Index

A

absolute_frequency_threshold (scine_chemoton.gears.compound.ThermoAggregateHousekeeping.Options attribute) AcetalX (class in scine_chemoton.reaction_rules.reaction_rule_library) ActivatedAggregateFilter (class in scine_chemoton.filters.aggregate_filters) add_reaction() (scine_chemoton.gears.pathfinder.Pathfinder.BarrierBasedHandler method) (scine_chemoton.gears.pathfinder.Pathfinder.BasicHandler method) additional_catalyst_elements (scine_chemoton.steering_wheel.selections.organometallic_complexes.CentralMetalSelection.Options attribute) Aggregate (class in scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper) aggregate_enabling (scine_chemoton.gears.compound.BasicAggregateHousekeeping.Options attribute) (scine_chemoton.gears.compound.ThermoAggregateHousekeeping.Options attribute) (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement attribute) aggregate_energy_window (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) aggregate_filter (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps attribute) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps attribute) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps attribute) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps attribute) (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement attribute) (scine_chemoton.steering_wheel.datastructures.SelectionResult attribute) aggregate_validation (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement attribute) AggregateBasedRefinement (class in scine_chemoton.gears.network_refinement.aggregate_based_refinement) AggregateBasedRefinement.Options (class in scine_chemoton.gears.network_refinement.aggregate_based_refinement) AggregateCache (class in scine_chemoton.utilities.db_object_wrappers.aggregate_cache) AggregateDisabling (class in scine_chemoton.gears.network_refinement.disabling) AggregateEnabling (class in scine_chemoton.gears.network_refinement.enabling) AggregateFilter (class in scine_chemoton.filters.aggregate_filters) AggregateFilterAndArray (class in scine_chemoton.filters.aggregate_filters) AggregateFilterOrArray (class in scine_chemoton.filters.aggregate_filters) AllBarrierLessDissociationsFilter (class in scine_chemoton.filters.further_exploration_filters) AllFromPreviousResultSelection (class in scine_chemoton.steering_wheel.selections.basics) AllFromPreviousResultSelection.Options (class in scine_chemoton.steering_wheel.selections.basics)

allow_unsolved_compound_costs (scine_chemoton.gears.kinetics.PathfinderKinetics.Options attribute) allowed_labels (scine_chemoton.gears.single_point.SinglePoint.Options attribute) AllUserInputsSelection (class in scine_chemoton.steering_wheel.selections.basics) AllUserInputsSelection.Options (class in scine_chemoton.steering_wheel.selections.basics) AllylicSp3X (class in scine_chemoton.reaction_rules.reaction_rule_library) always_further_explore_dissociative_reactions (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.UnimolOptions attribute) AlwaysFalse (class in scine_chemoton.reaction_rules.distance_rules) AlwaysTrue (class in scine_chemoton.reaction_rules.distance_rules) AmidH (class in scine_chemoton.reaction_rules.reaction_rule_library) AmidX (class in scine_chemoton.reaction_rules.reaction_rule_library) AminX (class in scine_chemoton.reaction_rules.reaction_rule_library) AmmoniumX (class in scine_chemoton.reaction_rules.reaction_rule_library) analyze() (scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper.Aggregate method) (scine_chemoton.utilities.db_object_wrappers.ensemble_wrapper.Ensemble method) (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) AND (scine_chemoton.steering_wheel.datastructures.LogicCoupling attribute) append() (scine_chemoton.engine.EngineHandler method) apply_to_protocol() (scine_chemoton.steering_wheel.datastructures.GearOptions method) ApplyToAllStepsInReaction (class in scine_chemoton.gears.network_refinement.enabling) ApplyToAllStructuresInAggregate (class in scine_chemoton.gears.network_refinement.enabling) args (scine_chemoton.gears.pathfinder.DifferentSubgraphsError attribute) assemble_reactive_complex() (in module scine_chemoton.utilities.reactive_complexes.inter_reactive_complexes) assert_non_negative_barriers() (scine_chemoton.gears.kinetic_modeling.rms_kinetic_modeling.RMSKineticModelingJobFactory method) Association (class in scine_chemoton.steering_wheel.network_expansions.reactions) Association.Options (class in scine_chemoton.steering_wheel.network_expansions.reactions) Associative (scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer.ReactionType attribute) AtomEnergyReference (class in scine_chemoton.gears.kinetic_modeling.atomization) AtomNumberFilter (class in scine_chemoton.filters.aggregate_filters) (class in scine_chemoton.filters.structure_filters) AtomPairFunctionalGroupFilter (class in scine_chemoton.filters.reactive_site_filters) AtomRuleBasedFilter (class in scine_chemoton.filters.reactive_site_filters)

B

barrier_limit (scine_chemoton.gears.pathfinder.Pathfinder.Options attribute) barrierless() (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) barrierless_weight (scine_chemoton.gears.kinetics.PathfinderKinetics.Options attribute) (scine_chemoton.gears.pathfinder.Pathfinder.Options attribute) BarrierlessElementaryStepFilter (class in scine_chemoton.filters.elementary_step_filters) BarrierlessReactionFilter (class in scine_chemoton.filters.reaction_filters) BarriersWithinRangeSelection (class in scine_chemoton.steering_wheel.selections.basics) BarriersWithinRangeSelection.Options (class in scine_chemoton.steering_wheel.selections.basics) base_job_settings (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.ElementaryStepGear.Options attribute) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options attribute) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased.Options attribute) (scine_chemoton.gears.elementary_steps.trial_generator.TrialGenerator.Options attribute) BaseRule (class in scine_chemoton.reaction_rules) BasicAggregateHousekeeping (class in scine_chemoton.gears.compound) BasicAggregateHousekeeping.Options (class in scine_chemoton.gears.compound) BasicBarrierHeightKinetics (class in scine_chemoton.gears.kinetics) BasicBarrierHeightKinetics.Options (class in scine_chemoton.gears.kinetics) BasicReactionHousekeeping (class in scine_chemoton.gears.reaction) BasicReactionHousekeeping.Options (class in scine_chemoton.gears.reaction) BasicThermoDataCompletion (class in scine_chemoton.gears.thermo) BasicThermoDataCompletion.Options (class in scine_chemoton.gears.thermo) bimolecular_association_options (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options attribute) bimolecular_coordinates() (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps method) (scine_chemoton.gears.elementary_steps.ElementaryStepGear method) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps method) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps method) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps method) (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased method) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations method) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased method) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased method) (scine_chemoton.gears.elementary_steps.trial_generator.TrialGenerator method)

bimolecular_options (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options attribute) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased.Options attribute) bimolecular_reactions() (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased method) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations method) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased method) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased method) (scine_chemoton.gears.elementary_steps.trial_generator.TrialGenerator method) bond_order_job (scine_chemoton.gears.compound.BasicAggregateHousekeeping.Options attribute) (scine_chemoton.gears.compound.ThermoAggregateHousekeeping.Options attribute) bond_order_settings (scine_chemoton.gears.compound.BasicAggregateHousekeeping.Options attribute) (scine_chemoton.gears.compound.ThermoAggregateHousekeeping.Options attribute) BondBased (class in scine_chemoton.gears.elementary_steps.trial_generator.bond_based) BondBased.Options (class in scine_chemoton.gears.elementary_steps.trial_generator.bond_based) BondBased.Options.BimolOptions (class in scine_chemoton.gears.elementary_steps.trial_generator.bond_based) BondBased.Options.UnimolOptions (class in scine_chemoton.gears.elementary_steps.trial_generator.bond_based) BruteForceConformers (class in scine_chemoton.gears.conformers.brute_force) BruteForceConformers.Options (class in scine_chemoton.gears.conformers.brute_force) BruteForceElementarySteps (class in scine_chemoton.gears.elementary_steps.brute_force) BruteForceElementarySteps.Options (class in scine_chemoton.gears.elementary_steps.brute_force) build_graph() (scine_chemoton.gears.pathfinder.Pathfinder method)

C

cache_file_name (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement.Options attribute) caching_file_name (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) calculate_compound_costs() (scine_chemoton.gears.pathfinder.Pathfinder method) CALCULATING (scine_chemoton.steering_wheel.datastructures.Status attribute) calculation_id_list (scine_chemoton.gears.rerun_calculations.RerunCalculations.Options attribute) calculation_model (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) CalculationBasedRefinement (class in scine_chemoton.gears.network_refinement.calculation_based_refinement) CalculationBasedRefinement.Options (class in scine_chemoton.gears.network_refinement.calculation_based_refinement) can_cache() (scine_chemoton.filters.aggregate_filters.ActivatedAggregateFilter method) (scine_chemoton.filters.aggregate_filters.AggregateFilter method) (scine_chemoton.filters.aggregate_filters.AggregateFilterAndArray method) (scine_chemoton.filters.aggregate_filters.AggregateFilterOrArray method) (scine_chemoton.filters.aggregate_filters.AtomNumberFilter method) (scine_chemoton.filters.aggregate_filters.CatalystFilter method) (scine_chemoton.filters.aggregate_filters.ChargeCombinationFilter method) (scine_chemoton.filters.aggregate_filters.CompleteSubstructureFilter method) (scine_chemoton.filters.aggregate_filters.CompoundCostPropertyFilter method) (scine_chemoton.filters.aggregate_filters.ConcentrationPropertyFilter method) (scine_chemoton.filters.aggregate_filters.ElementCountFilter method) (scine_chemoton.filters.aggregate_filters.ElementSumCountFilter method) (scine_chemoton.filters.aggregate_filters.HasStructureWithModel method) (scine_chemoton.filters.aggregate_filters.IdFilter method) (scine_chemoton.filters.aggregate_filters.LastKineticModelingFilter method) (scine_chemoton.filters.aggregate_filters.MolecularWeightFilter method) (scine_chemoton.filters.aggregate_filters.OneAggregateIdFilter method) (scine_chemoton.filters.aggregate_filters.OnePotentialEnergySurface method) (scine_chemoton.filters.aggregate_filters.PlaceHolderAggregateFilter method) (scine_chemoton.filters.aggregate_filters.SelectedAggregateIdFilter method) (scine_chemoton.filters.aggregate_filters.SelectedStructureIdFilter method) (scine_chemoton.filters.aggregate_filters.SelfReactionFilter method) (scine_chemoton.filters.aggregate_filters.SpecificChargeFilter method) (scine_chemoton.filters.aggregate_filters.StopDuringExploration method) (scine_chemoton.filters.aggregate_filters.TrueMinimumFilter method) (scine_chemoton.filters.structure_filters.AtomNumberFilter method) (scine_chemoton.filters.structure_filters.CatalystFilter method) (scine_chemoton.filters.structure_filters.ChargeCombinationFilter method) (scine_chemoton.filters.structure_filters.ElementCountFilter method) (scine_chemoton.filters.structure_filters.ElementSumCountFilter method) (scine_chemoton.filters.structure_filters.ModelFilter method) (scine_chemoton.filters.structure_filters.MolecularWeightFilter method) (scine_chemoton.filters.structure_filters.SpecificChargeFilter method) (scine_chemoton.filters.structure_filters.StructureFilter method) (scine_chemoton.filters.structure_filters.StructureFilterAndArray method) (scine_chemoton.filters.structure_filters.StructureFilterOrArray method) (scine_chemoton.filters.structure_filters.StructureLabelFilter method) (scine_chemoton.filters.structure_filters.TrueMinimumFilter method) CarbonylX (class in scine_chemoton.reaction_rules.reaction_rule_library) CarboxylH (class in scine_chemoton.reaction_rules.reaction_rule_library) CarboxylX (class in scine_chemoton.reaction_rules.reaction_rule_library) CatalystFilter (class in scine_chemoton.filters.aggregate_filters) (class in scine_chemoton.filters.structure_filters) CentralMetalSelection (class in scine_chemoton.steering_wheel.selections.organometallic_complexes) CentralMetalSelection.Options (class in scine_chemoton.steering_wheel.selections.organometallic_complexes) CentralSiteFilter (class in scine_chemoton.filters.reactive_site_filters) CentroidConformerSelection (class in scine_chemoton.steering_wheel.selections.conformers) CentroidConformerSelection.Options (class in scine_chemoton.steering_wheel.selections.conformers) change_model (scine_chemoton.gears.rerun_calculations.RerunCalculations.Options attribute) charge (scine_chemoton.steering_wheel.datastructures.StructureInformation attribute) ChargeCombinationFilter (class in scine_chemoton.filters.aggregate_filters) (class in scine_chemoton.filters.structure_filters) checkrules() (scine_chemoton.filters.reactive_site_filters.AtomPairFunctionalGroupFilter static method) ChemicalReaction (class in scine_chemoton.steering_wheel.network_expansions.reactions) ChemicalReaction.Options (class in scine_chemoton.steering_wheel.network_expansions.reactions) CHOlefinC (class in scine_chemoton.reaction_rules.reaction_rule_library) circle_reaction() (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) clear() (scine_chemoton.reaction_rules.distance_rules.DistanceRuleSet method) (scine_chemoton.reaction_rules.element_rules.ElementRuleSet method) (scine_chemoton.reaction_rules.polarization_rules.PolarizationRuleSet method) (scine_chemoton.reaction_rules.reaction_rule_library.DefaultOrganicChemistry method) (scine_chemoton.reaction_rules.RuleSet method) (scine_chemoton.steering_wheel.datastructures.GearOptions method) (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicPropertiesCache method) (scine_chemoton.utilities.db_object_wrappers.wrapper_caches.MultiModelCacheFactory method) clear_cache() (scine_chemoton.gears.conformers.brute_force.BruteForceConformers method) (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps method) (scine_chemoton.gears.elementary_steps.ElementaryStepGear method) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps method) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps method) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps method) (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased method) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations method) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased method) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased method) (scine_chemoton.gears.elementary_steps.trial_generator.TrialGenerator method) (scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics method) (scine_chemoton.gears.kinetics.KineticsBase method) (scine_chemoton.gears.kinetics.MaximumFluxKinetics method) (scine_chemoton.gears.kinetics.MinimalConnectivityKinetics method) (scine_chemoton.gears.kinetics.PathfinderKinetics method) (scine_chemoton.gears.kinetics.ReactionFilterBasedKinetics method) (scine_chemoton.gears.thermo.BasicThermoDataCompletion method) (scine_chemoton.steering_wheel.SteeringWheel method) ClusterCentroidConformerSelection (class in scine_chemoton.steering_wheel.selections.conformers) ClusterCentroidConformerSelection.Options (class in scine_chemoton.steering_wheel.selections.conformers) ClusterSelection (class in scine_chemoton.steering_wheel.selections.conformers) ClusterSelection.Options (class in scine_chemoton.steering_wheel.selections.conformers) comment_filter (scine_chemoton.gears.rerun_calculations.RerunCalculations.Options attribute) complete() (scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper.Aggregate method) (scine_chemoton.utilities.db_object_wrappers.ensemble_wrapper.Ensemble method) (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method)

CompleteSubstructureFilter (class in scine_chemoton.filters.aggregate_filters) complex_generator (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.BimolAssociationOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased.Options.BimolOptions attribute) ComponentDistanceTuple (class in scine_chemoton.utilities.masm) components (scine_chemoton.utilities.masm.ComponentDistanceTuple attribute) CompoundCostPropertyFilter (class in scine_chemoton.filters.aggregate_filters) compounds (scine_chemoton.steering_wheel.datastructures.NetworkExpansionResult attribute) ConcentrationPropertyFilter (class in scine_chemoton.filters.aggregate_filters) conformer_job (scine_chemoton.gears.conformers.brute_force.BruteForceConformers.Options attribute) conformer_settings (scine_chemoton.gears.conformers.brute_force.BruteForceConformers.Options attribute) ConformerCreation (class in scine_chemoton.steering_wheel.network_expansions.conformers) ConformerCreation.Options (class in scine_chemoton.steering_wheel.network_expansions.conformers) ConformerSelection (class in scine_chemoton.steering_wheel.selections.conformers) ConformerSelection.Options (class in scine_chemoton.steering_wheel.selections.conformers) ConnectivityAnalyzer (class in scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer) consider_diatomic_fragments (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.BimolAssociationOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.UnimolAssociationOptions attribute) ConsistentEnergyModelFilter (class in scine_chemoton.filters.elementary_step_filters) copy() (scine_chemoton.reaction_rules.distance_rules.DistanceRuleSet method) (scine_chemoton.reaction_rules.element_rules.ElementRuleSet method) (scine_chemoton.reaction_rules.polarization_rules.PolarizationRuleSet method) (scine_chemoton.reaction_rules.reaction_rule_library.DefaultOrganicChemistry method) (scine_chemoton.reaction_rules.RuleSet method) (scine_chemoton.steering_wheel.datastructures.GearOptions method) correction_name (scine_chemoton.gears.thermo.BasicThermoDataCompletion attribute) count() (scine_chemoton.utilities.masm.ComponentDistanceTuple method) create_kinetic_modeling_job() (scine_chemoton.gears.kinetic_modeling.kinetx_kinetic_modeling.KinetxKineticModelingJobFactory method) (scine_chemoton.gears.kinetic_modeling.prepare_kinetic_modeling_job.KineticModelingJobFactory method) (scine_chemoton.gears.kinetic_modeling.rms_kinetic_modeling.RMSKineticModelingJobFactory method) credentials (scine_chemoton.steering_wheel.datastructures.ProtocolEntry attribute) current_gears() (scine_chemoton.steering_wheel.network_expansions.basics.SimpleOptimization method) (scine_chemoton.steering_wheel.network_expansions.basics.ThermochemistryGeneration method) (scine_chemoton.steering_wheel.network_expansions.conformers.ConformerCreation method) (scine_chemoton.steering_wheel.network_expansions.NetworkExpansion method) (scine_chemoton.steering_wheel.network_expansions.reactions.Association method) (scine_chemoton.steering_wheel.network_expansions.reactions.ChemicalReaction method) (scine_chemoton.steering_wheel.network_expansions.reactions.Dissociation method) (scine_chemoton.steering_wheel.network_expansions.reactions.Rearrangement method) currently_caches() (scine_chemoton.filters.aggregate_filters.ActivatedAggregateFilter method) (scine_chemoton.filters.aggregate_filters.AggregateFilter method) (scine_chemoton.filters.aggregate_filters.AggregateFilterAndArray method) (scine_chemoton.filters.aggregate_filters.AggregateFilterOrArray method) (scine_chemoton.filters.aggregate_filters.AtomNumberFilter method) (scine_chemoton.filters.aggregate_filters.CatalystFilter method) (scine_chemoton.filters.aggregate_filters.ChargeCombinationFilter method) (scine_chemoton.filters.aggregate_filters.CompleteSubstructureFilter method) (scine_chemoton.filters.aggregate_filters.CompoundCostPropertyFilter method) (scine_chemoton.filters.aggregate_filters.ConcentrationPropertyFilter method) (scine_chemoton.filters.aggregate_filters.ElementCountFilter method) (scine_chemoton.filters.aggregate_filters.ElementSumCountFilter method) (scine_chemoton.filters.aggregate_filters.HasStructureWithModel method) (scine_chemoton.filters.aggregate_filters.IdFilter method) (scine_chemoton.filters.aggregate_filters.LastKineticModelingFilter method) (scine_chemoton.filters.aggregate_filters.MolecularWeightFilter method) (scine_chemoton.filters.aggregate_filters.OneAggregateIdFilter method) (scine_chemoton.filters.aggregate_filters.OnePotentialEnergySurface method) (scine_chemoton.filters.aggregate_filters.PlaceHolderAggregateFilter method) (scine_chemoton.filters.aggregate_filters.SelectedAggregateIdFilter method) (scine_chemoton.filters.aggregate_filters.SelectedStructureIdFilter method) (scine_chemoton.filters.aggregate_filters.SelfReactionFilter method) (scine_chemoton.filters.aggregate_filters.SpecificChargeFilter method) (scine_chemoton.filters.aggregate_filters.StopDuringExploration method) (scine_chemoton.filters.aggregate_filters.TrueMinimumFilter method) (scine_chemoton.filters.structure_filters.AtomNumberFilter method) (scine_chemoton.filters.structure_filters.CatalystFilter method) (scine_chemoton.filters.structure_filters.ChargeCombinationFilter method) (scine_chemoton.filters.structure_filters.ElementCountFilter method) (scine_chemoton.filters.structure_filters.ElementSumCountFilter method) (scine_chemoton.filters.structure_filters.ModelFilter method) (scine_chemoton.filters.structure_filters.MolecularWeightFilter method) (scine_chemoton.filters.structure_filters.SpecificChargeFilter method) (scine_chemoton.filters.structure_filters.StructureFilter method) (scine_chemoton.filters.structure_filters.StructureFilterAndArray method) (scine_chemoton.filters.structure_filters.StructureFilterOrArray method) (scine_chemoton.filters.structure_filters.StructureLabelFilter method) (scine_chemoton.filters.structure_filters.TrueMinimumFilter method) cutting_job_settings (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.UnimolOptions attribute) cycle_time (scine_chemoton.gears.compound.BasicAggregateHousekeeping.Options attribute) (scine_chemoton.gears.compound.ThermoAggregateHousekeeping.Options attribute) (scine_chemoton.gears.conformers.brute_force.BruteForceConformers.Options attribute) (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.ElementaryStepGear.Options attribute) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps.Options attribute) (scine_chemoton.gears.Gear.Options attribute) (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling.Options attribute) (scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics.Options attribute) (scine_chemoton.gears.kinetics.KineticsBase.Options attribute) (scine_chemoton.gears.kinetics.MaximumFluxKinetics.Options attribute) (scine_chemoton.gears.kinetics.MinimalConnectivityKinetics.Options attribute) (scine_chemoton.gears.kinetics.PathfinderKinetics.Options attribute) (scine_chemoton.gears.kinetics.ReactionFilterBasedKinetics.Options attribute) (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) (scine_chemoton.gears.reaction.BasicReactionHousekeeping.Options attribute) (scine_chemoton.gears.rerun_calculations.RerunCalculations.Options attribute) (scine_chemoton.gears.scheduler.Scheduler.Options attribute) (scine_chemoton.gears.single_point.SinglePoint.Options attribute) (scine_chemoton.gears.thermo.BasicThermoDataCompletion.Options attribute)

