenance) restore_provenance() (in module orthonym.metrics.provenance) restore_withdrawn() (in module orthonym.validation.opsin_ambiguity) result (orthonym.assembly.inner_dispatch.InnerDispatchResult attribute) result_obj (orthonym.assembly.offer_pool.Offer attribute) retained (orthonym.rules.amides.RingAmideParts attribute) retained_c2_name() (in module orthonym.assembly.retained_c2_chain)

retained_c2_unit_carries_isotope() (in module orthonym.rules.isotope_licence) retained_c2_unit_has_isotope_label() (in module orthonym.assembly.locant_omission) RETAINED_C2_WORD (in module orthonym.assembly.retained_c2_chain) retained_component() (in module orthonym.rules.bridged_fused_pin.fusion_components) retained_group_prefix() (in module orthonym.assembly.book_prefixes) 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) RETRY_DROP_ORDER (in module orthonym.assembly.book_prefixes) RETRY_KEEP_ORDER (in module orthonym.assembly.book_prefixes) retry_keeps() (in module orthonym.assembly.book_prefixes) retry_rungs() (in module orthonym.assembly.book_prefixes) retry_spelling() (in module orthonym.assembly.book_prefixes) ring_adj() (in module orthonym.validation.spelling.indicated_hydrogen) ring_amide_parts() (in module orthonym.rules.amides) ring_aminide() (in module orthonym.rules.amine_anion_label) ring_anchored_pg_atoms() (in module orthonym.assembly.composer) RING_ASSEMBLY (orthonym.rules.ring_selection.RingSystemType attribute) ring_assembly_groups() (in module orthonym.validation.spelling.checks_assembly) ring_assembly_info (orthonym.namer.MolecularFeatures attribute) ring_assembly_named_as_such_check() (in module orthonym.validation.spelling.checks_assembly) 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_blocks() (in module orthonym.rules.spiro_polyspiro) ring_cation_locants() (in module orthonym.rules.ring_cation_hydro) ring_cation_prefix() (in module orthonym.rules.ring_cation_hydro) RING_CHALCOGEN_OXIDE (orthonym.routing.dispatch_table.StoutClass attribute) (orthonym.routing.StoutClass attribute) ring_chalcogen_oxide_has_lambda() (in module orthonym.validation.spelling.checks_ring_prefix) ring_count (orthonym.rules.polycyclic.PolycyclicDescriptor attribute) (orthonym.rules.polycyclic_bridged.PolycyclicInfo attribute) ring_count_neg (orthonym.rules.fused_ring_selection.ComponentRank attribute) ring_cycle() (in module orthonym.rules.bridged_fused_pin.fusion_components) 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_forms_enabled() (in module orthonym.assembly.book_prefixes) ring_has_multiple_bond() (in module orthonym.assembly.strict_ring_prefix) ring_has_other_nh_heteroatom() (in module orthonym.rules.azolium_cations) ring_hydride (orthonym.rules.amides.RingAmideParts attribute) ring_hydrogen() (in module orthonym.rules.ring_hydrogen) ring_info (orthonym.assembly.coverage_scoring.CandidateName attribute) ring_is_in_biphenyl_assembly() (in module orthonym.rules.ring_assembly_screen) ring_lambda_valence() (in module orthonym.rules.lambda_convention) ring_numbering_tie_key() (in module orthonym.rules.ring_cation_hydro) ring_on_chain_substituent_name() (in module orthonym.rules.ring_ylidene_carrier) ring_or_chain_model() (in module orthonym.validation.spelling.models) ring_prefix_sequence() (in module orthonym.rules.ring_prefix_sequence) 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_skeleton_units_resolved() (in module orthonym.rules.seniority) ring_stereo_prefix() (in module orthonym.rules.ring_cation_hydro) ring_substituents (orthonym.namer.MolecularFeatures attribute) ring_substituents_as_groups (orthonym.namer.MolecularFeatures attribute) ring_suffix_atoms_the_assembler_cites() (in module orthonym.rules.heterocycles) ring_system() (in module orthonym.rules.bridged_fused_pin.selection) ring_system_key() (in module orthonym.rules.ring_assembly_screen) ring_system_score() (in module orthonym.rules.ring_selection) ring_systems (orthonym.namer.MolecularFeatures attribute) (orthonym.validation.spelling.linear_phane.LinearPhaneVerdict attribute) ring_systems() (in module orthonym.metrics.breadth) (in module orthonym.rules.bridged_fused_pin.selection) (in module orthonym.validation.spelling.indicated_hydrogen) ring_triple_bond_locants (orthonym.namer.MolecularFeatures attribute) ring_triple_bonds (orthonym.namer.MolecularFeatures attribute) ring_type (orthonym.namer.MolecularFeatures attribute) ring_unsaturation() (in module orthonym.rules.bridged_fused_pin.selection) ring_yl_attachment_descriptor() (in module orthonym.assembly.substituent_naming) ring_ylidene_bonds() (in module orthonym.rules.stereochemistry) ring_ylidene_descriptors() (in module orthonym.assembly.ring_ylidene_stereo) ring_ylidene_on_chain_substituent() (in module orthonym.rules.ring_ylidene_carrier) ring_ylidene_suspended() (in module orthonym.assembly.ring_ylidene_stereo) ring_ylium_may_be_locant_free() (in module orthonym.rules.ion_locants) RingAmideParts (class in orthonym.rules.amides) RingAnalysis (class in orthonym.rules.vonbaeyer_universal) RingGraph (class in orthonym.rules.main_ring_paths) RingHydrogen (class in orthonym.rules.ring_hydrogen) RINGS (in module orthonym.validation.spelling.models) rings (orthonym.rules.bridged_fused_pin.fusion_components.Component attribute) (orthonym.rules.main_ring_paths.RingGraph attribute) RingSystemType (class in orthonym.rules.ring_selection) RingUnsaturation (class in orthonym.rules.ring_unsaturation) RingYlidene (class in orthonym.assembly.ring_ylidene_stereo) 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) rows_in_line() (in module orthonym.rules.bridged_fused_pin.fusion_components) 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) rule (orthonym.validation.pin_spelling.SpellingFailure attribute) (orthonym.validation.thioperoxol_twin.ThioperoxolTwin attribute) rule_name() (in module orthonym.rules.bridged_fused_pin.hetero_fusion) (in module orthonym.rules.bridged_fused_pin.poly_fusion)

