Chemoton APIΒΆ
- Engine
- Gears
- Interface
- Implementations
- scine_chemoton.gears
GearHasNameHoldsCollections- scine_chemoton.gears.compound
- scine_chemoton.gears.conformers
- scine_chemoton.gears.elementary_steps
- scine_chemoton.gears.kinetic_modeling
- scine_chemoton.gears.kinetics
- scine_chemoton.gears.network_refinement
- scine_chemoton.gears.pathfinder
- scine_chemoton.gears.reaction
- scine_chemoton.gears.rerun_calculations
- scine_chemoton.gears.scheduler
- scine_chemoton.gears.single_point
- scine_chemoton.gears.thermo
- scine_chemoton.gears
- Filters
- scine_chemoton.filters
- scine_chemoton.filters.aggregate_filters
ActivatedAggregateFilterAggregateFilterAggregateFilterAndArrayAggregateFilterOrArrayAtomNumberFilterCatalystFilterChargeCombinationFilterCompleteSubstructureFilterCompoundCostPropertyFilterConcentrationPropertyFilterElementCountFilterElementSumCountFilterHasStructureWithModelIdFilterLastKineticModelingFilterMolecularWeightFilterOneAggregateIdFilterOnePotentialEnergySurfacePlaceHolderAggregateFilterSelectedAggregateIdFilterSelectedStructureIdFilterSelfReactionFilterSpecificChargeFilterStopDuringExplorationTrueMinimumFilter
- scine_chemoton.filters.elementary_step_filters
- scine_chemoton.filters.further_exploration_filters
- scine_chemoton.filters.reaction_filters
- scine_chemoton.filters.reactive_site_filters
- scine_chemoton.filters.structure_filters
- scine_chemoton.filters.aggregate_filters
- scine_chemoton.filters
- Optional Reaction Rules
- Steering Wheel
- Data Structures
ExplorationResultExplorationSchemeStepGearOptionsGearOptions.apply_to_protocol()GearOptions.clear()GearOptions.copy()GearOptions.fromkeys()GearOptions.generate_value()GearOptions.get()GearOptions.items()GearOptions.key_check()GearOptions.keys()GearOptions.pop()GearOptions.popitem()GearOptions.setdefault()GearOptions.update()GearOptions.values()
LogicCouplingNetworkExpansionResultNoRestartInfoPresentProtocolEntryProtocolEntry.credentialsProtocolEntry.engineProtocolEntry.forkProtocolEntry.gearProtocolEntry.is_running()ProtocolEntry.limited_runsProtocolEntry.n_runsProtocolEntry.nameProtocolEntry.run()ProtocolEntry.stop()ProtocolEntry.terminate()ProtocolEntry.wait_for_calculation_finishProtocolEntry.was_stopped
RestartPartialExpansionInfoSelectionResultStatusStopPreviousProtocolEntriesStopSplitCommunicationMethodStructureInformation
- Interfaces
SteeringWheelSteeringWheel.clear_cache()SteeringWheel.delete_results()SteeringWheel.get_partial_restart_info()SteeringWheel.get_results()SteeringWheel.get_status_report()SteeringWheel.is_running()SteeringWheel.join()SteeringWheel.nameSteeringWheel.pop()SteeringWheel.remove_global_selection()SteeringWheel.restart_fileSteeringWheel.run()SteeringWheel.save()SteeringWheel.set_global_selection()SteeringWheel.set_partial_restart_info()SteeringWheel.start()SteeringWheel.stop()SteeringWheel.terminate()
SelectionSelectionAndArraySelectionAndArray.OptionsSelectionAndArray.get_result()SelectionAndArray.get_step_result()SelectionAndArray.initialize_collections()SelectionAndArray.lowest_barrier_per_reaction()SelectionAndArray.nameSelectionAndArray.optionsSelectionAndArray.possible_attributes()SelectionAndArray.set_result()SelectionAndArray.set_step_result()SelectionAndArray.unset_collections()
SelectionOrArraySelectionOrArray.OptionsSelectionOrArray.get_result()SelectionOrArray.get_step_result()SelectionOrArray.initialize_collections()SelectionOrArray.lowest_barrier_per_reaction()SelectionOrArray.nameSelectionOrArray.optionsSelectionOrArray.possible_attributes()SelectionOrArray.set_result()SelectionOrArray.set_step_result()SelectionOrArray.unset_collections()