D

DBObjectDisabling (class in scine_chemoton.gears.network_refinement.disabling) DBObjectEnabling (class in scine_chemoton.gears.network_refinement.enabling) DefaultOrganicChemistry (class in scine_chemoton.reaction_rules.reaction_rule_library) DefaultOrganicChemistry.C (class in scine_chemoton.reaction_rules.reaction_rule_library) DefaultOrganicChemistry.H (class in scine_chemoton.reaction_rules.reaction_rule_library) delete_results() (scine_chemoton.steering_wheel.SteeringWheel method) deserialize_molecules() (in module scine_chemoton.utilities.masm) DifferentSubgraphsError disable() (scine_chemoton.gears.network_refinement.disabling.AggregateDisabling static method) (scine_chemoton.gears.network_refinement.disabling.DBObjectDisabling static method) (scine_chemoton.gears.network_refinement.disabling.DisableAllAggregates static method) (scine_chemoton.gears.network_refinement.disabling.DisableAllReactions static method) (scine_chemoton.gears.network_refinement.disabling.DisableAllSteps static method) (scine_chemoton.gears.network_refinement.disabling.DisableAllStepsByModel static method) (scine_chemoton.gears.network_refinement.disabling.DisableReactionByJob static method) (scine_chemoton.gears.network_refinement.disabling.DisableStepByJob static method) (scine_chemoton.gears.network_refinement.disabling.ReactionDisabling static method) (scine_chemoton.gears.network_refinement.disabling.StepDisabling static method) disable_aggregate() (scine_chemoton.gears.network_refinement.disabling.AggregateDisabling method) (scine_chemoton.gears.network_refinement.disabling.DisableAllAggregates method) disable_caching() (scine_chemoton.filters.aggregate_filters.ActivatedAggregateFilter method) (scine_chemoton.filters.aggregate_filters.AggregateFilter method) (scine_chemoton.filters.aggregate_filters.AggregateFilterAndArray method) (scine_chemoton.filters.aggregate_filters.AggregateFilterOrArray method) (scine_chemoton.filters.aggregate_filters.AtomNumberFilter method) (scine_chemoton.filters.aggregate_filters.CatalystFilter method) (scine_chemoton.filters.aggregate_filters.ChargeCombinationFilter method) (scine_chemoton.filters.aggregate_filters.CompleteSubstructureFilter method) (scine_chemoton.filters.aggregate_filters.CompoundCostPropertyFilter method) (scine_chemoton.filters.aggregate_filters.ConcentrationPropertyFilter method) (scine_chemoton.filters.aggregate_filters.ElementCountFilter method) (scine_chemoton.filters.aggregate_filters.ElementSumCountFilter method) (scine_chemoton.filters.aggregate_filters.HasStructureWithModel method) (scine_chemoton.filters.aggregate_filters.IdFilter method) (scine_chemoton.filters.aggregate_filters.LastKineticModelingFilter method) (scine_chemoton.filters.aggregate_filters.MolecularWeightFilter method) (scine_chemoton.filters.aggregate_filters.OneAggregateIdFilter method) (scine_chemoton.filters.aggregate_filters.OnePotentialEnergySurface method) (scine_chemoton.filters.aggregate_filters.PlaceHolderAggregateFilter method) (scine_chemoton.filters.aggregate_filters.SelectedAggregateIdFilter method) (scine_chemoton.filters.aggregate_filters.SelectedStructureIdFilter method) (scine_chemoton.filters.aggregate_filters.SelfReactionFilter method) (scine_chemoton.filters.aggregate_filters.SpecificChargeFilter method) (scine_chemoton.filters.aggregate_filters.StopDuringExploration method) (scine_chemoton.filters.aggregate_filters.TrueMinimumFilter method) (scine_chemoton.filters.structure_filters.AtomNumberFilter method) (scine_chemoton.filters.structure_filters.CatalystFilter method) (scine_chemoton.filters.structure_filters.ChargeCombinationFilter method) (scine_chemoton.filters.structure_filters.ElementCountFilter method) (scine_chemoton.filters.structure_filters.ElementSumCountFilter method) (scine_chemoton.filters.structure_filters.ModelFilter method) (scine_chemoton.filters.structure_filters.MolecularWeightFilter method) (scine_chemoton.filters.structure_filters.SpecificChargeFilter method) (scine_chemoton.filters.structure_filters.StructureFilter method) (scine_chemoton.filters.structure_filters.StructureFilterAndArray method) (scine_chemoton.filters.structure_filters.StructureFilterOrArray method) (scine_chemoton.filters.structure_filters.StructureLabelFilter method) (scine_chemoton.filters.structure_filters.TrueMinimumFilter method) (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps method) (scine_chemoton.gears.elementary_steps.ElementaryStepGear method) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps method) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps method) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps method)

disable_reaction() (scine_chemoton.gears.network_refinement.disabling.DisableAllReactions method) (scine_chemoton.gears.network_refinement.disabling.DisableReactionByJob method) (scine_chemoton.gears.network_refinement.disabling.ReactionDisabling method) DisableAllAggregates (class in scine_chemoton.gears.network_refinement.disabling) DisableAllReactions (class in scine_chemoton.gears.network_refinement.disabling) DisableAllSteps (class in scine_chemoton.gears.network_refinement.disabling) DisableAllStepsByModel (class in scine_chemoton.gears.network_refinement.disabling) DisableReactionByJob (class in scine_chemoton.gears.network_refinement.disabling) DisableStepByJob (class in scine_chemoton.gears.network_refinement.disabling) Disconnective (scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer.ReactionType attribute) Dissociation (class in scine_chemoton.steering_wheel.network_expansions.reactions) Dissociation.Options (class in scine_chemoton.steering_wheel.network_expansions.reactions) dissociation_setting_from_reaction_coordinate() (scine_chemoton.filters.further_exploration_filters.AllBarrierLessDissociationsFilter static method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilter static method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilterAndArray static method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilterOrArray static method) (scine_chemoton.filters.further_exploration_filters.ReactionCoordinateMaxDissociationEnergyFilter static method) Dissociative (scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer.ReactionType attribute) distance (scine_chemoton.utilities.masm.ComponentDistanceTuple attribute) DistanceBaseRule (class in scine_chemoton.reaction_rules.distance_rules) DistanceRuleAndArray (class in scine_chemoton.reaction_rules.distance_rules) DistanceRuleOrArray (class in scine_chemoton.reaction_rules.distance_rules) DistanceRuleSet (class in scine_chemoton.reaction_rules.distance_rules) distinct_atoms() (in module scine_chemoton.utilities.masm) distinct_components() (in module scine_chemoton.utilities.masm) distinguish_components() (in module scine_chemoton.utilities.masm) double_ended_job (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) double_ended_job_settings (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) dry_setup_protocol() (scine_chemoton.steering_wheel.network_expansions.basics.SimpleOptimization method) (scine_chemoton.steering_wheel.network_expansions.basics.ThermochemistryGeneration method) (scine_chemoton.steering_wheel.network_expansions.conformers.ConformerCreation method) (scine_chemoton.steering_wheel.network_expansions.NetworkExpansion method) (scine_chemoton.steering_wheel.network_expansions.reactions.Association method) (scine_chemoton.steering_wheel.network_expansions.reactions.ChemicalReaction method) (scine_chemoton.steering_wheel.network_expansions.reactions.Dissociation method) (scine_chemoton.steering_wheel.network_expansions.reactions.Rearrangement method)

E

elementary_step_filter (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement attribute) elementary_step_index_file_name (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) ElementaryStepBarrierFilter (class in scine_chemoton.filters.elementary_step_filters) ElementaryStepFilter (class in scine_chemoton.filters.elementary_step_filters) ElementaryStepFilterAndArray (class in scine_chemoton.filters.elementary_step_filters) ElementaryStepFilterOrArray (class in scine_chemoton.filters.elementary_step_filters) ElementaryStepGear (class in scine_chemoton.gears.elementary_steps) ElementaryStepGear.Options (class in scine_chemoton.gears.elementary_steps) ElementBaseRule (class in scine_chemoton.reaction_rules.element_rules) ElementCountFilter (class in scine_chemoton.filters.aggregate_filters) (class in scine_chemoton.filters.structure_filters) ElementRuleSet (class in scine_chemoton.reaction_rules.element_rules) ElementSumCountFilter (class in scine_chemoton.filters.aggregate_filters) (class in scine_chemoton.filters.structure_filters) ElementWiseReactionCoordinateFilter (class in scine_chemoton.filters.reactive_site_filters) enable() (scine_chemoton.gears.network_refinement.enabling.AggregateEnabling static method) (scine_chemoton.gears.network_refinement.enabling.ApplyToAllStepsInReaction static method) (scine_chemoton.gears.network_refinement.enabling.ApplyToAllStructuresInAggregate static method) (scine_chemoton.gears.network_refinement.enabling.DBObjectEnabling static method) (scine_chemoton.gears.network_refinement.enabling.EnableAllAggregates static method) (scine_chemoton.gears.network_refinement.enabling.EnableAllReactions static method) (scine_chemoton.gears.network_refinement.enabling.EnableAllSteps static method) (scine_chemoton.gears.network_refinement.enabling.EnableAllStructures static method) (scine_chemoton.gears.network_refinement.enabling.EnableCalculationResults static method) (scine_chemoton.gears.network_refinement.enabling.EnableJobSpecificCalculations static method) (scine_chemoton.gears.network_refinement.enabling.EnableStructureByModel static method) (scine_chemoton.gears.network_refinement.enabling.FilteredStepEnabling static method) (scine_chemoton.gears.network_refinement.enabling.PlaceHolderAggregateEnabling static method) (scine_chemoton.gears.network_refinement.enabling.PlaceHolderCalculationEnabling static method) (scine_chemoton.gears.network_refinement.enabling.PlaceHolderReactionEnabling static method) (scine_chemoton.gears.network_refinement.enabling.ReactionEnabling static method) (scine_chemoton.gears.network_refinement.enabling.StepEnabling static method) (scine_chemoton.gears.network_refinement.enabling.StructureEnabling static method) enable_bimolecular_trials (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.ElementaryStepGear.Options attribute) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps.Options attribute) enable_caching() (scine_chemoton.filters.aggregate_filters.ActivatedAggregateFilter method) (scine_chemoton.filters.aggregate_filters.AggregateFilter method) (scine_chemoton.filters.aggregate_filters.AggregateFilterAndArray method) (scine_chemoton.filters.aggregate_filters.AggregateFilterOrArray method) (scine_chemoton.filters.aggregate_filters.AtomNumberFilter method) (scine_chemoton.filters.aggregate_filters.CatalystFilter method) (scine_chemoton.filters.aggregate_filters.ChargeCombinationFilter method) (scine_chemoton.filters.aggregate_filters.CompleteSubstructureFilter method) (scine_chemoton.filters.aggregate_filters.CompoundCostPropertyFilter method) (scine_chemoton.filters.aggregate_filters.ConcentrationPropertyFilter method) (scine_chemoton.filters.aggregate_filters.ElementCountFilter method) (scine_chemoton.filters.aggregate_filters.ElementSumCountFilter method) (scine_chemoton.filters.aggregate_filters.HasStructureWithModel method) (scine_chemoton.filters.aggregate_filters.IdFilter method) (scine_chemoton.filters.aggregate_filters.LastKineticModelingFilter method) (scine_chemoton.filters.aggregate_filters.MolecularWeightFilter method) (scine_chemoton.filters.aggregate_filters.OneAggregateIdFilter method) (scine_chemoton.filters.aggregate_filters.OnePotentialEnergySurface method) (scine_chemoton.filters.aggregate_filters.PlaceHolderAggregateFilter method) (scine_chemoton.filters.aggregate_filters.SelectedAggregateIdFilter method) (scine_chemoton.filters.aggregate_filters.SelectedStructureIdFilter method) (scine_chemoton.filters.aggregate_filters.SelfReactionFilter method) (scine_chemoton.filters.aggregate_filters.SpecificChargeFilter method) (scine_chemoton.filters.aggregate_filters.StopDuringExploration method) (scine_chemoton.filters.aggregate_filters.TrueMinimumFilter method) (scine_chemoton.filters.structure_filters.AtomNumberFilter method) (scine_chemoton.filters.structure_filters.CatalystFilter method) (scine_chemoton.filters.structure_filters.ChargeCombinationFilter method) (scine_chemoton.filters.structure_filters.ElementCountFilter method) (scine_chemoton.filters.structure_filters.ElementSumCountFilter method) (scine_chemoton.filters.structure_filters.ModelFilter method) (scine_chemoton.filters.structure_filters.MolecularWeightFilter method) (scine_chemoton.filters.structure_filters.SpecificChargeFilter method) (scine_chemoton.filters.structure_filters.StructureFilter method) (scine_chemoton.filters.structure_filters.StructureFilterAndArray method) (scine_chemoton.filters.structure_filters.StructureFilterOrArray method) (scine_chemoton.filters.structure_filters.StructureLabelFilter method) (scine_chemoton.filters.structure_filters.TrueMinimumFilter method) (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps method) (scine_chemoton.gears.elementary_steps.ElementaryStepGear method) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps method) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps method) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps method)

enable_further_explorations (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.UnimolOptions attribute) enable_structure() (scine_chemoton.gears.network_refinement.enabling.EnableAllStructures method) (scine_chemoton.gears.network_refinement.enabling.EnableStructureByModel method) (scine_chemoton.gears.network_refinement.enabling.StructureEnabling method) enable_unimolecular_trials (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.ElementaryStepGear.Options attribute) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps.Options attribute) EnableAllAggregates (class in scine_chemoton.gears.network_refinement.enabling) EnableAllReactions (class in scine_chemoton.gears.network_refinement.enabling) EnableAllSteps (class in scine_chemoton.gears.network_refinement.enabling) EnableAllStructures (class in scine_chemoton.gears.network_refinement.enabling) EnableCalculationResults (class in scine_chemoton.gears.network_refinement.enabling) enabled (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.UnimolAssociationOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.UnimolDissociationOptions attribute) EnableJobSpecificCalculations (class in scine_chemoton.gears.network_refinement.enabling) EnableStructureByModel (class in scine_chemoton.gears.network_refinement.enabling) energy_cutoff (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased.Options attribute) energy_reference_type (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling.Options attribute) energy_references (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling.Options attribute) energy_tolerance (scine_chemoton.gears.reaction.BasicReactionHousekeeping.Options attribute) energy_upper_bound (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps.Options attribute) energy_window (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement.Options attribute) enforce_atom_shapes (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased.Options attribute) enforce_free_energies (scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics.Options attribute) Engine (class in scine_chemoton.engine) engine (scine_chemoton.steering_wheel.datastructures.ProtocolEntry attribute) EngineHandler (class in scine_chemoton.engine) Ensemble (class in scine_chemoton.utilities.db_object_wrappers.ensemble_wrapper) estimate_n_bimolecular_trials() (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased method) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations method) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased method) estimate_n_unimolecular_trials() (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased method) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations method) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased method) exclude_misguided_conformer_optimizations (scine_chemoton.gears.compound.BasicAggregateHousekeeping.Options attribute) (scine_chemoton.gears.compound.ThermoAggregateHousekeeping.Options attribute) ExplorationResult (class in scine_chemoton.steering_wheel.datastructures) ExplorationSchemeStep (class in scine_chemoton.steering_wheel.datastructures) ExplorationSchemeStep.Options (class in scine_chemoton.steering_wheel.datastructures) explore() (scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper.Aggregate method) (scine_chemoton.utilities.db_object_wrappers.ensemble_wrapper.Ensemble method) (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) export_compound_costs() (scine_chemoton.gears.pathfinder.Pathfinder method) export_graph() (scine_chemoton.gears.pathfinder.Pathfinder method) extract_connected_graph() (scine_chemoton.gears.pathfinder.Pathfinder method)

F

FAILED (scine_chemoton.steering_wheel.datastructures.Status attribute) FastDissociations (class in scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations) FastDissociations.Options (class in scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations) FastDissociations.Options.BimolOptions (class in scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations) FastDissociations.Options.UnimolOptions (class in scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations) FileInputSelection (class in scine_chemoton.steering_wheel.selections.input_selections) FileInputSelection.Options (class in scine_chemoton.steering_wheel.selections.input_selections) filter() (scine_chemoton.filters.aggregate_filters.ActivatedAggregateFilter method) (scine_chemoton.filters.aggregate_filters.AggregateFilter method) (scine_chemoton.filters.aggregate_filters.AggregateFilterAndArray method) (scine_chemoton.filters.aggregate_filters.AggregateFilterOrArray method) (scine_chemoton.filters.aggregate_filters.AtomNumberFilter method) (scine_chemoton.filters.aggregate_filters.CatalystFilter method) (scine_chemoton.filters.aggregate_filters.ChargeCombinationFilter method) (scine_chemoton.filters.aggregate_filters.CompleteSubstructureFilter method) (scine_chemoton.filters.aggregate_filters.CompoundCostPropertyFilter method) (scine_chemoton.filters.aggregate_filters.ConcentrationPropertyFilter method) (scine_chemoton.filters.aggregate_filters.ElementCountFilter method) (scine_chemoton.filters.aggregate_filters.ElementSumCountFilter method) (scine_chemoton.filters.aggregate_filters.HasStructureWithModel method) (scine_chemoton.filters.aggregate_filters.IdFilter method) (scine_chemoton.filters.aggregate_filters.LastKineticModelingFilter method) (scine_chemoton.filters.aggregate_filters.MolecularWeightFilter method) (scine_chemoton.filters.aggregate_filters.OneAggregateIdFilter method) (scine_chemoton.filters.aggregate_filters.OnePotentialEnergySurface method) (scine_chemoton.filters.aggregate_filters.PlaceHolderAggregateFilter method) (scine_chemoton.filters.aggregate_filters.SelectedAggregateIdFilter method) (scine_chemoton.filters.aggregate_filters.SelectedStructureIdFilter method) (scine_chemoton.filters.aggregate_filters.SelfReactionFilter method) (scine_chemoton.filters.aggregate_filters.SpecificChargeFilter method) (scine_chemoton.filters.aggregate_filters.StopDuringExploration method) (scine_chemoton.filters.aggregate_filters.TrueMinimumFilter method) (scine_chemoton.filters.elementary_step_filters.BarrierlessElementaryStepFilter method) (scine_chemoton.filters.elementary_step_filters.ConsistentEnergyModelFilter method) (scine_chemoton.filters.elementary_step_filters.ElementaryStepBarrierFilter method) (scine_chemoton.filters.elementary_step_filters.ElementaryStepFilter method) (scine_chemoton.filters.elementary_step_filters.ElementaryStepFilterAndArray method) (scine_chemoton.filters.elementary_step_filters.ElementaryStepFilterOrArray method) (scine_chemoton.filters.elementary_step_filters.PlaceHolderElementaryStepFilter method) (scine_chemoton.filters.elementary_step_filters.StopDuringExploration method) (scine_chemoton.filters.elementary_step_filters.StructureModelFilter method) (scine_chemoton.filters.reaction_filters.BarrierlessReactionFilter method) (scine_chemoton.filters.reaction_filters.MaximumTransitionStateEnergyFilter method) (scine_chemoton.filters.reaction_filters.PlaceHolderReactionFilter method) (scine_chemoton.filters.reaction_filters.ReactionBarrierFilter method) (scine_chemoton.filters.reaction_filters.ReactionCachedBasedFilter method) (scine_chemoton.filters.reaction_filters.ReactionFilter method) (scine_chemoton.filters.reaction_filters.ReactionFilterAndArray method) (scine_chemoton.filters.reaction_filters.ReactionFilterOrArray method) (scine_chemoton.filters.reaction_filters.ReactionHasStepWithModel method) (scine_chemoton.filters.reaction_filters.ReactionIDFilter method) (scine_chemoton.filters.reaction_filters.ReactionNumberPropertyFilter method) (scine_chemoton.filters.reaction_filters.StopDuringExploration method) (scine_chemoton.filters.structure_filters.AtomNumberFilter method) (scine_chemoton.filters.structure_filters.CatalystFilter method) (scine_chemoton.filters.structure_filters.ChargeCombinationFilter method) (scine_chemoton.filters.structure_filters.ElementCountFilter method) (scine_chemoton.filters.structure_filters.ElementSumCountFilter method) (scine_chemoton.filters.structure_filters.ModelFilter method) (scine_chemoton.filters.structure_filters.MolecularWeightFilter method) (scine_chemoton.filters.structure_filters.SpecificChargeFilter method) (scine_chemoton.filters.structure_filters.StructureFilter method) (scine_chemoton.filters.structure_filters.StructureFilterAndArray method) (scine_chemoton.filters.structure_filters.StructureFilterOrArray method) (scine_chemoton.filters.structure_filters.StructureLabelFilter method) (scine_chemoton.filters.structure_filters.TrueMinimumFilter method) filter_atom_pairs() (scine_chemoton.filters.further_exploration_filters.AllBarrierLessDissociationsFilter method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilter method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilterAndArray method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilterOrArray method) (scine_chemoton.filters.further_exploration_filters.ReactionCoordinateMaxDissociationEnergyFilter method) (scine_chemoton.filters.reactive_site_filters.AtomPairFunctionalGroupFilter method) (scine_chemoton.filters.reactive_site_filters.AtomRuleBasedFilter method) (scine_chemoton.filters.reactive_site_filters.CentralSiteFilter method) (scine_chemoton.filters.reactive_site_filters.ElementWiseReactionCoordinateFilter method) (scine_chemoton.filters.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter method) (scine_chemoton.filters.reactive_site_filters.MasmChemicalRankingFilter method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilter method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilterAndArray method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilterOrArray method) (scine_chemoton.filters.reactive_site_filters.SimpleRankingFilter method) (scine_chemoton.filters.reactive_site_filters.SubStructureFilter method)