S

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_block() (in module orthonym.assembly.ring_ylidene_stereo) scope_cites_stereo_locants() (in module orthonym.assembly.locant_omission) 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_orientation_grid() (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) seeded_scopes() (in module orthonym.assembly.memo) 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_rt_passing() (in module orthonym.assembly.offer_pool) SENIOR_A (in module orthonym.rules.bridged_fused_pin.fusion_components) 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) settle_confidence() (in module orthonym.failure_mode) severity (orthonym.validation.binding_spine.Finding attribute) sha256 (orthonym.jars.JarSpec attribute) shareable_entries() (in module orthonym.assembly.memo) shared_prefix_entries() (in module orthonym.assembly.identical_prefixes) shared_prefix_groups() (in module orthonym.assembly.identical_prefixes) ships_at_general_tier() (in module orthonym.validation.thioperoxol_twin) should_omit_locant_one() (in module orthonym.assembly.naming_utils) show() (in module orthonym.validation.spelling.models) 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_letters() (in module orthonym.rules.bridged_fused_pin.fusion_components) side_put() (in module orthonym.assembly.memo) SIMPLE (in module orthonym.validation.spelling.units) simple_multiplier_word() (in module orthonym.assembly.naming_utils) single_attachment() (in module orthonym.assembly.strict_ring_prefix) single_carbon_hosts_suffix() (in module orthonym.rules.parent_selection) site (orthonym.metrics.candidate_ledger.LedgerEntry attribute) sites (orthonym.perception.lipids.BackboneMatch attribute) (orthonym.rules.pin_vocabulary.PromotionProbe attribute) size (orthonym.rules.main_ring_paths.RingGraph attribute) skeletal_lambda_floor_name() (in module orthonym.assembly.radical_floor) 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) skeleton_twin() (in module orthonym.assembly.strict_ring_prefix) SkeletonClass (class in orthonym.rules.phane) slot_dir() (in module orthonym.jvm_budget) smiles (orthonym.metrics.coverage_metrics.RowResult attribute) (orthonym.namer.MolecularFeatures attribute) (orthonym.rules.bridged_fused_pin.derived_parents.DerivedParent attribute) smiles_for() (in module orthonym.input_mol) smiles_has_radical_electrons() (in module orthonym.validation.read_back_policy) sort_heteroatoms_by_priority() (in module orthonym.data.hw_heteroatoms) source (orthonym.assembly.offer_pool.Offer attribute) (orthonym.rules.bridged_fused_pin.parents.FusedParent attribute) span (orthonym.validation.stereo_descriptors.StereoBlockUnits attribute) species_type (orthonym.namer.MolecularFeatures attribute) specific_method_cation_name() (in module orthonym.rules.ions) speculative_fragment_naming() (in module orthonym.assembly.fragment_naming) spelled_offring_atoms (orthonym.rules.polycyclics.PartialSatName attribute) SpellingFailure (class in orthonym.validation.pin_spelling) 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) split_front_stereo() (in module orthonym.decomposition.fragment_assembly) split_locants() (in module orthonym.rules.bridged_fused_pin.fusion_components) split_prefix_zone() (in module orthonym.assembly.identical_prefixes) split_secondary_amine_name() (in module orthonym.decomposition.amide_n_substituents)