NetworkExpansionNetworkExpansion.OptionsNetworkExpansion.current_gears()NetworkExpansion.dry_setup_protocol()NetworkExpansion.get_result()NetworkExpansion.initialize_collections()NetworkExpansion.nameNetworkExpansion.optionsNetworkExpansion.possible_attributes()NetworkExpansion.set_result()NetworkExpansion.thermochemistry_gearNetworkExpansion.unset_collections()
- Implementations
- Selections
FileInputSelectionInputSelectionScineGeometryInputSelectionAllFromPreviousResultSelectionAllUserInputsSelectionBarriersWithinRangeSelectionLowestBarrierSelectionProductsSelectionCentroidConformerSelectionClusterCentroidConformerSelectionClusterSelectionConformerSelectionLowestEnergyConformerPerClusterSelectionLowestEnergyConformerSelectionCentralMetalSelection
- Network Expansions
- Selections
- Data Structures
- Utilities
- Methods for structure manipulations
ReactiveComplexesInterReactiveComplexesassemble_reactive_complex()LebedevSphereUnitCircleinsert_initial_structure()ComponentDistanceTupledeserialize_molecules()distinct_atoms()distinct_components()distinguish_components()get_atom_pairs()make_sorted_pair()mol_from_cbor()mol_to_cbor()mols_from_properties()pruned_atom_pairs()unpruned_atom_pairs()
- Database Object Wrappers
AggregateCacheAggregateAggregate.analyze()Aggregate.complete()Aggregate.explore()Aggregate.get_aggregate_type()Aggregate.get_concentration_flux()Aggregate.get_db_id()Aggregate.get_db_object()Aggregate.get_electronic_model()Aggregate.get_element_count()Aggregate.get_enthalpy()Aggregate.get_entropy()Aggregate.get_free_energy()Aggregate.get_lowest_n_structures()Aggregate.get_manager()Aggregate.get_model_combination()Aggregate.get_sorted_structure_list()Aggregate.get_starting_concentration()
EnsembleReactionCacheReactionReaction.analyze()Reaction.barrierless()Reaction.circle_reaction()Reaction.complete()Reaction.explore()Reaction.get_arrhenius_prefactor()Reaction.get_db_id()Reaction.get_db_object()Reaction.get_electronic_model()Reaction.get_element_count()Reaction.get_free_energy_of_activation()Reaction.get_lhs_aggregates()Reaction.get_lhs_free_energy()Reaction.get_lowest_n_steps()Reaction.get_lowest_n_structures()Reaction.get_manager()Reaction.get_model_combination()Reaction.get_reaction_free_energy()Reaction.get_rhs_aggregates()Reaction.get_rhs_free_energy()Reaction.get_sorted_structure_list()Reaction.get_sorted_structure_step_list()Reaction.get_transition_state_free_energy()Reaction.get_ts_theory_rate_constants()
PlaceHolderReferenceStateReferenceStateThermodynamicPropertiesThermodynamicProperties.get_electronic_energy()ThermodynamicProperties.get_enthalpy()ThermodynamicProperties.get_entropy()ThermodynamicProperties.get_gibbs_free_energy()ThermodynamicProperties.get_gibbs_free_energy_correction()ThermodynamicProperties.get_reference_state()ThermodynamicProperties.get_thermochemistry_calculator()ThermodynamicProperties.get_zero_point_energy()ThermodynamicProperties.get_zero_point_energy_correction()ThermodynamicProperties.id()
ThermodynamicPropertiesCacheThermodynamicPropertiesCache.clear()ThermodynamicPropertiesCache.get_ensemble_enthalpy()ThermodynamicPropertiesCache.get_ensemble_entropy()ThermodynamicPropertiesCache.get_ensemble_gibbs_free_energy()ThermodynamicPropertiesCache.get_n_cached()ThermodynamicPropertiesCache.get_or_produce()ThermodynamicPropertiesCache.get_sorted_structure_list()ThermodynamicPropertiesCache.minimum_values_need_update()ThermodynamicPropertiesCache.provides_values()
MultiModelAggregateCacheMultiModelCacheFactoryMultiModelReactionCacheMultipleModelCache
- Methods for structure manipulations