filter_atoms() (scine_chemoton.filters.further_exploration_filters.AllBarrierLessDissociationsFilter method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilter method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilterAndArray method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilterOrArray method) (scine_chemoton.filters.further_exploration_filters.ReactionCoordinateMaxDissociationEnergyFilter method) (scine_chemoton.filters.reactive_site_filters.AtomPairFunctionalGroupFilter method) (scine_chemoton.filters.reactive_site_filters.AtomRuleBasedFilter method) (scine_chemoton.filters.reactive_site_filters.CentralSiteFilter method) (scine_chemoton.filters.reactive_site_filters.ElementWiseReactionCoordinateFilter method) (scine_chemoton.filters.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter method) (scine_chemoton.filters.reactive_site_filters.MasmChemicalRankingFilter method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilter method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilterAndArray method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilterOrArray method) (scine_chemoton.filters.reactive_site_filters.SimpleRankingFilter method) (scine_chemoton.filters.reactive_site_filters.SubStructureFilter method) filter_by_rule() (scine_chemoton.reaction_rules.distance_rules.AlwaysFalse method) (scine_chemoton.reaction_rules.distance_rules.AlwaysTrue method) (scine_chemoton.reaction_rules.distance_rules.DistanceBaseRule method) (scine_chemoton.reaction_rules.distance_rules.DistanceRuleAndArray method) (scine_chemoton.reaction_rules.distance_rules.DistanceRuleOrArray method) (scine_chemoton.reaction_rules.distance_rules.FunctionalGroupRule method) (scine_chemoton.reaction_rules.distance_rules.SimpleDistanceRule method) (scine_chemoton.reaction_rules.reaction_rule_library.AcetalX method) (scine_chemoton.reaction_rules.reaction_rule_library.AllylicSp3X method) (scine_chemoton.reaction_rules.reaction_rule_library.AmidH method) (scine_chemoton.reaction_rules.reaction_rule_library.AmidX method) (scine_chemoton.reaction_rules.reaction_rule_library.AminX method) (scine_chemoton.reaction_rules.reaction_rule_library.AmmoniumX method) (scine_chemoton.reaction_rules.reaction_rule_library.CarbonylX method) (scine_chemoton.reaction_rules.reaction_rule_library.CarboxylH method) (scine_chemoton.reaction_rules.reaction_rule_library.CarboxylX method) (scine_chemoton.reaction_rules.reaction_rule_library.CHOlefinC method) (scine_chemoton.reaction_rules.reaction_rule_library.DefaultOrganicChemistry.C method) (scine_chemoton.reaction_rules.reaction_rule_library.DefaultOrganicChemistry.H method) (scine_chemoton.reaction_rules.reaction_rule_library.SpNCX method) filter_negative_barriers (scine_chemoton.gears.kinetics.PathfinderKinetics.Options attribute) (scine_chemoton.gears.pathfinder.Pathfinder.Options attribute) filter_reaction_coordinates() (scine_chemoton.filters.further_exploration_filters.AllBarrierLessDissociationsFilter method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilter method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilterAndArray method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilterOrArray method) (scine_chemoton.filters.further_exploration_filters.ReactionCoordinateMaxDissociationEnergyFilter method) (scine_chemoton.filters.reactive_site_filters.AtomPairFunctionalGroupFilter method) (scine_chemoton.filters.reactive_site_filters.AtomRuleBasedFilter method) (scine_chemoton.filters.reactive_site_filters.CentralSiteFilter method) (scine_chemoton.filters.reactive_site_filters.ElementWiseReactionCoordinateFilter method) (scine_chemoton.filters.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter method) (scine_chemoton.filters.reactive_site_filters.MasmChemicalRankingFilter method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilter method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilterAndArray method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilterOrArray method) (scine_chemoton.filters.reactive_site_filters.SimpleRankingFilter method) (scine_chemoton.filters.reactive_site_filters.SubStructureFilter method) FilteredStepEnabling (class in scine_chemoton.gears.network_refinement.enabling) find_paths() (scine_chemoton.gears.pathfinder.Pathfinder method) find_unique_paths() (scine_chemoton.gears.pathfinder.Pathfinder method) FINISHED (scine_chemoton.steering_wheel.datastructures.Status attribute) flasks (scine_chemoton.steering_wheel.datastructures.NetworkExpansionResult attribute) flux_variance_label (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling.Options attribute) fork (scine_chemoton.steering_wheel.datastructures.ProtocolEntry attribute) FragmentBased (class in scine_chemoton.gears.elementary_steps.trial_generator.fragment_based) FragmentBased.Options (class in scine_chemoton.gears.elementary_steps.trial_generator.fragment_based) FragmentBased.Options.BimolAssociationOptions (class in scine_chemoton.gears.elementary_steps.trial_generator.fragment_based) FragmentBased.Options.UnimolAssociationOptions (class in scine_chemoton.gears.elementary_steps.trial_generator.fragment_based) FragmentBased.Options.UnimolDissociationOptions (class in scine_chemoton.gears.elementary_steps.trial_generator.fragment_based) from_split_results() (scine_chemoton.steering_wheel.datastructures.ExplorationResult class method) (scine_chemoton.steering_wheel.datastructures.NetworkExpansionResult class method) (scine_chemoton.steering_wheel.datastructures.SelectionResult class method) from_structure() (scine_chemoton.filters.aggregate_filters.OnePotentialEnergySurface class method) fromkeys() (scine_chemoton.reaction_rules.distance_rules.DistanceRuleSet class method) (scine_chemoton.reaction_rules.element_rules.ElementRuleSet class method) (scine_chemoton.reaction_rules.polarization_rules.PolarizationRuleSet class method) (scine_chemoton.reaction_rules.reaction_rule_library.DefaultOrganicChemistry class method) (scine_chemoton.reaction_rules.RuleSet class method) (scine_chemoton.steering_wheel.datastructures.GearOptions class method) FunctionalGroupRule (class in scine_chemoton.reaction_rules.distance_rules) further_exploration_filter (scine_chemoton.steering_wheel.datastructures.SelectionResult attribute) further_job (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.UnimolOptions attribute) further_job_settings (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.UnimolOptions attribute) FurtherExplorationFilter (class in scine_chemoton.filters.further_exploration_filters) FurtherExplorationFilterAndArray (class in scine_chemoton.filters.further_exploration_filters) FurtherExplorationFilterOrArray (class in scine_chemoton.filters.further_exploration_filters)

G

Gear (class in scine_chemoton.gears) gear (scine_chemoton.steering_wheel.datastructures.ProtocolEntry attribute) Gear.Options (class in scine_chemoton.gears) GearOptions (class in scine_chemoton.steering_wheel.datastructures) generate_reactive_complexes() (scine_chemoton.utilities.reactive_complexes.inter_reactive_complexes.InterReactiveComplexes method) generate_value() (scine_chemoton.steering_wheel.datastructures.GearOptions static method) geometry (scine_chemoton.steering_wheel.datastructures.StructureInformation attribute) get() (scine_chemoton.reaction_rules.distance_rules.DistanceRuleSet method) (scine_chemoton.reaction_rules.element_rules.ElementRuleSet method) (scine_chemoton.reaction_rules.polarization_rules.PolarizationRuleSet method) (scine_chemoton.reaction_rules.reaction_rule_library.DefaultOrganicChemistry method) (scine_chemoton.reaction_rules.RuleSet method) (scine_chemoton.steering_wheel.datastructures.GearOptions method) get_adjacency_matrix() (scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer.ConnectivityAnalyzer method) get_aggregate_type() (scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper.Aggregate method) get_aggregates_cache() (scine_chemoton.utilities.db_object_wrappers.wrapper_caches.MultiModelCacheFactory method) get_allowed_reaction_sides() (scine_chemoton.gears.pathfinder.Pathfinder.BarrierBasedHandler method) (scine_chemoton.gears.pathfinder.Pathfinder.BasicHandler method) get_arrhenius_prefactor() (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction static method) get_atom_energy() (scine_chemoton.gears.kinetic_modeling.atomization.AtomEnergyReference method) get_atom_pairs() (in module scine_chemoton.utilities.masm) get_barrier_limit() (scine_chemoton.gears.pathfinder.Pathfinder.BarrierBasedHandler method) get_bimolecular_job_order() (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased method) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations method) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased method) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased method) (scine_chemoton.gears.elementary_steps.trial_generator.TrialGenerator method) get_cache() (scine_chemoton.filters.reaction_filters.BarrierlessReactionFilter method) (scine_chemoton.filters.reaction_filters.MaximumTransitionStateEnergyFilter method) (scine_chemoton.filters.reaction_filters.ReactionBarrierFilter method) (scine_chemoton.filters.reaction_filters.ReactionCachedBasedFilter method) (scine_chemoton.utilities.db_object_wrappers.wrapper_caches.MultiModelAggregateCache method) (scine_chemoton.utilities.db_object_wrappers.wrapper_caches.MultiModelReactionCache method) (scine_chemoton.utilities.db_object_wrappers.wrapper_caches.MultipleModelCache method) get_caches() (scine_chemoton.utilities.db_object_wrappers.wrapper_caches.MultiModelAggregateCache method) (scine_chemoton.utilities.db_object_wrappers.wrapper_caches.MultiModelReactionCache method) (scine_chemoton.utilities.db_object_wrappers.wrapper_caches.MultipleModelCache method) get_concentration_flux() (scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper.Aggregate method) get_db_id() (scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper.Aggregate method) (scine_chemoton.utilities.db_object_wrappers.ensemble_wrapper.Ensemble method) (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) get_db_object() (scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper.Aggregate method) (scine_chemoton.utilities.db_object_wrappers.ensemble_wrapper.Ensemble method) (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) get_default_settings() (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling static method) (scine_chemoton.gears.kinetic_modeling.kinetx_kinetic_modeling.KinetxKineticModelingJobFactory static method) (scine_chemoton.gears.kinetic_modeling.prepare_kinetic_modeling_job.KineticModelingJobFactory static method) (scine_chemoton.gears.kinetic_modeling.rms_kinetic_modeling.RMSKineticModelingJobFactory static method) get_electronic_energy() (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicProperties method) get_electronic_model() (scine_chemoton.utilities.db_object_wrappers.aggregate_cache.AggregateCache method) (scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper.Aggregate method) (scine_chemoton.utilities.db_object_wrappers.ensemble_wrapper.Ensemble method) (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) get_element_count() (scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper.Aggregate method) (scine_chemoton.utilities.db_object_wrappers.ensemble_wrapper.Ensemble method) (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) get_elementary_step_sequence() (scine_chemoton.gears.pathfinder.Pathfinder method) get_energy_reference() (scine_chemoton.gears.kinetic_modeling.atomization.MultiModelEnergyReferences method) (scine_chemoton.gears.kinetic_modeling.atomization.PlaceHolderMultiModelEnergyReferences method) get_ensemble_enthalpy() (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicPropertiesCache method) get_ensemble_entropy() (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicPropertiesCache method) get_ensemble_gibbs_free_energy() (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicPropertiesCache method) get_enthalpy() (scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper.Aggregate method) (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicProperties method) get_entropy() (scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper.Aggregate method) (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicProperties method) get_free_energy() (scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper.Aggregate method) get_free_energy_of_activation() (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) get_gibbs_free_energy() (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicProperties method) get_gibbs_free_energy_correction() (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicProperties method) get_graph_distance() (scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer.ConnectivityAnalyzer method) get_job() (scine_chemoton.gears.kinetic_modeling.kinetx_kinetic_modeling.KinetxKineticModelingJobFactory static method) (scine_chemoton.gears.kinetic_modeling.prepare_kinetic_modeling_job.KineticModelingJobFactory static method) (scine_chemoton.gears.kinetic_modeling.rms_kinetic_modeling.RMSKineticModelingJobFactory static method) get_lhs_aggregates() (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) get_lhs_free_energy() (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) get_lowest_n_steps() (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) get_lowest_n_structures() (scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper.Aggregate method) (scine_chemoton.utilities.db_object_wrappers.ensemble_wrapper.Ensemble method) (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) get_manager() (scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper.Aggregate method) (scine_chemoton.utilities.db_object_wrappers.ensemble_wrapper.Ensemble method) (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) get_model() (scine_chemoton.gears.kinetic_modeling.atomization.AtomEnergyReference method) (scine_chemoton.gears.kinetic_modeling.atomization.ZeroEnergyReference method) get_model_combination() (scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper.Aggregate method) (scine_chemoton.utilities.db_object_wrappers.ensemble_wrapper.Ensemble method) (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) get_model_combinations() (scine_chemoton.utilities.db_object_wrappers.wrapper_caches.MultiModelAggregateCache method) (scine_chemoton.utilities.db_object_wrappers.wrapper_caches.MultiModelReactionCache method) (scine_chemoton.utilities.db_object_wrappers.wrapper_caches.MultipleModelCache method) get_n_cached() (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicPropertiesCache method) get_number_of_gear_loops() (scine_chemoton.engine.Engine method) get_or_produce() (scine_chemoton.utilities.db_object_wrappers.aggregate_cache.AggregateCache method) (scine_chemoton.utilities.db_object_wrappers.reaction_cache.ReactionCache method) (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicPropertiesCache method) (scine_chemoton.utilities.db_object_wrappers.wrapper_caches.MultiModelAggregateCache method) (scine_chemoton.utilities.db_object_wrappers.wrapper_caches.MultiModelReactionCache method) (scine_chemoton.utilities.db_object_wrappers.wrapper_caches.MultipleModelCache method)

get_overall_reactants() (scine_chemoton.gears.pathfinder.Pathfinder method) get_overall_reaction_equation() (scine_chemoton.gears.pathfinder.Pathfinder method) get_partial_restart_info() (scine_chemoton.steering_wheel.SteeringWheel method) get_reaction_cache() (scine_chemoton.utilities.db_object_wrappers.wrapper_caches.MultiModelCacheFactory method) get_reaction_free_energy() (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) get_reaction_type() (scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer.ConnectivityAnalyzer method) get_reactions() (scine_chemoton.gears.kinetic_modeling.kinetx_kinetic_modeling.KinetxKineticModelingJobFactory method) (scine_chemoton.gears.kinetic_modeling.prepare_kinetic_modeling_job.KineticModelingJobFactory method) (scine_chemoton.gears.kinetic_modeling.rms_kinetic_modeling.RMSKineticModelingJobFactory method) get_reference_energy() (scine_chemoton.gears.kinetic_modeling.atomization.AtomEnergyReference method) (scine_chemoton.gears.kinetic_modeling.atomization.ZeroEnergyReference method) get_reference_state() (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicProperties method) get_restart_ids() (scine_chemoton.gears.rerun_calculations.RerunCalculations static method) get_result() (scine_chemoton.steering_wheel.datastructures.ExplorationSchemeStep method) (scine_chemoton.steering_wheel.network_expansions.basics.SimpleOptimization method) (scine_chemoton.steering_wheel.network_expansions.basics.ThermochemistryGeneration method) (scine_chemoton.steering_wheel.network_expansions.conformers.ConformerCreation method) (scine_chemoton.steering_wheel.network_expansions.NetworkExpansion method) (scine_chemoton.steering_wheel.network_expansions.reactions.Association method) (scine_chemoton.steering_wheel.network_expansions.reactions.ChemicalReaction method) (scine_chemoton.steering_wheel.network_expansions.reactions.Dissociation method) (scine_chemoton.steering_wheel.network_expansions.reactions.Rearrangement method) (scine_chemoton.steering_wheel.selections.basics.AllFromPreviousResultSelection method) (scine_chemoton.steering_wheel.selections.basics.AllUserInputsSelection method) (scine_chemoton.steering_wheel.selections.basics.BarriersWithinRangeSelection method) (scine_chemoton.steering_wheel.selections.basics.LowestBarrierSelection method) (scine_chemoton.steering_wheel.selections.basics.ProductsSelection method) (scine_chemoton.steering_wheel.selections.conformers.CentroidConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.ClusterCentroidConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.ClusterSelection method) (scine_chemoton.steering_wheel.selections.conformers.ConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerPerClusterSelection method) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerSelection method) (scine_chemoton.steering_wheel.selections.input_selections.FileInputSelection method) (scine_chemoton.steering_wheel.selections.input_selections.InputSelection method) (scine_chemoton.steering_wheel.selections.input_selections.ScineGeometryInputSelection method) (scine_chemoton.steering_wheel.selections.organometallic_complexes.CentralMetalSelection method) (scine_chemoton.steering_wheel.selections.Selection method) (scine_chemoton.steering_wheel.selections.SelectionAndArray method) (scine_chemoton.steering_wheel.selections.SelectionOrArray method) get_results() (scine_chemoton.steering_wheel.SteeringWheel method) get_rhs_aggregates() (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) get_rhs_free_energy() (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) get_sorted_structure_list() (scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper.Aggregate method) (scine_chemoton.utilities.db_object_wrappers.ensemble_wrapper.Ensemble method) (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicPropertiesCache method) get_sorted_structure_step_list() (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) get_starting_concentration() (scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper.Aggregate method) get_status_report() (scine_chemoton.steering_wheel.SteeringWheel method) get_step_result() (scine_chemoton.steering_wheel.selections.basics.AllFromPreviousResultSelection method) (scine_chemoton.steering_wheel.selections.basics.AllUserInputsSelection method) (scine_chemoton.steering_wheel.selections.basics.BarriersWithinRangeSelection method) (scine_chemoton.steering_wheel.selections.basics.LowestBarrierSelection method) (scine_chemoton.steering_wheel.selections.basics.ProductsSelection method) (scine_chemoton.steering_wheel.selections.conformers.CentroidConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.ClusterCentroidConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.ClusterSelection method) (scine_chemoton.steering_wheel.selections.conformers.ConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerPerClusterSelection method) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerSelection method) (scine_chemoton.steering_wheel.selections.input_selections.FileInputSelection method) (scine_chemoton.steering_wheel.selections.input_selections.InputSelection method) (scine_chemoton.steering_wheel.selections.input_selections.ScineGeometryInputSelection method) (scine_chemoton.steering_wheel.selections.organometallic_complexes.CentralMetalSelection method) (scine_chemoton.steering_wheel.selections.Selection method) (scine_chemoton.steering_wheel.selections.SelectionAndArray method) (scine_chemoton.steering_wheel.selections.SelectionOrArray method) get_temperature() (scine_chemoton.gears.pathfinder.Pathfinder.BarrierBasedHandler method) get_thermochemistry_calculator() (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicProperties method) get_transition_state_free_energy() (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) get_ts_theory_rate_constants() (scine_chemoton.utilities.db_object_wrappers.reaction_wrapper.Reaction method) get_unimolecular_job_order() (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased method) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations method) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased method) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased method) (scine_chemoton.gears.elementary_steps.trial_generator.TrialGenerator method) get_valid_graph_handler_options() (scine_chemoton.gears.pathfinder.Pathfinder static method) get_valid_reaction_ids() (scine_chemoton.gears.pathfinder.Pathfinder.BarrierBasedHandler method) (scine_chemoton.gears.pathfinder.Pathfinder.BasicHandler method) get_value() (scine_chemoton.gears.kinetic_modeling.atomization.MultiModelEnergyReferences method) (scine_chemoton.gears.kinetic_modeling.atomization.PlaceHolderMultiModelEnergyReferences method) get_zero_point_energy() (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicProperties method) get_zero_point_energy_correction() (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicProperties method) graph_handler (scine_chemoton.gears.pathfinder.Pathfinder.Options attribute) graph_job (scine_chemoton.gears.compound.BasicAggregateHousekeeping.Options attribute) (scine_chemoton.gears.compound.ThermoAggregateHousekeeping.Options attribute) graph_settings (scine_chemoton.gears.compound.BasicAggregateHousekeeping.Options attribute) (scine_chemoton.gears.compound.ThermoAggregateHousekeeping.Options attribute)

H

hardcoded_gear_options (scine_chemoton.steering_wheel.network_expansions.basics.SimpleOptimization attribute) (scine_chemoton.steering_wheel.network_expansions.basics.ThermochemistryGeneration attribute) (scine_chemoton.steering_wheel.network_expansions.conformers.ConformerCreation attribute) (scine_chemoton.steering_wheel.network_expansions.reactions.Association attribute) (scine_chemoton.steering_wheel.network_expansions.reactions.ChemicalReaction attribute) (scine_chemoton.steering_wheel.network_expansions.reactions.Dissociation attribute) (scine_chemoton.steering_wheel.network_expansions.reactions.Rearrangement attribute) has_cache() (scine_chemoton.utilities.db_object_wrappers.wrapper_caches.MultiModelAggregateCache method) (scine_chemoton.utilities.db_object_wrappers.wrapper_caches.MultiModelReactionCache method) (scine_chemoton.utilities.db_object_wrappers.wrapper_caches.MultipleModelCache method)

has_reference() (scine_chemoton.gears.kinetic_modeling.atomization.MultiModelEnergyReferences method) (scine_chemoton.gears.kinetic_modeling.atomization.PlaceHolderMultiModelEnergyReferences method) HasName (class in scine_chemoton.gears) HasStructureWithModel (class in scine_chemoton.filters.aggregate_filters) hessian_model (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) HeuristicPolarizationReactionCoordinateFilter (class in scine_chemoton.filters.reactive_site_filters) HoldsCollections (class in scine_chemoton.gears)