split_simple() (in module orthonym.validation.spelling.units) 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) STAND_IN (in module orthonym.perception.lone_pair_reading) stand_in_string() (in module orthonym.perception.lone_pair_reading) standard_centres_labels() (in module orthonym.perception.lone_pair_reading) standard_reading_flips() (in module orthonym.perception.lone_pair_reading) standard_reading_inchikey() (in module orthonym.perception.lone_pair_reading) standard_reading_mol() (in module orthonym.perception.lone_pair_reading) start (orthonym.validation.spelling.lexer.Encl 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) state (orthonym.rules.ring_hydrogen.RingHydrogen attribute) stated_charge() (in module orthonym.rules.organometallics) STATS (in module orthonym.perception.centres_mancude) stats (orthonym.validation.binding_spine.SpineProof attribute) status() (in module orthonym.jvm_budget) stem (orthonym.assembly.universal_halane.HalaneUnit attribute) stereo (orthonym.assembly.handlers.NameTreeNode attribute) (orthonym.assembly.name_tree.NameTreeNode attribute) (orthonym.validation.spelling.units.Parsed attribute) stereo_atom_to_locant (orthonym.assembly.general_engine.GeneralEngineResult attribute) (orthonym.validation.binding_spine.BindingSpine attribute) stereo_block_units() (in module orthonym.validation.stereo_descriptors) stereo_bond (orthonym.assembly.hetero_group_prefixes.GroupShape attribute) stereo_decides_below_pin() (in module orthonym.assembly.form_choice) stereo_descriptors_verified() (in module orthonym.validation.stereo_descriptors) stereo_elements() (in module orthonym.perception.charge_shift) stereo_in_key (orthonym.data.triviality_controller_seed.SeedEntry attribute) stereo_layer_row() (in module orthonym.assembly.default_tier_offer) StereoBlockUnits (class in orthonym.validation.stereo_descriptors) 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) strict_ring_substituent_name() (in module orthonym.assembly.strict_ring_prefix) StrictRingPolicy (class in orthonym.assembly.strict_ring_prefix) 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) substituted (orthonym.assembly.prefix_derivation.PrefixDerivation attribute) 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) (orthonym.rules.fused_forms.FusedKetoneForm attribute) SUFFIX (orthonym.validation.binding_spine.BindingKind attribute) suffix_leaves_no_room_for_a_prefix() (in module orthonym.rules.locant_validation) suffix_nitrogen_gains_hydron() (in module orthonym.assembly.locant_omission) suffix_nitrogen_hydrogens_are_caps() (in module orthonym.assembly.locant_omission) suffix_nitrogen_hydron_var (in module orthonym.assembly.memo) 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) SULFENIC_RULE (in module orthonym.validation.thioperoxol_twin) 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) suspended() (in module orthonym.metrics.producer_trail) system_type (orthonym.rules.polycyclic_bridged.PolycyclicInfo attribute)

