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  • Your first name

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  • How every name is checked
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Reference

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

Project

  • Contributing to Orthonym
  • Changelog
  • How to cite
  • Licence
  • llms.txt
  1. Orthonym /
  2. Internals /
  3. Engine and tools

Engine and tools#

Note

Internal API. Names and behaviour may change between releases.

The top level: the naming pipeline, the command line, the jars and the Java runtime bridge. 12 modules.

  • orthonym
  • orthonym.__main__
  • orthonym.cli
  • orthonym.diagnostics
  • orthonym.errors
  • orthonym.jars
  • orthonym.jvm_bridge
  • orthonym.jvm_budget
  • orthonym.jvm_flags
  • orthonym.namer
  • orthonym.runtime_tuning
  • orthonym.wallclock
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Made with coffee by Kohulan.R at Beilstein-InstitutBeilstein-Institut and Steinbeck-Lab

Orthonym 1.0.3. MIT licence.

Source on GitHub · Web app · llms.txt