I

id() (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicProperties method) IdFilter (class in scine_chemoton.filters.aggregate_filters) ignore_explore_bool (scine_chemoton.gears.thermo.BasicThermoDataCompletion.Options attribute) index() (scine_chemoton.utilities.masm.ComponentDistanceTuple method) initialize_collections() (scine_chemoton.filters.aggregate_filters.ActivatedAggregateFilter method) (scine_chemoton.filters.aggregate_filters.AggregateFilter method) (scine_chemoton.filters.aggregate_filters.AggregateFilterAndArray method) (scine_chemoton.filters.aggregate_filters.AggregateFilterOrArray method) (scine_chemoton.filters.aggregate_filters.AtomNumberFilter method) (scine_chemoton.filters.aggregate_filters.CatalystFilter method) (scine_chemoton.filters.aggregate_filters.ChargeCombinationFilter method) (scine_chemoton.filters.aggregate_filters.CompleteSubstructureFilter method) (scine_chemoton.filters.aggregate_filters.CompoundCostPropertyFilter method) (scine_chemoton.filters.aggregate_filters.ConcentrationPropertyFilter method) (scine_chemoton.filters.aggregate_filters.ElementCountFilter method) (scine_chemoton.filters.aggregate_filters.ElementSumCountFilter method) (scine_chemoton.filters.aggregate_filters.HasStructureWithModel method) (scine_chemoton.filters.aggregate_filters.IdFilter method) (scine_chemoton.filters.aggregate_filters.LastKineticModelingFilter method) (scine_chemoton.filters.aggregate_filters.MolecularWeightFilter method) (scine_chemoton.filters.aggregate_filters.OneAggregateIdFilter method) (scine_chemoton.filters.aggregate_filters.OnePotentialEnergySurface method) (scine_chemoton.filters.aggregate_filters.PlaceHolderAggregateFilter method) (scine_chemoton.filters.aggregate_filters.SelectedAggregateIdFilter method) (scine_chemoton.filters.aggregate_filters.SelectedStructureIdFilter method) (scine_chemoton.filters.aggregate_filters.SelfReactionFilter method) (scine_chemoton.filters.aggregate_filters.SpecificChargeFilter method) (scine_chemoton.filters.aggregate_filters.StopDuringExploration method) (scine_chemoton.filters.aggregate_filters.TrueMinimumFilter method) (scine_chemoton.filters.elementary_step_filters.BarrierlessElementaryStepFilter method) (scine_chemoton.filters.elementary_step_filters.ConsistentEnergyModelFilter method) (scine_chemoton.filters.elementary_step_filters.ElementaryStepBarrierFilter method) (scine_chemoton.filters.elementary_step_filters.ElementaryStepFilter method) (scine_chemoton.filters.elementary_step_filters.ElementaryStepFilterAndArray method) (scine_chemoton.filters.elementary_step_filters.ElementaryStepFilterOrArray method) (scine_chemoton.filters.elementary_step_filters.PlaceHolderElementaryStepFilter method) (scine_chemoton.filters.elementary_step_filters.StopDuringExploration method) (scine_chemoton.filters.elementary_step_filters.StructureModelFilter method) (scine_chemoton.filters.further_exploration_filters.AllBarrierLessDissociationsFilter method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilter method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilterAndArray method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilterOrArray method) (scine_chemoton.filters.further_exploration_filters.ReactionCoordinateMaxDissociationEnergyFilter method) (scine_chemoton.filters.reaction_filters.BarrierlessReactionFilter method) (scine_chemoton.filters.reaction_filters.MaximumTransitionStateEnergyFilter method) (scine_chemoton.filters.reaction_filters.PlaceHolderReactionFilter method) (scine_chemoton.filters.reaction_filters.ReactionBarrierFilter method) (scine_chemoton.filters.reaction_filters.ReactionCachedBasedFilter method) (scine_chemoton.filters.reaction_filters.ReactionFilter method) (scine_chemoton.filters.reaction_filters.ReactionFilterAndArray method) (scine_chemoton.filters.reaction_filters.ReactionFilterOrArray method) (scine_chemoton.filters.reaction_filters.ReactionHasStepWithModel method) (scine_chemoton.filters.reaction_filters.ReactionIDFilter method) (scine_chemoton.filters.reaction_filters.ReactionNumberPropertyFilter method) (scine_chemoton.filters.reaction_filters.StopDuringExploration method) (scine_chemoton.filters.reactive_site_filters.AtomPairFunctionalGroupFilter method) (scine_chemoton.filters.reactive_site_filters.AtomRuleBasedFilter method) (scine_chemoton.filters.reactive_site_filters.CentralSiteFilter method) (scine_chemoton.filters.reactive_site_filters.ElementWiseReactionCoordinateFilter method) (scine_chemoton.filters.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter method) (scine_chemoton.filters.reactive_site_filters.MasmChemicalRankingFilter method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilter method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilterAndArray method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilterOrArray method) (scine_chemoton.filters.reactive_site_filters.SimpleRankingFilter method) (scine_chemoton.filters.reactive_site_filters.SubStructureFilter method) (scine_chemoton.filters.structure_filters.AtomNumberFilter method) (scine_chemoton.filters.structure_filters.CatalystFilter method) (scine_chemoton.filters.structure_filters.ChargeCombinationFilter method) (scine_chemoton.filters.structure_filters.ElementCountFilter method) (scine_chemoton.filters.structure_filters.ElementSumCountFilter method) (scine_chemoton.filters.structure_filters.ModelFilter method) (scine_chemoton.filters.structure_filters.MolecularWeightFilter method) (scine_chemoton.filters.structure_filters.SpecificChargeFilter method) (scine_chemoton.filters.structure_filters.StructureFilter method) (scine_chemoton.filters.structure_filters.StructureFilterAndArray method) (scine_chemoton.filters.structure_filters.StructureFilterOrArray method) (scine_chemoton.filters.structure_filters.StructureLabelFilter method) (scine_chemoton.filters.structure_filters.TrueMinimumFilter method) (scine_chemoton.gears.compound.BasicAggregateHousekeeping method) (scine_chemoton.gears.compound.ThermoAggregateHousekeeping method) (scine_chemoton.gears.conformers.brute_force.BruteForceConformers method) (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps method) (scine_chemoton.gears.elementary_steps.ElementaryStepGear method) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps method) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps method) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps method) (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased method) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations method) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased method) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased method) (scine_chemoton.gears.elementary_steps.trial_generator.TrialGenerator method) (scine_chemoton.gears.Gear method) (scine_chemoton.gears.HoldsCollections method) (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling method) (scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics method) (scine_chemoton.gears.kinetics.KineticsBase method) (scine_chemoton.gears.kinetics.MaximumFluxKinetics method) (scine_chemoton.gears.kinetics.MinimalConnectivityKinetics method) (scine_chemoton.gears.kinetics.PathfinderKinetics method) (scine_chemoton.gears.kinetics.ReactionFilterBasedKinetics method) (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement method) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement method) (scine_chemoton.gears.network_refinement.disabling.AggregateDisabling method) (scine_chemoton.gears.network_refinement.disabling.DisableAllAggregates method) (scine_chemoton.gears.network_refinement.disabling.DisableAllReactions method) (scine_chemoton.gears.network_refinement.disabling.DisableAllSteps method) (scine_chemoton.gears.network_refinement.disabling.DisableAllStepsByModel method) (scine_chemoton.gears.network_refinement.disabling.DisableReactionByJob method) (scine_chemoton.gears.network_refinement.disabling.DisableStepByJob method) (scine_chemoton.gears.network_refinement.disabling.ReactionDisabling method) (scine_chemoton.gears.network_refinement.disabling.StepDisabling method) (scine_chemoton.gears.network_refinement.enabling.ApplyToAllStepsInReaction method) (scine_chemoton.gears.network_refinement.enabling.ApplyToAllStructuresInAggregate method) (scine_chemoton.gears.network_refinement.enabling.EnableAllSteps method) (scine_chemoton.gears.network_refinement.enabling.EnableAllStructures method) (scine_chemoton.gears.network_refinement.enabling.EnableCalculationResults method) (scine_chemoton.gears.network_refinement.enabling.EnableJobSpecificCalculations method) (scine_chemoton.gears.network_refinement.enabling.EnableStructureByModel method) (scine_chemoton.gears.network_refinement.enabling.FilteredStepEnabling method) (scine_chemoton.gears.network_refinement.enabling.PlaceHolderCalculationEnabling method) (scine_chemoton.gears.network_refinement.enabling.StepEnabling method) (scine_chemoton.gears.network_refinement.enabling.StructureEnabling method) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement method) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement method) (scine_chemoton.gears.pathfinder.Pathfinder method) (scine_chemoton.gears.pathfinder.Pathfinder.BarrierBasedHandler method) (scine_chemoton.gears.pathfinder.Pathfinder.BasicHandler method) (scine_chemoton.gears.reaction.BasicReactionHousekeeping method) (scine_chemoton.gears.rerun_calculations.RerunCalculations method) (scine_chemoton.gears.scheduler.Scheduler method) (scine_chemoton.gears.single_point.SinglePoint method) (scine_chemoton.gears.thermo.BasicThermoDataCompletion method) (scine_chemoton.steering_wheel.datastructures.ExplorationSchemeStep method) (scine_chemoton.steering_wheel.network_expansions.basics.SimpleOptimization method) (scine_chemoton.steering_wheel.network_expansions.basics.ThermochemistryGeneration method) (scine_chemoton.steering_wheel.network_expansions.conformers.ConformerCreation method) (scine_chemoton.steering_wheel.network_expansions.NetworkExpansion method) (scine_chemoton.steering_wheel.network_expansions.reactions.Association method) (scine_chemoton.steering_wheel.network_expansions.reactions.ChemicalReaction method) (scine_chemoton.steering_wheel.network_expansions.reactions.Dissociation method) (scine_chemoton.steering_wheel.network_expansions.reactions.Rearrangement method) (scine_chemoton.steering_wheel.selections.basics.AllFromPreviousResultSelection method) (scine_chemoton.steering_wheel.selections.basics.AllUserInputsSelection method) (scine_chemoton.steering_wheel.selections.basics.BarriersWithinRangeSelection method) (scine_chemoton.steering_wheel.selections.basics.LowestBarrierSelection method) (scine_chemoton.steering_wheel.selections.basics.ProductsSelection method) (scine_chemoton.steering_wheel.selections.conformers.CentroidConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.ClusterCentroidConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.ClusterSelection method) (scine_chemoton.steering_wheel.selections.conformers.ConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerPerClusterSelection method) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerSelection method) (scine_chemoton.steering_wheel.selections.input_selections.FileInputSelection method) (scine_chemoton.steering_wheel.selections.input_selections.InputSelection method) (scine_chemoton.steering_wheel.selections.input_selections.ScineGeometryInputSelection method) (scine_chemoton.steering_wheel.selections.organometallic_complexes.CentralMetalSelection method) (scine_chemoton.steering_wheel.selections.Selection method) (scine_chemoton.steering_wheel.selections.SelectionAndArray method) (scine_chemoton.steering_wheel.selections.SelectionOrArray method)

InputSelection (class in scine_chemoton.steering_wheel.selections.input_selections) InputSelection.Options (class in scine_chemoton.steering_wheel.selections.input_selections) insert_initial_structure() (in module scine_chemoton.utilities.insert_initial_structure) INTERACTION_REQUIRED (scine_chemoton.steering_wheel.datastructures.Status attribute) InterReactiveComplexes (class in scine_chemoton.utilities.reactive_complexes.inter_reactive_complexes) InterReactiveComplexes.Options (class in scine_chemoton.utilities.reactive_complexes.inter_reactive_complexes) is_running() (scine_chemoton.engine.Engine method) (scine_chemoton.steering_wheel.datastructures.ProtocolEntry method) (scine_chemoton.steering_wheel.SteeringWheel method) items() (scine_chemoton.reaction_rules.distance_rules.DistanceRuleSet method) (scine_chemoton.reaction_rules.element_rules.ElementRuleSet method) (scine_chemoton.reaction_rules.polarization_rules.PolarizationRuleSet method) (scine_chemoton.reaction_rules.reaction_rule_library.DefaultOrganicChemistry method) (scine_chemoton.reaction_rules.RuleSet method) (scine_chemoton.steering_wheel.datastructures.GearOptions method)

J

job (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.UnimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.UnimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.BimolAssociationOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.UnimolAssociationOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.UnimolDissociationOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased.Options.UnimolOptions attribute) (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling.Options attribute) (scine_chemoton.gears.single_point.SinglePoint.Options attribute) (scine_chemoton.gears.thermo.BasicThermoDataCompletion.Options attribute) job_counts (scine_chemoton.gears.scheduler.Scheduler.Options attribute) job_priorities (scine_chemoton.gears.scheduler.Scheduler.Options attribute) job_settings (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.BimolAssociationOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.UnimolAssociationOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased.Options.BimolOptions attribute) (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling.Options attribute) (scine_chemoton.gears.single_point.SinglePoint.Options attribute)

job_settings_associative (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.UnimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.UnimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased.Options.UnimolOptions attribute) job_settings_disconnective (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.UnimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.UnimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.UnimolDissociationOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased.Options.UnimolOptions attribute) job_settings_dissociative (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.UnimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.UnimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.UnimolDissociationOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased.Options.UnimolOptions attribute) join() (scine_chemoton.engine.Engine method) (scine_chemoton.steering_wheel.SteeringWheel method)

K

key_check() (scine_chemoton.steering_wheel.datastructures.GearOptions method) keys() (scine_chemoton.reaction_rules.distance_rules.DistanceRuleSet method) (scine_chemoton.reaction_rules.element_rules.ElementRuleSet method) (scine_chemoton.reaction_rules.polarization_rules.PolarizationRuleSet method) (scine_chemoton.reaction_rules.reaction_rule_library.DefaultOrganicChemistry method) (scine_chemoton.reaction_rules.RuleSet method) (scine_chemoton.steering_wheel.datastructures.GearOptions method)

KineticModeling (class in scine_chemoton.gears.kinetic_modeling.kinetic_modeling) KineticModeling.Options (class in scine_chemoton.gears.kinetic_modeling.kinetic_modeling) KineticModelingJobFactory (class in scine_chemoton.gears.kinetic_modeling.prepare_kinetic_modeling_job) KineticsBase (class in scine_chemoton.gears.kinetics) KineticsBase.Options (class in scine_chemoton.gears.kinetics) KinetxKineticModelingJobFactory (class in scine_chemoton.gears.kinetic_modeling.kinetx_kinetic_modeling)

L

LastKineticModelingFilter (class in scine_chemoton.filters.aggregate_filters) LebedevSphere (class in scine_chemoton.utilities.reactive_complexes.lebedev_sphere) legacy_existence_check (scine_chemoton.gears.rerun_calculations.RerunCalculations.Options attribute) ligand_without_metal_reactive (scine_chemoton.steering_wheel.selections.organometallic_complexes.CentralMetalSelection.Options attribute) limited_runs (scine_chemoton.steering_wheel.datastructures.ProtocolEntry attribute) list_valid_input_type (scine_chemoton.steering_wheel.selections.input_selections.FileInputSelection attribute) (scine_chemoton.steering_wheel.selections.input_selections.InputSelection attribute) (scine_chemoton.steering_wheel.selections.input_selections.ScineGeometryInputSelection attribute) load_graph() (scine_chemoton.gears.pathfinder.Pathfinder method) LogicCoupling (class in scine_chemoton.steering_wheel.datastructures) looped_collection (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.ElementaryStepGear.Options attribute) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps.Options attribute) lowest_barrier_per_reaction() (scine_chemoton.steering_wheel.selections.basics.AllFromPreviousResultSelection method) (scine_chemoton.steering_wheel.selections.basics.AllUserInputsSelection method) (scine_chemoton.steering_wheel.selections.basics.BarriersWithinRangeSelection method) (scine_chemoton.steering_wheel.selections.basics.LowestBarrierSelection method) (scine_chemoton.steering_wheel.selections.basics.ProductsSelection method) (scine_chemoton.steering_wheel.selections.conformers.CentroidConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.ClusterCentroidConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.ClusterSelection method) (scine_chemoton.steering_wheel.selections.conformers.ConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerPerClusterSelection method) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerSelection method) (scine_chemoton.steering_wheel.selections.input_selections.FileInputSelection method) (scine_chemoton.steering_wheel.selections.input_selections.InputSelection method) (scine_chemoton.steering_wheel.selections.input_selections.ScineGeometryInputSelection method) (scine_chemoton.steering_wheel.selections.organometallic_complexes.CentralMetalSelection method) (scine_chemoton.steering_wheel.selections.Selection method) (scine_chemoton.steering_wheel.selections.SelectionAndArray method) (scine_chemoton.steering_wheel.selections.SelectionOrArray method)

LowestBarrierSelection (class in scine_chemoton.steering_wheel.selections.basics) LowestBarrierSelection.Options (class in scine_chemoton.steering_wheel.selections.basics) LowestEnergyConformerPerClusterSelection (class in scine_chemoton.steering_wheel.selections.conformers) LowestEnergyConformerPerClusterSelection.Options (class in scine_chemoton.steering_wheel.selections.conformers) LowestEnergyConformerSelection (class in scine_chemoton.steering_wheel.selections.conformers) LowestEnergyConformerSelection.Options (class in scine_chemoton.steering_wheel.selections.conformers)

M

make_sorted_pair() (in module scine_chemoton.utilities.masm) MasmChemicalRankingFilter (class in scine_chemoton.filters.reactive_site_filters) max_allowed_barrier (scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics.Options attribute) max_allowed_energy (scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics.Options attribute) max_barrier (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling.Options attribute) max_bond_dissociations (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.UnimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.UnimolOptions attribute) max_bond_formations (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.UnimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.UnimolOptions attribute) max_bond_modifications (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.UnimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.UnimolOptions attribute) max_compound_cost (scine_chemoton.gears.kinetics.PathfinderKinetics.Options attribute) max_graph_distance (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.UnimolDissociationOptions attribute) max_inter_bond_formations (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.BimolOptions attribute) max_inter_fragment_graph_distance (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.UnimolAssociationOptions attribute) max_intra_bond_formations (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.BimolOptions attribute) max_number_structures (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps.Options attribute) max_within_fragment_graph_distance (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.BimolAssociationOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.UnimolAssociationOptions attribute) MaximumFluxKinetics (class in scine_chemoton.gears.kinetics) MaximumFluxKinetics.Options (class in scine_chemoton.gears.kinetics) MaximumTransitionStateEnergyFilter (class in scine_chemoton.filters.reaction_filters) metal (scine_chemoton.steering_wheel.selections.organometallic_complexes.CentralMetalSelection.Options attribute) min_allowed_concentration (scine_chemoton.gears.kinetics.MaximumFluxKinetics.Options attribute) min_bond_dissociations (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.UnimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.UnimolOptions attribute) min_bond_formations (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.UnimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.UnimolOptions attribute) min_bond_modifications (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.UnimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.UnimolOptions attribute) min_flux_truncation (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling.Options attribute) min_inter_bond_formations (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.BimolOptions attribute) min_inter_fragment_graph_distance (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.UnimolAssociationOptions attribute) min_intra_bond_formations (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.BimolOptions attribute) minimal_spin_multiplicity (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.BimolOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.BimolAssociationOptions attribute) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased.Options.BimolOptions attribute) MinimalConnectivityKinetics (class in scine_chemoton.gears.kinetics) MinimalConnectivityKinetics.Options (class in scine_chemoton.gears.kinetics) MinimalElementarySteps (class in scine_chemoton.gears.elementary_steps.minimal) MinimalElementarySteps.Options (class in scine_chemoton.gears.elementary_steps.minimal) minimization_job (scine_chemoton.gears.conformers.brute_force.BruteForceConformers.Options attribute) minimization_settings (scine_chemoton.gears.conformers.brute_force.BruteForceConformers.Options attribute) minimum_values_need_update() (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicPropertiesCache method) MinimumEnergyConformerElementarySteps (class in scine_chemoton.gears.elementary_steps.minimum_energy_conformer) MinimumEnergyConformerElementarySteps.Options (class in scine_chemoton.gears.elementary_steps.minimum_energy_conformer) Mixed (scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer.ReactionType attribute) model (scine_chemoton.gears.compound.BasicAggregateHousekeeping.Options attribute) (scine_chemoton.gears.compound.ThermoAggregateHousekeeping.Options attribute) (scine_chemoton.gears.conformers.brute_force.BruteForceConformers.Options attribute) (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.ElementaryStepGear.Options attribute) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options attribute) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased.Options attribute) (scine_chemoton.gears.elementary_steps.trial_generator.TrialGenerator.Options attribute) (scine_chemoton.gears.Gear.Options attribute) (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling.Options attribute) (scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics.Options attribute) (scine_chemoton.gears.kinetics.KineticsBase.Options attribute) (scine_chemoton.gears.kinetics.MaximumFluxKinetics.Options attribute) (scine_chemoton.gears.kinetics.MinimalConnectivityKinetics.Options attribute) (scine_chemoton.gears.kinetics.PathfinderKinetics.Options attribute) (scine_chemoton.gears.kinetics.ReactionFilterBasedKinetics.Options attribute) (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) (scine_chemoton.gears.pathfinder.Pathfinder.Options attribute) (scine_chemoton.gears.reaction.BasicReactionHousekeeping.Options attribute) (scine_chemoton.gears.rerun_calculations.RerunCalculations.Options attribute) (scine_chemoton.gears.scheduler.Scheduler.Options attribute) (scine_chemoton.gears.single_point.SinglePoint.Options attribute) (scine_chemoton.gears.thermo.BasicThermoDataCompletion.Options attribute)