T

t4_rescue_name() (in module orthonym.assembly.budget_rescue) tautomer_accepted() (in module orthonym.rules.isotope_compare) tautomer_of() (in module orthonym.rules.isotope_compare) tautomer_passes() (in module orthonym.rules.isotope_compare) TAUTOMER_READING (in module orthonym.rules.isotope_compare) tautomer_verdict() (in module orthonym.validation.protonation_identity) 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) terminal_yl_prefix() (in module orthonym.assembly.capped_name) TerminalFragmentName (class in orthonym.rules.terminal_fragment) TerminalRingName (class in orthonym.rules.terminal_ring) tert_butyl_check() (in module orthonym.validation.spelling.checks_prefixes) tetravalent_fusion_atoms() (in module orthonym.rules.bridged_fused_pin.fusion_components) text (orthonym.assembly.composer.NameFragment attribute) (orthonym.assembly.resolvers.SuffixInfo attribute) (orthonym.validation.spelling.lexer.Tok attribute) (orthonym.validation.spelling.lexer.Unit attribute) (orthonym.validation.stereo_descriptors.StereoBlockUnits 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) thioperoxol_twin() (in module orthonym.validation.thioperoxol_twin) thioperoxol_twin_outcome() (in module orthonym.validation.thioperoxol_twin) thioperoxol_twin_round_trip() (in module orthonym.validation.thioperoxol_twin) ThioperoxolTwin (class in orthonym.validation.thioperoxol_twin) tied_amine_parent() (in module orthonym.assembly.strict_ring_prefix) 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) Tok (class in orthonym.validation.spelling.lexer) 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) toks (orthonym.validation.spelling.lexer.Unit attribute) top_level_text() (in module orthonym.assembly.naming_utils) top_level_tokens() (in module orthonym.assembly.naming_utils) 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) TRADITIONAL_NUMBERING (in module orthonym.rules.bridged_fused_pin.parents) 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) twin_gate_ships() (in module orthonym.validation.twin_spellings) twin_last_resort_row() (in module orthonym.assembly.default_tier_offer) twin_licensed() (in module orthonym.rules.isotope_licence) twin_of() (in module orthonym.validation.twin_spellings) twin_offer_holds() (in module orthonym.validation.twin_spellings) twin_opsin_parse() (in module orthonym.validation.twin_spellings) twin_outcome() (in module orthonym.metrics.provenance) twin_outcome_holds() (in module orthonym.validation.twin_spellings) twin_round_trip() (in module orthonym.validation.twin_spellings) TWIN_RULES (in module orthonym.validation.twin_spellings) two_component_name() (in module orthonym.rules.bridged_fused_pin.fusion_names) typ (orthonym.validation.spelling.lexer.Encl attribute) 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

uide_twin() (in module orthonym.validation.uide_twin) uide_twin_outcome() (in module orthonym.validation.uide_twin) uide_twin_round_trip() (in module orthonym.validation.uide_twin) UIDE_TWIN_RULE (in module orthonym.validation.uide_twin) UnbalancedMarksError 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) unexpressed (orthonym.rules.ring_replacement.ReplacementPrefix attribute) Unit (class in orthonym.validation.spelling.lexer) unit (orthonym.assembly.hetero_group_prefixes.GroupShape attribute) (orthonym.validation.spelling.units.Parsed attribute) UNIT_TERMS (in module orthonym.data.chain_names) units (orthonym.validation.stereo_descriptors.StereoBlockUnits attribute) units() (in module orthonym.validation.spelling.lexer)

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) unsaturated_monocycle_ylidene_prefix() (in module orthonym.rules.ring_ylidene_prefix) 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) unspecified_carbohydrate() (in module orthonym.assembly.strict_ring_prefix) 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) uses_bound() (in module orthonym.rules.main_ring_paths)

V

valences (orthonym.data.metal_scope.MetalScope attribute) 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_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) vector() (in module orthonym.validation.spelling.models) Verdict (class in orthonym.validation.reconstruct)

verdict (orthonym.validation.reconstruct.ReconResult attribute) verified_field() (in module orthonym.metrics.provenance) VERIFIED_FIELD_BY_OPSIN_LABEL (in module orthonym.metrics.provenance) VERIFIED_FIELD_FOR_TIER (in module orthonym.metrics.provenance) VERIFIED_OPSIN_LABELS (in module orthonym.metrics.provenance) 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 warn_unnamed() (in module orthonym.failure_mode) watch_book_forms() (in module orthonym.assembly.book_prefixes) weave_is_verified() (in module orthonym.decomposition.weave)

with_derivation() (in module orthonym.assembly.prefix_derivation) withdrawn_name() (in module orthonym.validation.opsin_ambiguity) withdrawn_names() (in module orthonym.rules.relative_stereo) within_ring_ceiling() (in module orthonym.rules.vonbaeyer_universal) without_ring_skeleton_amidine() (in module orthonym.rules.seniority) word (orthonym.validation.spelling.lexer.Unit attribute) write_prefix() (in module orthonym.assembly.identical_prefixes)

Y

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

Z

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