model_combination (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement attribute) model_combinations (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling.Options attribute) model_combinations_reactions (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling.Options attribute) model_matches() (scine_chemoton.gears.kinetic_modeling.atomization.AtomEnergyReference method) (scine_chemoton.gears.kinetic_modeling.atomization.ZeroEnergyReference method) ModelFilter (class in scine_chemoton.filters.structure_filters) module scine_chemoton.engine scine_chemoton.filters scine_chemoton.filters.aggregate_filters 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.gears scine_chemoton.gears.compound scine_chemoton.gears.conformers scine_chemoton.gears.conformers.brute_force scine_chemoton.gears.elementary_steps scine_chemoton.gears.elementary_steps.brute_force scine_chemoton.gears.elementary_steps.minimal scine_chemoton.gears.elementary_steps.minimum_energy_conformer scine_chemoton.gears.elementary_steps.selected_structures scine_chemoton.gears.elementary_steps.trial_generator scine_chemoton.gears.elementary_steps.trial_generator.bond_based scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations scine_chemoton.gears.elementary_steps.trial_generator.fragment_based scine_chemoton.gears.elementary_steps.trial_generator.template_based scine_chemoton.gears.kinetic_modeling scine_chemoton.gears.kinetic_modeling.atomization scine_chemoton.gears.kinetic_modeling.kinetic_modeling scine_chemoton.gears.kinetic_modeling.kinetx_kinetic_modeling scine_chemoton.gears.kinetic_modeling.prepare_kinetic_modeling_job scine_chemoton.gears.kinetic_modeling.rms_kinetic_modeling scine_chemoton.gears.kinetic_modeling.rms_network_extractor scine_chemoton.gears.kinetics scine_chemoton.gears.network_refinement scine_chemoton.gears.network_refinement.aggregate_based_refinement scine_chemoton.gears.network_refinement.calculation_based_refinement scine_chemoton.gears.network_refinement.disabling scine_chemoton.gears.network_refinement.enabling scine_chemoton.gears.network_refinement.reaction_based_refinement scine_chemoton.gears.network_refinement.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.reaction_rules scine_chemoton.reaction_rules.distance_rules scine_chemoton.reaction_rules.element_rules scine_chemoton.reaction_rules.polarization_rules scine_chemoton.reaction_rules.reaction_rule_library scine_chemoton.steering_wheel.datastructures scine_chemoton.steering_wheel.network_expansions.basics scine_chemoton.steering_wheel.network_expansions.conformers scine_chemoton.steering_wheel.network_expansions.reactions scine_chemoton.steering_wheel.selections.basics scine_chemoton.steering_wheel.selections.conformers scine_chemoton.steering_wheel.selections.input_selections scine_chemoton.steering_wheel.selections.organometallic_complexes scine_chemoton.utilities.db_object_wrappers.aggregate_cache scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper scine_chemoton.utilities.db_object_wrappers.ensemble_wrapper scine_chemoton.utilities.db_object_wrappers.reaction_cache scine_chemoton.utilities.db_object_wrappers.reaction_wrapper scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties scine_chemoton.utilities.db_object_wrappers.wrapper_caches scine_chemoton.utilities.insert_initial_structure scine_chemoton.utilities.masm scine_chemoton.utilities.reactive_complexes scine_chemoton.utilities.reactive_complexes.inter_reactive_complexes scine_chemoton.utilities.reactive_complexes.lebedev_sphere scine_chemoton.utilities.reactive_complexes.unit_circle mol_from_cbor() (in module scine_chemoton.utilities.masm) mol_idx (scine_chemoton.utilities.masm.ComponentDistanceTuple attribute) mol_to_cbor() (in module scine_chemoton.utilities.masm) MolecularWeightFilter (class in scine_chemoton.filters.aggregate_filters) (class in scine_chemoton.filters.structure_filters) mols_from_properties() (in module scine_chemoton.utilities.masm) MultiModelAggregateCache (class in scine_chemoton.utilities.db_object_wrappers.wrapper_caches) MultiModelCacheFactory (class in scine_chemoton.utilities.db_object_wrappers.wrapper_caches) MultiModelEnergyReferences (class in scine_chemoton.gears.kinetic_modeling.atomization) MultiModelReactionCache (class in scine_chemoton.utilities.db_object_wrappers.wrapper_caches) multiple_attack_points (scine_chemoton.utilities.reactive_complexes.inter_reactive_complexes.InterReactiveComplexes.Options attribute) MultipleModelCache (class in scine_chemoton.utilities.db_object_wrappers.wrapper_caches) multiplicity (scine_chemoton.steering_wheel.datastructures.StructureInformation attribute)

N

n_already_executed_protocol_steps (scine_chemoton.steering_wheel.datastructures.RestartPartialExpansionInfo attribute) n_lowest (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement.Options attribute) n_runs (scine_chemoton.steering_wheel.datastructures.ProtocolEntry attribute) name (scine_chemoton.filters.aggregate_filters.ActivatedAggregateFilter property) (scine_chemoton.filters.aggregate_filters.AggregateFilter property) (scine_chemoton.filters.aggregate_filters.AggregateFilterAndArray property) (scine_chemoton.filters.aggregate_filters.AggregateFilterOrArray property) (scine_chemoton.filters.aggregate_filters.AtomNumberFilter property) (scine_chemoton.filters.aggregate_filters.CatalystFilter property) (scine_chemoton.filters.aggregate_filters.ChargeCombinationFilter property) (scine_chemoton.filters.aggregate_filters.CompleteSubstructureFilter property) (scine_chemoton.filters.aggregate_filters.CompoundCostPropertyFilter property) (scine_chemoton.filters.aggregate_filters.ConcentrationPropertyFilter property) (scine_chemoton.filters.aggregate_filters.ElementCountFilter property) (scine_chemoton.filters.aggregate_filters.ElementSumCountFilter property) (scine_chemoton.filters.aggregate_filters.HasStructureWithModel property) (scine_chemoton.filters.aggregate_filters.IdFilter property) (scine_chemoton.filters.aggregate_filters.LastKineticModelingFilter property) (scine_chemoton.filters.aggregate_filters.MolecularWeightFilter property) (scine_chemoton.filters.aggregate_filters.OneAggregateIdFilter property) (scine_chemoton.filters.aggregate_filters.OnePotentialEnergySurface property) (scine_chemoton.filters.aggregate_filters.PlaceHolderAggregateFilter property) (scine_chemoton.filters.aggregate_filters.SelectedAggregateIdFilter property) (scine_chemoton.filters.aggregate_filters.SelectedStructureIdFilter property) (scine_chemoton.filters.aggregate_filters.SelfReactionFilter property) (scine_chemoton.filters.aggregate_filters.SpecificChargeFilter property) (scine_chemoton.filters.aggregate_filters.StopDuringExploration property) (scine_chemoton.filters.aggregate_filters.TrueMinimumFilter property) (scine_chemoton.filters.elementary_step_filters.BarrierlessElementaryStepFilter property) (scine_chemoton.filters.elementary_step_filters.ConsistentEnergyModelFilter property) (scine_chemoton.filters.elementary_step_filters.ElementaryStepBarrierFilter property) (scine_chemoton.filters.elementary_step_filters.ElementaryStepFilter property) (scine_chemoton.filters.elementary_step_filters.ElementaryStepFilterAndArray property) (scine_chemoton.filters.elementary_step_filters.ElementaryStepFilterOrArray property) (scine_chemoton.filters.elementary_step_filters.PlaceHolderElementaryStepFilter property) (scine_chemoton.filters.elementary_step_filters.StopDuringExploration property) (scine_chemoton.filters.elementary_step_filters.StructureModelFilter property) (scine_chemoton.filters.further_exploration_filters.AllBarrierLessDissociationsFilter property) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilter property) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilterAndArray property) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilterOrArray property) (scine_chemoton.filters.further_exploration_filters.ReactionCoordinateMaxDissociationEnergyFilter property) (scine_chemoton.filters.reaction_filters.BarrierlessReactionFilter property) (scine_chemoton.filters.reaction_filters.MaximumTransitionStateEnergyFilter property) (scine_chemoton.filters.reaction_filters.PlaceHolderReactionFilter property) (scine_chemoton.filters.reaction_filters.ReactionBarrierFilter property) (scine_chemoton.filters.reaction_filters.ReactionCachedBasedFilter property) (scine_chemoton.filters.reaction_filters.ReactionFilter property) (scine_chemoton.filters.reaction_filters.ReactionFilterAndArray property) (scine_chemoton.filters.reaction_filters.ReactionFilterOrArray property) (scine_chemoton.filters.reaction_filters.ReactionHasStepWithModel property) (scine_chemoton.filters.reaction_filters.ReactionIDFilter property) (scine_chemoton.filters.reaction_filters.ReactionNumberPropertyFilter property) (scine_chemoton.filters.reaction_filters.StopDuringExploration property) (scine_chemoton.filters.reactive_site_filters.AtomPairFunctionalGroupFilter property) (scine_chemoton.filters.reactive_site_filters.AtomRuleBasedFilter property) (scine_chemoton.filters.reactive_site_filters.CentralSiteFilter property) (scine_chemoton.filters.reactive_site_filters.ElementWiseReactionCoordinateFilter property) (scine_chemoton.filters.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter property) (scine_chemoton.filters.reactive_site_filters.MasmChemicalRankingFilter property) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilter property) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilterAndArray property) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilterOrArray property) (scine_chemoton.filters.reactive_site_filters.SimpleRankingFilter property) (scine_chemoton.filters.reactive_site_filters.SubStructureFilter property) (scine_chemoton.filters.structure_filters.AtomNumberFilter property) (scine_chemoton.filters.structure_filters.CatalystFilter property) (scine_chemoton.filters.structure_filters.ChargeCombinationFilter property) (scine_chemoton.filters.structure_filters.ElementCountFilter property) (scine_chemoton.filters.structure_filters.ElementSumCountFilter property) (scine_chemoton.filters.structure_filters.ModelFilter property) (scine_chemoton.filters.structure_filters.MolecularWeightFilter property) (scine_chemoton.filters.structure_filters.SpecificChargeFilter property) (scine_chemoton.filters.structure_filters.StructureFilter property) (scine_chemoton.filters.structure_filters.StructureFilterAndArray property) (scine_chemoton.filters.structure_filters.StructureFilterOrArray property) (scine_chemoton.filters.structure_filters.StructureLabelFilter property) (scine_chemoton.filters.structure_filters.TrueMinimumFilter property) (scine_chemoton.gears.compound.BasicAggregateHousekeeping property) (scine_chemoton.gears.compound.ThermoAggregateHousekeeping property) (scine_chemoton.gears.conformers.brute_force.BruteForceConformers property) (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps property) (scine_chemoton.gears.elementary_steps.ElementaryStepGear property) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps property) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps property) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps property) (scine_chemoton.gears.Gear property) (scine_chemoton.gears.HasName property) (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling property) (scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics property) (scine_chemoton.gears.kinetics.KineticsBase property) (scine_chemoton.gears.kinetics.MaximumFluxKinetics property) (scine_chemoton.gears.kinetics.MinimalConnectivityKinetics property) (scine_chemoton.gears.kinetics.PathfinderKinetics property) (scine_chemoton.gears.kinetics.ReactionFilterBasedKinetics property) (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement property) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement property) (scine_chemoton.gears.network_refinement.disabling.AggregateDisabling property) (scine_chemoton.gears.network_refinement.disabling.DBObjectDisabling property) (scine_chemoton.gears.network_refinement.disabling.DisableAllAggregates property) (scine_chemoton.gears.network_refinement.disabling.DisableAllReactions property) (scine_chemoton.gears.network_refinement.disabling.DisableAllSteps property) (scine_chemoton.gears.network_refinement.disabling.DisableAllStepsByModel property) (scine_chemoton.gears.network_refinement.disabling.DisableReactionByJob property) (scine_chemoton.gears.network_refinement.disabling.DisableStepByJob property) (scine_chemoton.gears.network_refinement.disabling.ReactionDisabling property) (scine_chemoton.gears.network_refinement.disabling.StepDisabling property) (scine_chemoton.gears.network_refinement.enabling.AggregateEnabling property) (scine_chemoton.gears.network_refinement.enabling.ApplyToAllStepsInReaction property) (scine_chemoton.gears.network_refinement.enabling.ApplyToAllStructuresInAggregate property) (scine_chemoton.gears.network_refinement.enabling.DBObjectEnabling property) (scine_chemoton.gears.network_refinement.enabling.EnableAllAggregates property) (scine_chemoton.gears.network_refinement.enabling.EnableAllReactions property) (scine_chemoton.gears.network_refinement.enabling.EnableAllSteps property) (scine_chemoton.gears.network_refinement.enabling.EnableAllStructures property) (scine_chemoton.gears.network_refinement.enabling.EnableCalculationResults property) (scine_chemoton.gears.network_refinement.enabling.EnableJobSpecificCalculations property) (scine_chemoton.gears.network_refinement.enabling.EnableStructureByModel property) (scine_chemoton.gears.network_refinement.enabling.FilteredStepEnabling property) (scine_chemoton.gears.network_refinement.enabling.PlaceHolderAggregateEnabling property) (scine_chemoton.gears.network_refinement.enabling.PlaceHolderCalculationEnabling property) (scine_chemoton.gears.network_refinement.enabling.PlaceHolderReactionEnabling property) (scine_chemoton.gears.network_refinement.enabling.ReactionEnabling property) (scine_chemoton.gears.network_refinement.enabling.StepEnabling property) (scine_chemoton.gears.network_refinement.enabling.StructureEnabling property) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement property) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement property) (scine_chemoton.gears.reaction.BasicReactionHousekeeping property) (scine_chemoton.gears.rerun_calculations.RerunCalculations property) (scine_chemoton.gears.scheduler.Scheduler property) (scine_chemoton.gears.single_point.SinglePoint property) (scine_chemoton.gears.thermo.BasicThermoDataCompletion property) (scine_chemoton.reaction_rules.BaseRule property) (scine_chemoton.reaction_rules.distance_rules.AlwaysFalse property) (scine_chemoton.reaction_rules.distance_rules.AlwaysTrue property) (scine_chemoton.reaction_rules.distance_rules.DistanceBaseRule property) (scine_chemoton.reaction_rules.distance_rules.DistanceRuleAndArray property) (scine_chemoton.reaction_rules.distance_rules.DistanceRuleOrArray property) (scine_chemoton.reaction_rules.distance_rules.FunctionalGroupRule property) (scine_chemoton.reaction_rules.distance_rules.SimpleDistanceRule property) (scine_chemoton.reaction_rules.element_rules.ElementBaseRule property) (scine_chemoton.reaction_rules.element_rules.SimpleElementCombinationRule property) (scine_chemoton.reaction_rules.polarization_rules.PaulingElectronegativityRule property) (scine_chemoton.reaction_rules.polarization_rules.PolarizationBaseRule property) (scine_chemoton.reaction_rules.polarization_rules.PolarizationFunctionalGroupRule property) (scine_chemoton.reaction_rules.polarization_rules.PolarizationRuleAndArray property) (scine_chemoton.reaction_rules.reaction_rule_library.AcetalX property) (scine_chemoton.reaction_rules.reaction_rule_library.AllylicSp3X property) (scine_chemoton.reaction_rules.reaction_rule_library.AmidH property) (scine_chemoton.reaction_rules.reaction_rule_library.AmidX property) (scine_chemoton.reaction_rules.reaction_rule_library.AminX property) (scine_chemoton.reaction_rules.reaction_rule_library.AmmoniumX property) (scine_chemoton.reaction_rules.reaction_rule_library.CarbonylX property) (scine_chemoton.reaction_rules.reaction_rule_library.CarboxylH property) (scine_chemoton.reaction_rules.reaction_rule_library.CarboxylX property) (scine_chemoton.reaction_rules.reaction_rule_library.CHOlefinC property) (scine_chemoton.reaction_rules.reaction_rule_library.DefaultOrganicChemistry.C property) (scine_chemoton.reaction_rules.reaction_rule_library.DefaultOrganicChemistry.H property) (scine_chemoton.reaction_rules.reaction_rule_library.SpNCX property) (scine_chemoton.steering_wheel.datastructures.ExplorationSchemeStep property) (scine_chemoton.steering_wheel.datastructures.ProtocolEntry attribute) (scine_chemoton.steering_wheel.network_expansions.basics.SimpleOptimization property) (scine_chemoton.steering_wheel.network_expansions.basics.ThermochemistryGeneration property) (scine_chemoton.steering_wheel.network_expansions.conformers.ConformerCreation property) (scine_chemoton.steering_wheel.network_expansions.NetworkExpansion property) (scine_chemoton.steering_wheel.network_expansions.reactions.Association property) (scine_chemoton.steering_wheel.network_expansions.reactions.ChemicalReaction property) (scine_chemoton.steering_wheel.network_expansions.reactions.Dissociation property) (scine_chemoton.steering_wheel.network_expansions.reactions.Rearrangement property) (scine_chemoton.steering_wheel.selections.basics.AllFromPreviousResultSelection property) (scine_chemoton.steering_wheel.selections.basics.AllUserInputsSelection property) (scine_chemoton.steering_wheel.selections.basics.BarriersWithinRangeSelection property) (scine_chemoton.steering_wheel.selections.basics.LowestBarrierSelection property) (scine_chemoton.steering_wheel.selections.basics.ProductsSelection property) (scine_chemoton.steering_wheel.selections.conformers.CentroidConformerSelection property) (scine_chemoton.steering_wheel.selections.conformers.ClusterCentroidConformerSelection property) (scine_chemoton.steering_wheel.selections.conformers.ClusterSelection property) (scine_chemoton.steering_wheel.selections.conformers.ConformerSelection property) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerPerClusterSelection property) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerSelection property) (scine_chemoton.steering_wheel.selections.input_selections.FileInputSelection property) (scine_chemoton.steering_wheel.selections.input_selections.InputSelection property) (scine_chemoton.steering_wheel.selections.input_selections.ScineGeometryInputSelection property) (scine_chemoton.steering_wheel.selections.organometallic_complexes.CentralMetalSelection property) (scine_chemoton.steering_wheel.selections.Selection property) (scine_chemoton.steering_wheel.selections.SelectionAndArray property) (scine_chemoton.steering_wheel.selections.SelectionOrArray property) (scine_chemoton.steering_wheel.SteeringWheel property)

nearest_neighbors (scine_chemoton.utilities.reactive_complexes.lebedev_sphere.LebedevSphere property) (scine_chemoton.utilities.reactive_complexes.unit_circle.UnitCircle property) NetworkExpansion (class in scine_chemoton.steering_wheel.network_expansions) NetworkExpansion.Options (class in scine_chemoton.steering_wheel.network_expansions) NetworkExpansionResult (class in scine_chemoton.steering_wheel.datastructures) NetworkRefinement (class in scine_chemoton.gears.network_refinement.refinement) NetworkRefinement.Options (class in scine_chemoton.gears.network_refinement.refinement) new_job (scine_chemoton.gears.rerun_calculations.RerunCalculations.Options attribute) new_job_settings (scine_chemoton.gears.rerun_calculations.RerunCalculations.Options attribute) new_model (scine_chemoton.gears.rerun_calculations.RerunCalculations.Options attribute) NoRestartInfoPresent (class in scine_chemoton.steering_wheel.datastructures) number_rotamers (scine_chemoton.utilities.reactive_complexes.inter_reactive_complexes.InterReactiveComplexes.Options attribute) number_rotamers_two_on_two (scine_chemoton.utilities.reactive_complexes.inter_reactive_complexes.InterReactiveComplexes.Options attribute)

O

old_job (scine_chemoton.gears.rerun_calculations.RerunCalculations.Options attribute) old_job_settings (scine_chemoton.gears.rerun_calculations.RerunCalculations.Options attribute) old_settings_to_remove (scine_chemoton.gears.rerun_calculations.RerunCalculations.Options attribute) old_status (scine_chemoton.gears.rerun_calculations.RerunCalculations.Options attribute) OneAggregateIdFilter (class in scine_chemoton.filters.aggregate_filters) OnePotentialEnergySurface (class in scine_chemoton.filters.aggregate_filters) only_electronic (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling.Options attribute) only_electronic_energies (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) opt_job (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) opt_job_settings (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) options (scine_chemoton.gears.compound.BasicAggregateHousekeeping attribute) (scine_chemoton.gears.compound.ThermoAggregateHousekeeping attribute) (scine_chemoton.gears.conformers.brute_force.BruteForceConformers attribute) (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps attribute) (scine_chemoton.gears.elementary_steps.ElementaryStepGear attribute) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps attribute) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps attribute) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps attribute) (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased attribute) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased attribute) (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling attribute) (scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics attribute) (scine_chemoton.gears.kinetics.KineticsBase attribute) (scine_chemoton.gears.kinetics.MaximumFluxKinetics attribute) (scine_chemoton.gears.kinetics.MinimalConnectivityKinetics attribute) (scine_chemoton.gears.kinetics.PathfinderKinetics attribute) (scine_chemoton.gears.kinetics.ReactionFilterBasedKinetics attribute) (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement attribute) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement attribute) (scine_chemoton.gears.reaction.BasicReactionHousekeeping attribute) (scine_chemoton.gears.rerun_calculations.RerunCalculations attribute) (scine_chemoton.gears.scheduler.Scheduler attribute) (scine_chemoton.gears.single_point.SinglePoint attribute) (scine_chemoton.gears.thermo.BasicThermoDataCompletion attribute) (scine_chemoton.steering_wheel.datastructures.ExplorationSchemeStep attribute) (scine_chemoton.steering_wheel.network_expansions.basics.SimpleOptimization attribute) (scine_chemoton.steering_wheel.network_expansions.basics.ThermochemistryGeneration attribute) (scine_chemoton.steering_wheel.network_expansions.conformers.ConformerCreation attribute) (scine_chemoton.steering_wheel.network_expansions.NetworkExpansion attribute) (scine_chemoton.steering_wheel.network_expansions.reactions.Association attribute) (scine_chemoton.steering_wheel.network_expansions.reactions.ChemicalReaction attribute) (scine_chemoton.steering_wheel.network_expansions.reactions.Dissociation attribute) (scine_chemoton.steering_wheel.network_expansions.reactions.Rearrangement attribute) (scine_chemoton.steering_wheel.selections.basics.AllFromPreviousResultSelection attribute) (scine_chemoton.steering_wheel.selections.basics.AllUserInputsSelection attribute) (scine_chemoton.steering_wheel.selections.basics.BarriersWithinRangeSelection attribute) (scine_chemoton.steering_wheel.selections.basics.LowestBarrierSelection attribute) (scine_chemoton.steering_wheel.selections.basics.ProductsSelection attribute) (scine_chemoton.steering_wheel.selections.conformers.CentroidConformerSelection attribute) (scine_chemoton.steering_wheel.selections.conformers.ClusterCentroidConformerSelection attribute) (scine_chemoton.steering_wheel.selections.conformers.ClusterSelection attribute) (scine_chemoton.steering_wheel.selections.conformers.ConformerSelection attribute) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerPerClusterSelection attribute) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerSelection attribute) (scine_chemoton.steering_wheel.selections.input_selections.FileInputSelection attribute) (scine_chemoton.steering_wheel.selections.input_selections.InputSelection attribute) (scine_chemoton.steering_wheel.selections.input_selections.ScineGeometryInputSelection attribute) (scine_chemoton.steering_wheel.selections.organometallic_complexes.CentralMetalSelection attribute) (scine_chemoton.steering_wheel.selections.Selection attribute) (scine_chemoton.steering_wheel.selections.SelectionAndArray attribute) (scine_chemoton.steering_wheel.selections.SelectionOrArray attribute) (scine_chemoton.utilities.reactive_complexes.inter_reactive_complexes.InterReactiveComplexes attribute)

OR (scine_chemoton.steering_wheel.datastructures.LogicCoupling attribute) order_dependent_setting_keys() (scine_chemoton.gears.kinetic_modeling.kinetx_kinetic_modeling.KinetxKineticModelingJobFactory static method) (scine_chemoton.gears.kinetic_modeling.prepare_kinetic_modeling_job.KineticModelingJobFactory static method) (scine_chemoton.gears.kinetic_modeling.rms_kinetic_modeling.RMSKineticModelingJobFactory static method)

P

pair_is_bound() (scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer.ConnectivityAnalyzer method) Pathfinder (class in scine_chemoton.gears.pathfinder) Pathfinder.BarrierBasedHandler (class in scine_chemoton.gears.pathfinder) Pathfinder.BasicHandler (class in scine_chemoton.gears.pathfinder) Pathfinder.Options (class in scine_chemoton.gears.pathfinder) PathfinderKinetics (class in scine_chemoton.gears.kinetics) PathfinderKinetics.Options (class in scine_chemoton.gears.kinetics) PaulingElectronegativityRule (class in scine_chemoton.reaction_rules.polarization_rules) PlaceHolderAggregateEnabling (class in scine_chemoton.gears.network_refinement.enabling) PlaceHolderAggregateFilter (class in scine_chemoton.filters.aggregate_filters) PlaceHolderCalculationEnabling (class in scine_chemoton.gears.network_refinement.enabling) PlaceHolderElementaryStepFilter (class in scine_chemoton.filters.elementary_step_filters) PlaceHolderMultiModelEnergyReferences (class in scine_chemoton.gears.kinetic_modeling.atomization) PlaceHolderReactionEnabling (class in scine_chemoton.gears.network_refinement.enabling) PlaceHolderReactionFilter (class in scine_chemoton.filters.reaction_filters) PlaceHolderReferenceState (class in scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties) points (scine_chemoton.utilities.reactive_complexes.lebedev_sphere.LebedevSphere property) (scine_chemoton.utilities.reactive_complexes.unit_circle.UnitCircle property) PolarizationBaseRule (class in scine_chemoton.reaction_rules.polarization_rules) PolarizationFunctionalGroupRule (class in scine_chemoton.reaction_rules.polarization_rules) PolarizationRuleAndArray (class in scine_chemoton.reaction_rules.polarization_rules) PolarizationRuleSet (class in scine_chemoton.reaction_rules.polarization_rules) pop() (scine_chemoton.reaction_rules.distance_rules.DistanceRuleSet method) (scine_chemoton.reaction_rules.element_rules.ElementRuleSet method) (scine_chemoton.reaction_rules.polarization_rules.PolarizationRuleSet method) (scine_chemoton.reaction_rules.reaction_rule_library.DefaultOrganicChemistry method) (scine_chemoton.reaction_rules.RuleSet method) (scine_chemoton.steering_wheel.datastructures.GearOptions method) (scine_chemoton.steering_wheel.SteeringWheel method) popitem() (scine_chemoton.reaction_rules.distance_rules.DistanceRuleSet method) (scine_chemoton.reaction_rules.element_rules.ElementRuleSet method) (scine_chemoton.reaction_rules.polarization_rules.PolarizationRuleSet method) (scine_chemoton.reaction_rules.reaction_rule_library.DefaultOrganicChemistry method) (scine_chemoton.reaction_rules.RuleSet method) (scine_chemoton.steering_wheel.datastructures.GearOptions method) possible_attributes() (scine_chemoton.filters.aggregate_filters.ActivatedAggregateFilter static method) (scine_chemoton.filters.aggregate_filters.AggregateFilter static method) (scine_chemoton.filters.aggregate_filters.AggregateFilterAndArray static method) (scine_chemoton.filters.aggregate_filters.AggregateFilterOrArray static method) (scine_chemoton.filters.aggregate_filters.AtomNumberFilter static method) (scine_chemoton.filters.aggregate_filters.CatalystFilter static method) (scine_chemoton.filters.aggregate_filters.ChargeCombinationFilter static method) (scine_chemoton.filters.aggregate_filters.CompleteSubstructureFilter static method) (scine_chemoton.filters.aggregate_filters.CompoundCostPropertyFilter static method) (scine_chemoton.filters.aggregate_filters.ConcentrationPropertyFilter static method) (scine_chemoton.filters.aggregate_filters.ElementCountFilter static method) (scine_chemoton.filters.aggregate_filters.ElementSumCountFilter static method) (scine_chemoton.filters.aggregate_filters.HasStructureWithModel static method) (scine_chemoton.filters.aggregate_filters.IdFilter static method) (scine_chemoton.filters.aggregate_filters.LastKineticModelingFilter static method) (scine_chemoton.filters.aggregate_filters.MolecularWeightFilter static method) (scine_chemoton.filters.aggregate_filters.OneAggregateIdFilter static method) (scine_chemoton.filters.aggregate_filters.OnePotentialEnergySurface static method) (scine_chemoton.filters.aggregate_filters.PlaceHolderAggregateFilter static method) (scine_chemoton.filters.aggregate_filters.SelectedAggregateIdFilter static method) (scine_chemoton.filters.aggregate_filters.SelectedStructureIdFilter static method) (scine_chemoton.filters.aggregate_filters.SelfReactionFilter static method) (scine_chemoton.filters.aggregate_filters.SpecificChargeFilter static method) (scine_chemoton.filters.aggregate_filters.StopDuringExploration static method) (scine_chemoton.filters.aggregate_filters.TrueMinimumFilter static method) (scine_chemoton.filters.elementary_step_filters.BarrierlessElementaryStepFilter static method) (scine_chemoton.filters.elementary_step_filters.ConsistentEnergyModelFilter static method) (scine_chemoton.filters.elementary_step_filters.ElementaryStepBarrierFilter static method) (scine_chemoton.filters.elementary_step_filters.ElementaryStepFilter static method) (scine_chemoton.filters.elementary_step_filters.ElementaryStepFilterAndArray static method) (scine_chemoton.filters.elementary_step_filters.ElementaryStepFilterOrArray static method) (scine_chemoton.filters.elementary_step_filters.PlaceHolderElementaryStepFilter static method) (scine_chemoton.filters.elementary_step_filters.StopDuringExploration static method) (scine_chemoton.filters.elementary_step_filters.StructureModelFilter static method) (scine_chemoton.filters.further_exploration_filters.AllBarrierLessDissociationsFilter static method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilter static method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilterAndArray static method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilterOrArray static method) (scine_chemoton.filters.further_exploration_filters.ReactionCoordinateMaxDissociationEnergyFilter static method) (scine_chemoton.filters.reaction_filters.BarrierlessReactionFilter static method) (scine_chemoton.filters.reaction_filters.MaximumTransitionStateEnergyFilter static method) (scine_chemoton.filters.reaction_filters.PlaceHolderReactionFilter static method) (scine_chemoton.filters.reaction_filters.ReactionBarrierFilter static method) (scine_chemoton.filters.reaction_filters.ReactionCachedBasedFilter static method) (scine_chemoton.filters.reaction_filters.ReactionFilter static method) (scine_chemoton.filters.reaction_filters.ReactionFilterAndArray static method) (scine_chemoton.filters.reaction_filters.ReactionFilterOrArray static method) (scine_chemoton.filters.reaction_filters.ReactionHasStepWithModel static method) (scine_chemoton.filters.reaction_filters.ReactionIDFilter static method) (scine_chemoton.filters.reaction_filters.ReactionNumberPropertyFilter static method) (scine_chemoton.filters.reaction_filters.StopDuringExploration static method) (scine_chemoton.filters.reactive_site_filters.AtomPairFunctionalGroupFilter static method) (scine_chemoton.filters.reactive_site_filters.AtomRuleBasedFilter static method) (scine_chemoton.filters.reactive_site_filters.CentralSiteFilter static method) (scine_chemoton.filters.reactive_site_filters.ElementWiseReactionCoordinateFilter static method) (scine_chemoton.filters.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter static method) (scine_chemoton.filters.reactive_site_filters.MasmChemicalRankingFilter static method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilter static method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilterAndArray static method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilterOrArray static method) (scine_chemoton.filters.reactive_site_filters.SimpleRankingFilter static method) (scine_chemoton.filters.reactive_site_filters.SubStructureFilter static method) (scine_chemoton.filters.structure_filters.AtomNumberFilter static method) (scine_chemoton.filters.structure_filters.CatalystFilter static method) (scine_chemoton.filters.structure_filters.ChargeCombinationFilter static method) (scine_chemoton.filters.structure_filters.ElementCountFilter static method) (scine_chemoton.filters.structure_filters.ElementSumCountFilter static method) (scine_chemoton.filters.structure_filters.ModelFilter static method) (scine_chemoton.filters.structure_filters.MolecularWeightFilter static method) (scine_chemoton.filters.structure_filters.SpecificChargeFilter static method) (scine_chemoton.filters.structure_filters.StructureFilter static method) (scine_chemoton.filters.structure_filters.StructureFilterAndArray static method) (scine_chemoton.filters.structure_filters.StructureFilterOrArray static method) (scine_chemoton.filters.structure_filters.StructureLabelFilter static method) (scine_chemoton.filters.structure_filters.TrueMinimumFilter static method) (scine_chemoton.gears.compound.BasicAggregateHousekeeping static method) (scine_chemoton.gears.compound.ThermoAggregateHousekeeping static method) (scine_chemoton.gears.conformers.brute_force.BruteForceConformers static method) (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps static method) (scine_chemoton.gears.elementary_steps.ElementaryStepGear static method) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps static method) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps static method) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps static method) (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased static method) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations static method) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased static method) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased static method) (scine_chemoton.gears.elementary_steps.trial_generator.TrialGenerator static method) (scine_chemoton.gears.Gear static method) (scine_chemoton.gears.HoldsCollections static method) (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling static method) (scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics static method) (scine_chemoton.gears.kinetics.KineticsBase static method) (scine_chemoton.gears.kinetics.MaximumFluxKinetics static method) (scine_chemoton.gears.kinetics.MinimalConnectivityKinetics static method) (scine_chemoton.gears.kinetics.PathfinderKinetics static method) (scine_chemoton.gears.kinetics.ReactionFilterBasedKinetics static method) (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement static method) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement static method) (scine_chemoton.gears.network_refinement.disabling.AggregateDisabling static method) (scine_chemoton.gears.network_refinement.disabling.DisableAllAggregates static method) (scine_chemoton.gears.network_refinement.disabling.DisableAllReactions static method) (scine_chemoton.gears.network_refinement.disabling.DisableAllSteps static method) (scine_chemoton.gears.network_refinement.disabling.DisableAllStepsByModel static method) (scine_chemoton.gears.network_refinement.disabling.DisableReactionByJob static method) (scine_chemoton.gears.network_refinement.disabling.DisableStepByJob static method) (scine_chemoton.gears.network_refinement.disabling.ReactionDisabling static method) (scine_chemoton.gears.network_refinement.disabling.StepDisabling static method) (scine_chemoton.gears.network_refinement.enabling.ApplyToAllStepsInReaction static method) (scine_chemoton.gears.network_refinement.enabling.ApplyToAllStructuresInAggregate static method) (scine_chemoton.gears.network_refinement.enabling.EnableAllSteps static method) (scine_chemoton.gears.network_refinement.enabling.EnableAllStructures static method) (scine_chemoton.gears.network_refinement.enabling.EnableCalculationResults static method) (scine_chemoton.gears.network_refinement.enabling.EnableJobSpecificCalculations static method) (scine_chemoton.gears.network_refinement.enabling.EnableStructureByModel static method) (scine_chemoton.gears.network_refinement.enabling.FilteredStepEnabling static method) (scine_chemoton.gears.network_refinement.enabling.PlaceHolderCalculationEnabling static method) (scine_chemoton.gears.network_refinement.enabling.StepEnabling static method) (scine_chemoton.gears.network_refinement.enabling.StructureEnabling static method) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement static method) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement static method) (scine_chemoton.gears.pathfinder.Pathfinder static method) (scine_chemoton.gears.pathfinder.Pathfinder.BarrierBasedHandler static method) (scine_chemoton.gears.pathfinder.Pathfinder.BasicHandler static method) (scine_chemoton.gears.reaction.BasicReactionHousekeeping static method) (scine_chemoton.gears.rerun_calculations.RerunCalculations static method) (scine_chemoton.gears.scheduler.Scheduler static method) (scine_chemoton.gears.single_point.SinglePoint static method) (scine_chemoton.gears.thermo.BasicThermoDataCompletion static method) (scine_chemoton.steering_wheel.datastructures.ExplorationSchemeStep static method) (scine_chemoton.steering_wheel.network_expansions.basics.SimpleOptimization static method) (scine_chemoton.steering_wheel.network_expansions.basics.ThermochemistryGeneration static method) (scine_chemoton.steering_wheel.network_expansions.conformers.ConformerCreation static method) (scine_chemoton.steering_wheel.network_expansions.NetworkExpansion static method) (scine_chemoton.steering_wheel.network_expansions.reactions.Association static method) (scine_chemoton.steering_wheel.network_expansions.reactions.ChemicalReaction static method) (scine_chemoton.steering_wheel.network_expansions.reactions.Dissociation static method) (scine_chemoton.steering_wheel.network_expansions.reactions.Rearrangement static method) (scine_chemoton.steering_wheel.selections.basics.AllFromPreviousResultSelection static method) (scine_chemoton.steering_wheel.selections.basics.AllUserInputsSelection static method) (scine_chemoton.steering_wheel.selections.basics.BarriersWithinRangeSelection static method) (scine_chemoton.steering_wheel.selections.basics.LowestBarrierSelection static method) (scine_chemoton.steering_wheel.selections.basics.ProductsSelection static method) (scine_chemoton.steering_wheel.selections.conformers.CentroidConformerSelection static method) (scine_chemoton.steering_wheel.selections.conformers.ClusterCentroidConformerSelection static method) (scine_chemoton.steering_wheel.selections.conformers.ClusterSelection static method) (scine_chemoton.steering_wheel.selections.conformers.ConformerSelection static method) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerPerClusterSelection static method) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerSelection static method) (scine_chemoton.steering_wheel.selections.input_selections.FileInputSelection static method) (scine_chemoton.steering_wheel.selections.input_selections.InputSelection static method) (scine_chemoton.steering_wheel.selections.input_selections.ScineGeometryInputSelection static method) (scine_chemoton.steering_wheel.selections.organometallic_complexes.CentralMetalSelection static method) (scine_chemoton.steering_wheel.selections.Selection static method) (scine_chemoton.steering_wheel.selections.SelectionAndArray static method) (scine_chemoton.steering_wheel.selections.SelectionOrArray static method)

post_refine_model (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) process() (scine_chemoton.gears.network_refinement.disabling.AggregateDisabling method) (scine_chemoton.gears.network_refinement.disabling.DisableAllAggregates method) (scine_chemoton.gears.network_refinement.disabling.DisableAllReactions method) (scine_chemoton.gears.network_refinement.disabling.DisableAllSteps method) (scine_chemoton.gears.network_refinement.disabling.DisableAllStepsByModel method) (scine_chemoton.gears.network_refinement.disabling.DisableReactionByJob method) (scine_chemoton.gears.network_refinement.disabling.DisableStepByJob method) (scine_chemoton.gears.network_refinement.disabling.ReactionDisabling method) (scine_chemoton.gears.network_refinement.disabling.StepDisabling method) (scine_chemoton.gears.network_refinement.enabling.AggregateEnabling method) (scine_chemoton.gears.network_refinement.enabling.ApplyToAllStepsInReaction method) (scine_chemoton.gears.network_refinement.enabling.ApplyToAllStructuresInAggregate method) (scine_chemoton.gears.network_refinement.enabling.EnableAllAggregates method) (scine_chemoton.gears.network_refinement.enabling.EnableAllReactions method) (scine_chemoton.gears.network_refinement.enabling.EnableAllSteps method) (scine_chemoton.gears.network_refinement.enabling.EnableAllStructures method) (scine_chemoton.gears.network_refinement.enabling.EnableCalculationResults method) (scine_chemoton.gears.network_refinement.enabling.EnableJobSpecificCalculations method) (scine_chemoton.gears.network_refinement.enabling.EnableStructureByModel method) (scine_chemoton.gears.network_refinement.enabling.FilteredStepEnabling method) (scine_chemoton.gears.network_refinement.enabling.PlaceHolderAggregateEnabling method) (scine_chemoton.gears.network_refinement.enabling.PlaceHolderCalculationEnabling method) (scine_chemoton.gears.network_refinement.enabling.PlaceHolderReactionEnabling method) (scine_chemoton.gears.network_refinement.enabling.ReactionEnabling method) (scine_chemoton.gears.network_refinement.enabling.StepEnabling method) (scine_chemoton.gears.network_refinement.enabling.StructureEnabling method) process_calculations_of_structures() (scine_chemoton.gears.network_refinement.enabling.EnableJobSpecificCalculations method) ProductsSelection (class in scine_chemoton.steering_wheel.selections.basics) ProductsSelection.Options (class in scine_chemoton.steering_wheel.selections.basics) property_label (scine_chemoton.gears.kinetics.MaximumFluxKinetics.Options attribute) property_name (scine_chemoton.filters.structure_filters.TrueMinimumFilter attribute) protocol (scine_chemoton.steering_wheel.network_expansions.basics.SimpleOptimization attribute) (scine_chemoton.steering_wheel.network_expansions.basics.ThermochemistryGeneration attribute) (scine_chemoton.steering_wheel.network_expansions.conformers.ConformerCreation attribute) (scine_chemoton.steering_wheel.network_expansions.reactions.Association attribute) (scine_chemoton.steering_wheel.network_expansions.reactions.ChemicalReaction attribute) (scine_chemoton.steering_wheel.network_expansions.reactions.Dissociation attribute) (scine_chemoton.steering_wheel.network_expansions.reactions.Rearrangement attribute) protocol_step_index (scine_chemoton.steering_wheel.datastructures.RestartPartialExpansionInfo attribute) ProtocolEntry (class in scine_chemoton.steering_wheel.datastructures) provides_values() (scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties.ThermodynamicPropertiesCache method) pruned_atom_pairs() (in module scine_chemoton.utilities.masm)

R

Reaction (class in scine_chemoton.utilities.db_object_wrappers.reaction_wrapper) reaction_disabling (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement attribute) reaction_enabling (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement attribute) reaction_filter (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement attribute) reaction_template_file (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased.Options attribute) reaction_validation (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement attribute) ReactionBarrierFilter (class in scine_chemoton.filters.reaction_filters) ReactionBasedRefinement (class in scine_chemoton.gears.network_refinement.reaction_based_refinement) ReactionBasedRefinement.Options (class in scine_chemoton.gears.network_refinement.reaction_based_refinement) ReactionCache (class in scine_chemoton.utilities.db_object_wrappers.reaction_cache) ReactionCachedBasedFilter (class in scine_chemoton.filters.reaction_filters) ReactionCoordinateMaxDissociationEnergyFilter (class in scine_chemoton.filters.further_exploration_filters) ReactionDisabling (class in scine_chemoton.gears.network_refinement.disabling) ReactionEnabling (class in scine_chemoton.gears.network_refinement.enabling) ReactionFilter (class in scine_chemoton.filters.reaction_filters) ReactionFilterAndArray (class in scine_chemoton.filters.reaction_filters) ReactionFilterBasedKinetics (class in scine_chemoton.gears.kinetics) ReactionFilterBasedKinetics.Options (class in scine_chemoton.gears.kinetics) ReactionFilterOrArray (class in scine_chemoton.filters.reaction_filters) ReactionHasStepWithModel (class in scine_chemoton.filters.reaction_filters) ReactionIDFilter (class in scine_chemoton.filters.reaction_filters) ReactionNetworkData (class in scine_chemoton.gears.kinetic_modeling.rms_network_extractor) ReactionNumberPropertyFilter (class in scine_chemoton.filters.reaction_filters) reactions (scine_chemoton.steering_wheel.datastructures.NetworkExpansionResult attribute) ReactionType (class in scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer) reactive_site_filter (scine_chemoton.steering_wheel.datastructures.SelectionResult attribute) ReactiveComplexes (class in scine_chemoton.utilities.reactive_complexes) ReactiveComplexes.Options (class in scine_chemoton.utilities.reactive_complexes) ReactiveSiteFilter (class in scine_chemoton.filters.reactive_site_filters) ReactiveSiteFilterAndArray (class in scine_chemoton.filters.reactive_site_filters) ReactiveSiteFilterOrArray (class in scine_chemoton.filters.reactive_site_filters) Rearrangement (class in scine_chemoton.steering_wheel.network_expansions.reactions) Rearrangement.Options (class in scine_chemoton.steering_wheel.network_expansions.reactions) receive_from_pipe() (scine_chemoton.steering_wheel.datastructures.ExplorationResult class method) (scine_chemoton.steering_wheel.datastructures.NetworkExpansionResult class method) (scine_chemoton.steering_wheel.datastructures.SelectionResult class method) reference_state (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling.Options attribute) (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute)

ReferenceState (class in scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties) refine_n_per_reaction (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) refinement (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement.Options attribute) refinements (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) remove_global_selection() (scine_chemoton.steering_wheel.SteeringWheel method) RerunCalculations (class in scine_chemoton.gears.rerun_calculations) RerunCalculations.Options (class in scine_chemoton.gears.rerun_calculations) reset_graph_compound_costs() (scine_chemoton.gears.pathfinder.Pathfinder method) reset_job_factory() (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling method) restart (scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics.Options attribute) (scine_chemoton.gears.kinetics.KineticsBase.Options attribute) (scine_chemoton.gears.kinetics.MaximumFluxKinetics.Options attribute) (scine_chemoton.gears.kinetics.MinimalConnectivityKinetics.Options attribute) (scine_chemoton.gears.kinetics.PathfinderKinetics.Options attribute) (scine_chemoton.gears.kinetics.ReactionFilterBasedKinetics.Options attribute) restart_excess_ratio (scine_chemoton.gears.kinetics.PathfinderKinetics.Options attribute) restart_file (scine_chemoton.steering_wheel.SteeringWheel property) restart_info_key (scine_chemoton.gears.rerun_calculations.RerunCalculations attribute) RestartPartialExpansionInfo (class in scine_chemoton.steering_wheel.datastructures) result_enabling (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement attribute) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement attribute) (scine_chemoton.gears.rerun_calculations.RerunCalculations attribute) results_enabling_policy (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options attribute) rmsd_tolerance (scine_chemoton.gears.reaction.BasicReactionHousekeeping.Options attribute) RMSKineticModelingJobFactory (class in scine_chemoton.gears.kinetic_modeling.rms_kinetic_modeling) rule_applies() (scine_chemoton.reaction_rules.element_rules.ElementBaseRule method) (scine_chemoton.reaction_rules.element_rules.SimpleElementCombinationRule method) RuleSet (class in scine_chemoton.reaction_rules) run() (scine_chemoton.engine.Engine method) (scine_chemoton.engine.EngineHandler method) (scine_chemoton.steering_wheel.datastructures.ProtocolEntry method) (scine_chemoton.steering_wheel.SteeringWheel method) run_one_cycle_with_settings_enhancement (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.ElementaryStepGear.Options attribute) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps.Options attribute)

S

save() (scine_chemoton.steering_wheel.SteeringWheel method) Scheduler (class in scine_chemoton.gears.scheduler) Scheduler.Options (class in scine_chemoton.gears.scheduler) scine_chemoton.engine module scine_chemoton.filters module scine_chemoton.filters.aggregate_filters module scine_chemoton.filters.elementary_step_filters module scine_chemoton.filters.further_exploration_filters module scine_chemoton.filters.reaction_filters module scine_chemoton.filters.reactive_site_filters module scine_chemoton.filters.structure_filters module scine_chemoton.gears module scine_chemoton.gears.compound module scine_chemoton.gears.conformers module scine_chemoton.gears.conformers.brute_force module scine_chemoton.gears.elementary_steps module scine_chemoton.gears.elementary_steps.brute_force module scine_chemoton.gears.elementary_steps.minimal module scine_chemoton.gears.elementary_steps.minimum_energy_conformer module scine_chemoton.gears.elementary_steps.selected_structures module scine_chemoton.gears.elementary_steps.trial_generator module scine_chemoton.gears.elementary_steps.trial_generator.bond_based module scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer module scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations module scine_chemoton.gears.elementary_steps.trial_generator.fragment_based module scine_chemoton.gears.elementary_steps.trial_generator.template_based module scine_chemoton.gears.kinetic_modeling module scine_chemoton.gears.kinetic_modeling.atomization module scine_chemoton.gears.kinetic_modeling.kinetic_modeling module scine_chemoton.gears.kinetic_modeling.kinetx_kinetic_modeling module scine_chemoton.gears.kinetic_modeling.prepare_kinetic_modeling_job module scine_chemoton.gears.kinetic_modeling.rms_kinetic_modeling module scine_chemoton.gears.kinetic_modeling.rms_network_extractor module scine_chemoton.gears.kinetics module scine_chemoton.gears.network_refinement module scine_chemoton.gears.network_refinement.aggregate_based_refinement module scine_chemoton.gears.network_refinement.calculation_based_refinement module scine_chemoton.gears.network_refinement.disabling module scine_chemoton.gears.network_refinement.enabling module scine_chemoton.gears.network_refinement.reaction_based_refinement module scine_chemoton.gears.network_refinement.refinement module scine_chemoton.gears.pathfinder module scine_chemoton.gears.reaction module scine_chemoton.gears.rerun_calculations module scine_chemoton.gears.scheduler module scine_chemoton.gears.single_point module scine_chemoton.gears.thermo module scine_chemoton.reaction_rules module scine_chemoton.reaction_rules.distance_rules module scine_chemoton.reaction_rules.element_rules module scine_chemoton.reaction_rules.polarization_rules module scine_chemoton.reaction_rules.reaction_rule_library module scine_chemoton.steering_wheel.datastructures module scine_chemoton.steering_wheel.network_expansions.basics module scine_chemoton.steering_wheel.network_expansions.conformers module scine_chemoton.steering_wheel.network_expansions.reactions module scine_chemoton.steering_wheel.selections.basics module scine_chemoton.steering_wheel.selections.conformers module scine_chemoton.steering_wheel.selections.input_selections module scine_chemoton.steering_wheel.selections.organometallic_complexes module scine_chemoton.utilities.db_object_wrappers.aggregate_cache module scine_chemoton.utilities.db_object_wrappers.aggregate_wrapper module scine_chemoton.utilities.db_object_wrappers.ensemble_wrapper module scine_chemoton.utilities.db_object_wrappers.reaction_cache module scine_chemoton.utilities.db_object_wrappers.reaction_wrapper module scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties module scine_chemoton.utilities.db_object_wrappers.wrapper_caches module scine_chemoton.utilities.insert_initial_structure module scine_chemoton.utilities.masm module scine_chemoton.utilities.reactive_complexes module scine_chemoton.utilities.reactive_complexes.inter_reactive_complexes module scine_chemoton.utilities.reactive_complexes.lebedev_sphere module scine_chemoton.utilities.reactive_complexes.unit_circle module ScineGeometryInputSelection (class in scine_chemoton.steering_wheel.selections.input_selections) ScineGeometryInputSelection.Options (class in scine_chemoton.steering_wheel.selections.input_selections) selected_structures (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps.Options attribute) SelectedAggregateIdFilter (class in scine_chemoton.filters.aggregate_filters) SelectedStructureIdFilter (class in scine_chemoton.filters.aggregate_filters) SelectedStructuresElementarySteps (class in scine_chemoton.gears.elementary_steps.selected_structures) SelectedStructuresElementarySteps.Options (class in scine_chemoton.gears.elementary_steps.selected_structures) Selection (class in scine_chemoton.steering_wheel.selections) Selection.Options (class in scine_chemoton.steering_wheel.selections) SelectionAndArray (class in scine_chemoton.steering_wheel.selections) SelectionAndArray.Options (class in scine_chemoton.steering_wheel.selections) SelectionOrArray (class in scine_chemoton.steering_wheel.selections) SelectionOrArray.Options (class in scine_chemoton.steering_wheel.selections) SelectionResult (class in scine_chemoton.steering_wheel.datastructures) SelfReactionFilter (class in scine_chemoton.filters.aggregate_filters) send_in_pipe() (scine_chemoton.steering_wheel.datastructures.ExplorationResult method) (scine_chemoton.steering_wheel.datastructures.NetworkExpansionResult method) (scine_chemoton.steering_wheel.datastructures.SelectionResult method) set_barrier_limit() (scine_chemoton.gears.pathfinder.Pathfinder.BarrierBasedHandler method) set_cache() (scine_chemoton.filters.reaction_filters.BarrierlessReactionFilter method) (scine_chemoton.filters.reaction_filters.MaximumTransitionStateEnergyFilter method) (scine_chemoton.filters.reaction_filters.ReactionBarrierFilter method) (scine_chemoton.filters.reaction_filters.ReactionCachedBasedFilter method) set_gear() (scine_chemoton.engine.Engine method) set_global_selection() (scine_chemoton.steering_wheel.SteeringWheel method) set_options() (scine_chemoton.utilities.reactive_complexes.inter_reactive_complexes.InterReactiveComplexes method) (scine_chemoton.utilities.reactive_complexes.ReactiveComplexes method) set_partial_restart_info() (scine_chemoton.steering_wheel.SteeringWheel method) set_result() (scine_chemoton.steering_wheel.datastructures.ExplorationSchemeStep method) (scine_chemoton.steering_wheel.network_expansions.basics.SimpleOptimization method) (scine_chemoton.steering_wheel.network_expansions.basics.ThermochemistryGeneration method) (scine_chemoton.steering_wheel.network_expansions.conformers.ConformerCreation method) (scine_chemoton.steering_wheel.network_expansions.NetworkExpansion method) (scine_chemoton.steering_wheel.network_expansions.reactions.Association method) (scine_chemoton.steering_wheel.network_expansions.reactions.ChemicalReaction method) (scine_chemoton.steering_wheel.network_expansions.reactions.Dissociation method) (scine_chemoton.steering_wheel.network_expansions.reactions.Rearrangement method) (scine_chemoton.steering_wheel.selections.basics.AllFromPreviousResultSelection method) (scine_chemoton.steering_wheel.selections.basics.AllUserInputsSelection method) (scine_chemoton.steering_wheel.selections.basics.BarriersWithinRangeSelection method) (scine_chemoton.steering_wheel.selections.basics.LowestBarrierSelection method) (scine_chemoton.steering_wheel.selections.basics.ProductsSelection method) (scine_chemoton.steering_wheel.selections.conformers.CentroidConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.ClusterCentroidConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.ClusterSelection method) (scine_chemoton.steering_wheel.selections.conformers.ConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerPerClusterSelection method) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerSelection method) (scine_chemoton.steering_wheel.selections.input_selections.FileInputSelection method) (scine_chemoton.steering_wheel.selections.input_selections.InputSelection method) (scine_chemoton.steering_wheel.selections.input_selections.ScineGeometryInputSelection method) (scine_chemoton.steering_wheel.selections.organometallic_complexes.CentralMetalSelection method) (scine_chemoton.steering_wheel.selections.Selection method) (scine_chemoton.steering_wheel.selections.SelectionAndArray method) (scine_chemoton.steering_wheel.selections.SelectionOrArray method) set_start_conditions() (scine_chemoton.gears.pathfinder.Pathfinder method) set_step_result() (scine_chemoton.steering_wheel.selections.basics.AllFromPreviousResultSelection method) (scine_chemoton.steering_wheel.selections.basics.AllUserInputsSelection method) (scine_chemoton.steering_wheel.selections.basics.BarriersWithinRangeSelection method) (scine_chemoton.steering_wheel.selections.basics.LowestBarrierSelection method) (scine_chemoton.steering_wheel.selections.basics.ProductsSelection method) (scine_chemoton.steering_wheel.selections.conformers.CentroidConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.ClusterCentroidConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.ClusterSelection method) (scine_chemoton.steering_wheel.selections.conformers.ConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerPerClusterSelection method) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerSelection method) (scine_chemoton.steering_wheel.selections.input_selections.FileInputSelection method) (scine_chemoton.steering_wheel.selections.input_selections.InputSelection method) (scine_chemoton.steering_wheel.selections.input_selections.ScineGeometryInputSelection method) (scine_chemoton.steering_wheel.selections.organometallic_complexes.CentralMetalSelection method) (scine_chemoton.steering_wheel.selections.Selection method) (scine_chemoton.steering_wheel.selections.SelectionAndArray method) (scine_chemoton.steering_wheel.selections.SelectionOrArray method)

set_temperature() (scine_chemoton.gears.pathfinder.Pathfinder.BarrierBasedHandler method) set_up_atom_energy_calculations() (scine_chemoton.gears.kinetic_modeling.atomization.AtomEnergyReference method) setdefault() (scine_chemoton.reaction_rules.distance_rules.DistanceRuleSet method) (scine_chemoton.reaction_rules.element_rules.ElementRuleSet method) (scine_chemoton.reaction_rules.polarization_rules.PolarizationRuleSet method) (scine_chemoton.reaction_rules.reaction_rule_library.DefaultOrganicChemistry method) (scine_chemoton.reaction_rules.RuleSet method) (scine_chemoton.steering_wheel.datastructures.GearOptions method) settings (scine_chemoton.gears.thermo.BasicThermoDataCompletion.Options attribute) SimpleDistanceRule (class in scine_chemoton.reaction_rules.distance_rules) SimpleElementCombinationRule (class in scine_chemoton.reaction_rules.element_rules) SimpleOptimization (class in scine_chemoton.steering_wheel.network_expansions.basics) SimpleOptimization.Options (class in scine_chemoton.steering_wheel.network_expansions.basics) SimpleRankingFilter (class in scine_chemoton.filters.reactive_site_filters) single_ended_job (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) single_ended_job_settings (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) single_ended_step_refinement_job (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) single_ended_step_refinement_settings (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) single_structure_assertion() (in module scine_chemoton.filters.further_exploration_filters) SinglePoint (class in scine_chemoton.gears.single_point) SinglePoint.Options (class in scine_chemoton.gears.single_point) sp_job (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) sp_job_settings (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) SpecificChargeFilter (class in scine_chemoton.filters.aggregate_filters) (class in scine_chemoton.filters.structure_filters) SpNCX (class in scine_chemoton.reaction_rules.reaction_rule_library) STALLING (scine_chemoton.steering_wheel.datastructures.Status attribute) start() (scine_chemoton.steering_wheel.SteeringWheel method) start_conditions (scine_chemoton.gears.kinetics.PathfinderKinetics.Options attribute) start_conditions_are_met() (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling method) start_id (scine_chemoton.steering_wheel.datastructures.RestartPartialExpansionInfo attribute) start_time (scine_chemoton.steering_wheel.datastructures.RestartPartialExpansionInfo attribute) Status (class in scine_chemoton.steering_wheel.datastructures) SteeringWheel (class in scine_chemoton.steering_wheel) step_disabling (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement attribute) StepDisabling (class in scine_chemoton.gears.network_refinement.disabling) StepEnabling (class in scine_chemoton.gears.network_refinement.enabling) stop() (scine_chemoton.engine.Engine method) (scine_chemoton.gears.compound.BasicAggregateHousekeeping method) (scine_chemoton.gears.compound.ThermoAggregateHousekeeping method) (scine_chemoton.gears.conformers.brute_force.BruteForceConformers method) (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps method) (scine_chemoton.gears.elementary_steps.ElementaryStepGear method) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps method) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps method) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps method) (scine_chemoton.gears.Gear method) (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling method) (scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics method) (scine_chemoton.gears.kinetics.KineticsBase method) (scine_chemoton.gears.kinetics.MaximumFluxKinetics method) (scine_chemoton.gears.kinetics.MinimalConnectivityKinetics method) (scine_chemoton.gears.kinetics.PathfinderKinetics method) (scine_chemoton.gears.kinetics.ReactionFilterBasedKinetics method) (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement method) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement method) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement method) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement method) (scine_chemoton.gears.reaction.BasicReactionHousekeeping method) (scine_chemoton.gears.rerun_calculations.RerunCalculations method) (scine_chemoton.gears.scheduler.Scheduler method) (scine_chemoton.gears.single_point.SinglePoint method) (scine_chemoton.gears.thermo.BasicThermoDataCompletion method) (scine_chemoton.steering_wheel.datastructures.ProtocolEntry method) (scine_chemoton.steering_wheel.datastructures.StopPreviousProtocolEntries method) (scine_chemoton.steering_wheel.SteeringWheel method) stop_and_join() (scine_chemoton.engine.EngineHandler method) stop_at_next_break_point (scine_chemoton.gears.compound.BasicAggregateHousekeeping property) (scine_chemoton.gears.compound.ThermoAggregateHousekeeping property) (scine_chemoton.gears.conformers.brute_force.BruteForceConformers property) (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps property) (scine_chemoton.gears.elementary_steps.ElementaryStepGear property) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps property) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps property) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps property) (scine_chemoton.gears.Gear property) (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling property) (scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics property) (scine_chemoton.gears.kinetics.KineticsBase property) (scine_chemoton.gears.kinetics.MaximumFluxKinetics property) (scine_chemoton.gears.kinetics.MinimalConnectivityKinetics property) (scine_chemoton.gears.kinetics.PathfinderKinetics property) (scine_chemoton.gears.kinetics.ReactionFilterBasedKinetics property) (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement property) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement property) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement property) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement property) (scine_chemoton.gears.reaction.BasicReactionHousekeeping property) (scine_chemoton.gears.rerun_calculations.RerunCalculations property) (scine_chemoton.gears.scheduler.Scheduler property) (scine_chemoton.gears.single_point.SinglePoint property) (scine_chemoton.gears.thermo.BasicThermoDataCompletion property) stop_if_no_new_aggregates_are_activated (scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics.Options attribute) (scine_chemoton.gears.kinetics.KineticsBase.Options attribute) (scine_chemoton.gears.kinetics.MaximumFluxKinetics.Options attribute) (scine_chemoton.gears.kinetics.MinimalConnectivityKinetics.Options attribute) (scine_chemoton.gears.kinetics.PathfinderKinetics.Options attribute) (scine_chemoton.gears.kinetics.ReactionFilterBasedKinetics.Options attribute) StopDuringExploration (class in scine_chemoton.filters.aggregate_filters) (class in scine_chemoton.filters.elementary_step_filters) (class in scine_chemoton.filters.reaction_filters) STOPPING (scine_chemoton.steering_wheel.datastructures.Status attribute) StopPreviousProtocolEntries (class in scine_chemoton.steering_wheel.datastructures) StopSplitCommunicationMethod (class in scine_chemoton.steering_wheel.datastructures) store_pathfinder_output (scine_chemoton.gears.kinetics.PathfinderKinetics.Options attribute) string_from_rule() (scine_chemoton.reaction_rules.polarization_rules.PaulingElectronegativityRule method) (scine_chemoton.reaction_rules.polarization_rules.PolarizationBaseRule method) (scine_chemoton.reaction_rules.polarization_rules.PolarizationFunctionalGroupRule method) (scine_chemoton.reaction_rules.polarization_rules.PolarizationRuleAndArray method) structure_model (scine_chemoton.gears.compound.ThermoAggregateHousekeeping.Options attribute) (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.ElementaryStepGear.Options attribute) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps.Options attribute) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps.Options attribute) (scine_chemoton.gears.kinetics.PathfinderKinetics.Options attribute) (scine_chemoton.gears.pathfinder.Pathfinder.Options attribute) (scine_chemoton.gears.thermo.BasicThermoDataCompletion.Options attribute) StructureEnabling (class in scine_chemoton.gears.network_refinement.enabling) StructureFilter (class in scine_chemoton.filters.structure_filters) StructureFilterAndArray (class in scine_chemoton.filters.structure_filters) StructureFilterOrArray (class in scine_chemoton.filters.structure_filters) StructureInformation (class in scine_chemoton.steering_wheel.datastructures) StructureLabelFilter (class in scine_chemoton.filters.structure_filters) StructureModelFilter (class in scine_chemoton.filters.elementary_step_filters) structures (scine_chemoton.steering_wheel.datastructures.NetworkExpansionResult attribute) (scine_chemoton.steering_wheel.datastructures.SelectionResult attribute) SubStructureFilter (class in scine_chemoton.filters.reactive_site_filters) supports_flasks() (scine_chemoton.filters.aggregate_filters.ActivatedAggregateFilter method) (scine_chemoton.filters.aggregate_filters.AggregateFilter method) (scine_chemoton.filters.aggregate_filters.AggregateFilterAndArray method) (scine_chemoton.filters.aggregate_filters.AggregateFilterOrArray method) (scine_chemoton.filters.aggregate_filters.AtomNumberFilter method) (scine_chemoton.filters.aggregate_filters.CatalystFilter method) (scine_chemoton.filters.aggregate_filters.ChargeCombinationFilter method) (scine_chemoton.filters.aggregate_filters.CompleteSubstructureFilter method) (scine_chemoton.filters.aggregate_filters.CompoundCostPropertyFilter method) (scine_chemoton.filters.aggregate_filters.ConcentrationPropertyFilter method) (scine_chemoton.filters.aggregate_filters.ElementCountFilter method) (scine_chemoton.filters.aggregate_filters.ElementSumCountFilter method) (scine_chemoton.filters.aggregate_filters.HasStructureWithModel method) (scine_chemoton.filters.aggregate_filters.IdFilter method) (scine_chemoton.filters.aggregate_filters.LastKineticModelingFilter method) (scine_chemoton.filters.aggregate_filters.MolecularWeightFilter method) (scine_chemoton.filters.aggregate_filters.OneAggregateIdFilter method) (scine_chemoton.filters.aggregate_filters.OnePotentialEnergySurface method) (scine_chemoton.filters.aggregate_filters.PlaceHolderAggregateFilter method) (scine_chemoton.filters.aggregate_filters.SelectedAggregateIdFilter method) (scine_chemoton.filters.aggregate_filters.SelectedStructureIdFilter method) (scine_chemoton.filters.aggregate_filters.SelfReactionFilter method) (scine_chemoton.filters.aggregate_filters.SpecificChargeFilter method) (scine_chemoton.filters.aggregate_filters.StopDuringExploration method) (scine_chemoton.filters.aggregate_filters.TrueMinimumFilter method) (scine_chemoton.filters.further_exploration_filters.AllBarrierLessDissociationsFilter method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilter method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilterAndArray method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilterOrArray method) (scine_chemoton.filters.further_exploration_filters.ReactionCoordinateMaxDissociationEnergyFilter method) (scine_chemoton.filters.reactive_site_filters.AtomPairFunctionalGroupFilter method) (scine_chemoton.filters.reactive_site_filters.AtomRuleBasedFilter method) (scine_chemoton.filters.reactive_site_filters.CentralSiteFilter method) (scine_chemoton.filters.reactive_site_filters.ElementWiseReactionCoordinateFilter method) (scine_chemoton.filters.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter method) (scine_chemoton.filters.reactive_site_filters.MasmChemicalRankingFilter method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilter method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilterAndArray method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilterOrArray method) (scine_chemoton.filters.reactive_site_filters.SimpleRankingFilter method) (scine_chemoton.filters.reactive_site_filters.SubStructureFilter method)

T

temperature (scine_chemoton.gears.conformers.brute_force.BruteForceConformers.Options attribute) (scine_chemoton.gears.kinetics.PathfinderKinetics.Options attribute) (scine_chemoton.gears.pathfinder.Pathfinder.Options attribute) TemplateBased (class in scine_chemoton.gears.elementary_steps.trial_generator.template_based) TemplateBased.Options (class in scine_chemoton.gears.elementary_steps.trial_generator.template_based) TemplateBased.Options.BimolOptions (class in scine_chemoton.gears.elementary_steps.trial_generator.template_based) TemplateBased.Options.UnimolOptions (class in scine_chemoton.gears.elementary_steps.trial_generator.template_based) terminate() (scine_chemoton.engine.Engine method) (scine_chemoton.steering_wheel.datastructures.ProtocolEntry method) (scine_chemoton.steering_wheel.SteeringWheel method) ThermoAggregateHousekeeping (class in scine_chemoton.gears.compound) ThermoAggregateHousekeeping.Options (class in scine_chemoton.gears.compound) thermochemistry_gear (scine_chemoton.steering_wheel.network_expansions.basics.SimpleOptimization attribute) (scine_chemoton.steering_wheel.network_expansions.basics.ThermochemistryGeneration attribute) (scine_chemoton.steering_wheel.network_expansions.conformers.ConformerCreation attribute) (scine_chemoton.steering_wheel.network_expansions.NetworkExpansion attribute) (scine_chemoton.steering_wheel.network_expansions.reactions.Association attribute) (scine_chemoton.steering_wheel.network_expansions.reactions.ChemicalReaction attribute) (scine_chemoton.steering_wheel.network_expansions.reactions.Dissociation attribute) (scine_chemoton.steering_wheel.network_expansions.reactions.Rearrangement attribute) ThermochemistryGeneration (class in scine_chemoton.steering_wheel.network_expansions.basics) ThermochemistryGeneration.Options (class in scine_chemoton.steering_wheel.network_expansions.basics)

ThermodynamicProperties (class in scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties) ThermodynamicPropertiesCache (class in scine_chemoton.utilities.db_object_wrappers.thermodynamic_properties) to_split_results() (scine_chemoton.steering_wheel.datastructures.ExplorationResult method) (scine_chemoton.steering_wheel.datastructures.NetworkExpansionResult method) (scine_chemoton.steering_wheel.datastructures.SelectionResult method) transition_state_energy_window (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) trial_generator (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps attribute) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps attribute) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps attribute) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps attribute) TrialGenerator (class in scine_chemoton.gears.elementary_steps.trial_generator) TrialGenerator.Options (class in scine_chemoton.gears.elementary_steps.trial_generator) TrueMinimumFilter (class in scine_chemoton.filters.aggregate_filters) (class in scine_chemoton.filters.structure_filters) tsopt_job (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute) tsopt_job_settings (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options attribute) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options attribute)

U

uncertainty_estimator (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling.Options attribute) unimolecular_association_options (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options attribute) unimolecular_coordinates() (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps method) (scine_chemoton.gears.elementary_steps.ElementaryStepGear method) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps method) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps method) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps method) (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased method) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations method) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased method) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased method) (scine_chemoton.gears.elementary_steps.trial_generator.TrialGenerator method) unimolecular_dissociation_options (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options attribute) unimolecular_fast_coordinates() (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations method) unimolecular_further_explore_coordinates() (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations method) unimolecular_options (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options attribute) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options attribute) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased.Options attribute) unimolecular_reactions() (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased method) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations method) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased method) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased method) (scine_chemoton.gears.elementary_steps.trial_generator.TrialGenerator method) UnitCircle (class in scine_chemoton.utilities.reactive_complexes.unit_circle) unpruned_atom_pairs() (in module scine_chemoton.utilities.masm) unset_collections() (scine_chemoton.filters.aggregate_filters.ActivatedAggregateFilter method) (scine_chemoton.filters.aggregate_filters.AggregateFilter method) (scine_chemoton.filters.aggregate_filters.AggregateFilterAndArray method) (scine_chemoton.filters.aggregate_filters.AggregateFilterOrArray method) (scine_chemoton.filters.aggregate_filters.AtomNumberFilter method) (scine_chemoton.filters.aggregate_filters.CatalystFilter method) (scine_chemoton.filters.aggregate_filters.ChargeCombinationFilter method) (scine_chemoton.filters.aggregate_filters.CompleteSubstructureFilter method) (scine_chemoton.filters.aggregate_filters.CompoundCostPropertyFilter method) (scine_chemoton.filters.aggregate_filters.ConcentrationPropertyFilter method) (scine_chemoton.filters.aggregate_filters.ElementCountFilter method) (scine_chemoton.filters.aggregate_filters.ElementSumCountFilter method) (scine_chemoton.filters.aggregate_filters.HasStructureWithModel method) (scine_chemoton.filters.aggregate_filters.IdFilter method) (scine_chemoton.filters.aggregate_filters.LastKineticModelingFilter method) (scine_chemoton.filters.aggregate_filters.MolecularWeightFilter method) (scine_chemoton.filters.aggregate_filters.OneAggregateIdFilter method) (scine_chemoton.filters.aggregate_filters.OnePotentialEnergySurface method) (scine_chemoton.filters.aggregate_filters.PlaceHolderAggregateFilter method) (scine_chemoton.filters.aggregate_filters.SelectedAggregateIdFilter method) (scine_chemoton.filters.aggregate_filters.SelectedStructureIdFilter method) (scine_chemoton.filters.aggregate_filters.SelfReactionFilter method) (scine_chemoton.filters.aggregate_filters.SpecificChargeFilter method) (scine_chemoton.filters.aggregate_filters.StopDuringExploration method) (scine_chemoton.filters.aggregate_filters.TrueMinimumFilter method) (scine_chemoton.filters.elementary_step_filters.BarrierlessElementaryStepFilter method) (scine_chemoton.filters.elementary_step_filters.ConsistentEnergyModelFilter method) (scine_chemoton.filters.elementary_step_filters.ElementaryStepBarrierFilter method) (scine_chemoton.filters.elementary_step_filters.ElementaryStepFilter method) (scine_chemoton.filters.elementary_step_filters.ElementaryStepFilterAndArray method) (scine_chemoton.filters.elementary_step_filters.ElementaryStepFilterOrArray method) (scine_chemoton.filters.elementary_step_filters.PlaceHolderElementaryStepFilter method) (scine_chemoton.filters.elementary_step_filters.StopDuringExploration method) (scine_chemoton.filters.elementary_step_filters.StructureModelFilter method) (scine_chemoton.filters.further_exploration_filters.AllBarrierLessDissociationsFilter method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilter method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilterAndArray method) (scine_chemoton.filters.further_exploration_filters.FurtherExplorationFilterOrArray method) (scine_chemoton.filters.further_exploration_filters.ReactionCoordinateMaxDissociationEnergyFilter method) (scine_chemoton.filters.reaction_filters.BarrierlessReactionFilter method) (scine_chemoton.filters.reaction_filters.MaximumTransitionStateEnergyFilter method) (scine_chemoton.filters.reaction_filters.PlaceHolderReactionFilter method) (scine_chemoton.filters.reaction_filters.ReactionBarrierFilter method) (scine_chemoton.filters.reaction_filters.ReactionCachedBasedFilter method) (scine_chemoton.filters.reaction_filters.ReactionFilter method) (scine_chemoton.filters.reaction_filters.ReactionFilterAndArray method) (scine_chemoton.filters.reaction_filters.ReactionFilterOrArray method) (scine_chemoton.filters.reaction_filters.ReactionHasStepWithModel method) (scine_chemoton.filters.reaction_filters.ReactionIDFilter method) (scine_chemoton.filters.reaction_filters.ReactionNumberPropertyFilter method) (scine_chemoton.filters.reaction_filters.StopDuringExploration method) (scine_chemoton.filters.reactive_site_filters.AtomPairFunctionalGroupFilter method) (scine_chemoton.filters.reactive_site_filters.AtomRuleBasedFilter method) (scine_chemoton.filters.reactive_site_filters.CentralSiteFilter method) (scine_chemoton.filters.reactive_site_filters.ElementWiseReactionCoordinateFilter method) (scine_chemoton.filters.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter method) (scine_chemoton.filters.reactive_site_filters.MasmChemicalRankingFilter method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilter method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilterAndArray method) (scine_chemoton.filters.reactive_site_filters.ReactiveSiteFilterOrArray method) (scine_chemoton.filters.reactive_site_filters.SimpleRankingFilter method) (scine_chemoton.filters.reactive_site_filters.SubStructureFilter method) (scine_chemoton.filters.structure_filters.AtomNumberFilter method) (scine_chemoton.filters.structure_filters.CatalystFilter method) (scine_chemoton.filters.structure_filters.ChargeCombinationFilter method) (scine_chemoton.filters.structure_filters.ElementCountFilter method) (scine_chemoton.filters.structure_filters.ElementSumCountFilter method) (scine_chemoton.filters.structure_filters.ModelFilter method) (scine_chemoton.filters.structure_filters.MolecularWeightFilter method) (scine_chemoton.filters.structure_filters.SpecificChargeFilter method) (scine_chemoton.filters.structure_filters.StructureFilter method) (scine_chemoton.filters.structure_filters.StructureFilterAndArray method) (scine_chemoton.filters.structure_filters.StructureFilterOrArray method) (scine_chemoton.filters.structure_filters.StructureLabelFilter method) (scine_chemoton.filters.structure_filters.TrueMinimumFilter method) (scine_chemoton.gears.compound.BasicAggregateHousekeeping method) (scine_chemoton.gears.compound.BasicAggregateHousekeeping.Options method) (scine_chemoton.gears.compound.ThermoAggregateHousekeeping method) (scine_chemoton.gears.compound.ThermoAggregateHousekeeping.Options method) (scine_chemoton.gears.conformers.brute_force.BruteForceConformers method) (scine_chemoton.gears.conformers.brute_force.BruteForceConformers.Options method) (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps method) (scine_chemoton.gears.elementary_steps.brute_force.BruteForceElementarySteps.Options method) (scine_chemoton.gears.elementary_steps.ElementaryStepGear method) (scine_chemoton.gears.elementary_steps.ElementaryStepGear.Options method) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps method) (scine_chemoton.gears.elementary_steps.minimal.MinimalElementarySteps.Options method) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps method) (scine_chemoton.gears.elementary_steps.minimum_energy_conformer.MinimumEnergyConformerElementarySteps.Options method) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps method) (scine_chemoton.gears.elementary_steps.selected_structures.SelectedStructuresElementarySteps.Options method) (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased method) (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options method) (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.BimolOptions method) (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.UnimolOptions method) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations method) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options method) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.BimolOptions method) (scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations.FastDissociations.Options.UnimolOptions method) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased method) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options method) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.BimolAssociationOptions method) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.UnimolAssociationOptions method) (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.UnimolDissociationOptions method) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased method) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased.Options method) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased.Options.BimolOptions method) (scine_chemoton.gears.elementary_steps.trial_generator.template_based.TemplateBased.Options.UnimolOptions method) (scine_chemoton.gears.elementary_steps.trial_generator.TrialGenerator method) (scine_chemoton.gears.elementary_steps.trial_generator.TrialGenerator.Options method) (scine_chemoton.gears.Gear method) (scine_chemoton.gears.Gear.Options method) (scine_chemoton.gears.HoldsCollections method) (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling method) (scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling.Options method) (scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics method) (scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics.Options method) (scine_chemoton.gears.kinetics.KineticsBase method) (scine_chemoton.gears.kinetics.KineticsBase.Options method) (scine_chemoton.gears.kinetics.MaximumFluxKinetics method) (scine_chemoton.gears.kinetics.MaximumFluxKinetics.Options method) (scine_chemoton.gears.kinetics.MinimalConnectivityKinetics method) (scine_chemoton.gears.kinetics.MinimalConnectivityKinetics.Options method) (scine_chemoton.gears.kinetics.PathfinderKinetics method) (scine_chemoton.gears.kinetics.PathfinderKinetics.Options method) (scine_chemoton.gears.kinetics.ReactionFilterBasedKinetics method) (scine_chemoton.gears.kinetics.ReactionFilterBasedKinetics.Options method) (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement method) (scine_chemoton.gears.network_refinement.aggregate_based_refinement.AggregateBasedRefinement.Options method) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement method) (scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement.Options method) (scine_chemoton.gears.network_refinement.disabling.AggregateDisabling method) (scine_chemoton.gears.network_refinement.disabling.DisableAllAggregates method) (scine_chemoton.gears.network_refinement.disabling.DisableAllReactions method) (scine_chemoton.gears.network_refinement.disabling.DisableAllSteps method) (scine_chemoton.gears.network_refinement.disabling.DisableAllStepsByModel method) (scine_chemoton.gears.network_refinement.disabling.DisableReactionByJob method) (scine_chemoton.gears.network_refinement.disabling.DisableStepByJob method) (scine_chemoton.gears.network_refinement.disabling.ReactionDisabling method) (scine_chemoton.gears.network_refinement.disabling.StepDisabling method) (scine_chemoton.gears.network_refinement.enabling.ApplyToAllStepsInReaction method) (scine_chemoton.gears.network_refinement.enabling.ApplyToAllStructuresInAggregate method) (scine_chemoton.gears.network_refinement.enabling.EnableAllSteps method) (scine_chemoton.gears.network_refinement.enabling.EnableAllStructures method) (scine_chemoton.gears.network_refinement.enabling.EnableCalculationResults method) (scine_chemoton.gears.network_refinement.enabling.EnableJobSpecificCalculations method) (scine_chemoton.gears.network_refinement.enabling.EnableStructureByModel method) (scine_chemoton.gears.network_refinement.enabling.FilteredStepEnabling method) (scine_chemoton.gears.network_refinement.enabling.PlaceHolderCalculationEnabling method) (scine_chemoton.gears.network_refinement.enabling.StepEnabling method) (scine_chemoton.gears.network_refinement.enabling.StructureEnabling method) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement method) (scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement.Options method) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement method) (scine_chemoton.gears.network_refinement.refinement.NetworkRefinement.Options method) (scine_chemoton.gears.pathfinder.Pathfinder method) (scine_chemoton.gears.pathfinder.Pathfinder.BarrierBasedHandler method) (scine_chemoton.gears.pathfinder.Pathfinder.BasicHandler method) (scine_chemoton.gears.pathfinder.Pathfinder.Options method) (scine_chemoton.gears.reaction.BasicReactionHousekeeping method) (scine_chemoton.gears.reaction.BasicReactionHousekeeping.Options method) (scine_chemoton.gears.rerun_calculations.RerunCalculations method) (scine_chemoton.gears.rerun_calculations.RerunCalculations.Options method) (scine_chemoton.gears.scheduler.Scheduler method) (scine_chemoton.gears.scheduler.Scheduler.Options method) (scine_chemoton.gears.single_point.SinglePoint method) (scine_chemoton.gears.single_point.SinglePoint.Options method) (scine_chemoton.gears.thermo.BasicThermoDataCompletion method) (scine_chemoton.gears.thermo.BasicThermoDataCompletion.Options method) (scine_chemoton.steering_wheel.datastructures.ExplorationSchemeStep method) (scine_chemoton.steering_wheel.datastructures.ExplorationSchemeStep.Options method) (scine_chemoton.steering_wheel.network_expansions.basics.SimpleOptimization method) (scine_chemoton.steering_wheel.network_expansions.basics.SimpleOptimization.Options method) (scine_chemoton.steering_wheel.network_expansions.basics.ThermochemistryGeneration method) (scine_chemoton.steering_wheel.network_expansions.basics.ThermochemistryGeneration.Options method) (scine_chemoton.steering_wheel.network_expansions.conformers.ConformerCreation method) (scine_chemoton.steering_wheel.network_expansions.conformers.ConformerCreation.Options method) (scine_chemoton.steering_wheel.network_expansions.NetworkExpansion method) (scine_chemoton.steering_wheel.network_expansions.NetworkExpansion.Options method) (scine_chemoton.steering_wheel.network_expansions.reactions.Association method) (scine_chemoton.steering_wheel.network_expansions.reactions.Association.Options method) (scine_chemoton.steering_wheel.network_expansions.reactions.ChemicalReaction method) (scine_chemoton.steering_wheel.network_expansions.reactions.ChemicalReaction.Options method) (scine_chemoton.steering_wheel.network_expansions.reactions.Dissociation method) (scine_chemoton.steering_wheel.network_expansions.reactions.Dissociation.Options method) (scine_chemoton.steering_wheel.network_expansions.reactions.Rearrangement method) (scine_chemoton.steering_wheel.network_expansions.reactions.Rearrangement.Options method) (scine_chemoton.steering_wheel.selections.basics.AllFromPreviousResultSelection method) (scine_chemoton.steering_wheel.selections.basics.AllFromPreviousResultSelection.Options method) (scine_chemoton.steering_wheel.selections.basics.AllUserInputsSelection method) (scine_chemoton.steering_wheel.selections.basics.AllUserInputsSelection.Options method) (scine_chemoton.steering_wheel.selections.basics.BarriersWithinRangeSelection method) (scine_chemoton.steering_wheel.selections.basics.BarriersWithinRangeSelection.Options method) (scine_chemoton.steering_wheel.selections.basics.LowestBarrierSelection method) (scine_chemoton.steering_wheel.selections.basics.LowestBarrierSelection.Options method) (scine_chemoton.steering_wheel.selections.basics.ProductsSelection method) (scine_chemoton.steering_wheel.selections.basics.ProductsSelection.Options method) (scine_chemoton.steering_wheel.selections.conformers.CentroidConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.CentroidConformerSelection.Options method) (scine_chemoton.steering_wheel.selections.conformers.ClusterCentroidConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.ClusterCentroidConformerSelection.Options method) (scine_chemoton.steering_wheel.selections.conformers.ClusterSelection method) (scine_chemoton.steering_wheel.selections.conformers.ClusterSelection.Options method) (scine_chemoton.steering_wheel.selections.conformers.ConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.ConformerSelection.Options method) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerPerClusterSelection method) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerPerClusterSelection.Options method) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerSelection method) (scine_chemoton.steering_wheel.selections.conformers.LowestEnergyConformerSelection.Options method) (scine_chemoton.steering_wheel.selections.input_selections.FileInputSelection method) (scine_chemoton.steering_wheel.selections.input_selections.FileInputSelection.Options method) (scine_chemoton.steering_wheel.selections.input_selections.InputSelection method) (scine_chemoton.steering_wheel.selections.input_selections.InputSelection.Options method) (scine_chemoton.steering_wheel.selections.input_selections.ScineGeometryInputSelection method) (scine_chemoton.steering_wheel.selections.input_selections.ScineGeometryInputSelection.Options method) (scine_chemoton.steering_wheel.selections.organometallic_complexes.CentralMetalSelection method) (scine_chemoton.steering_wheel.selections.organometallic_complexes.CentralMetalSelection.Options method) (scine_chemoton.steering_wheel.selections.Selection method) (scine_chemoton.steering_wheel.selections.Selection.Options method) (scine_chemoton.steering_wheel.selections.SelectionAndArray method) (scine_chemoton.steering_wheel.selections.SelectionAndArray.Options method) (scine_chemoton.steering_wheel.selections.SelectionOrArray method) (scine_chemoton.steering_wheel.selections.SelectionOrArray.Options method)

update() (scine_chemoton.reaction_rules.distance_rules.DistanceRuleSet method) (scine_chemoton.reaction_rules.element_rules.ElementRuleSet method) (scine_chemoton.reaction_rules.polarization_rules.PolarizationRuleSet method) (scine_chemoton.reaction_rules.reaction_rule_library.DefaultOrganicChemistry method) (scine_chemoton.reaction_rules.RuleSet method) (scine_chemoton.steering_wheel.datastructures.GearOptions method) update_graph_compound_costs() (scine_chemoton.gears.pathfinder.Pathfinder method) use_energy_deduplication (scine_chemoton.gears.reaction.BasicReactionHousekeeping.Options attribute) use_only_enabled_aggregates (scine_chemoton.gears.pathfinder.Pathfinder.Options attribute) use_rmsd_deduplication (scine_chemoton.gears.reaction.BasicReactionHousekeeping.Options attribute) use_structure_deduplication (scine_chemoton.gears.reaction.BasicReactionHousekeeping.Options attribute) use_structure_model (scine_chemoton.gears.pathfinder.Pathfinder.Options attribute) user_input_only (scine_chemoton.gears.kinetics.MinimalConnectivityKinetics.Options attribute)

V

valid_compounds() (scine_chemoton.gears.conformers.brute_force.BruteForceConformers method) valid_element() (in module scine_chemoton.reaction_rules) valid_input_type (scine_chemoton.steering_wheel.selections.input_selections.FileInputSelection attribute) (scine_chemoton.steering_wheel.selections.input_selections.InputSelection attribute) (scine_chemoton.steering_wheel.selections.input_selections.ScineGeometryInputSelection attribute) validation_job (scine_chemoton.gears.compound.ThermoAggregateHousekeeping.Options attribute) validation_settings (scine_chemoton.gears.compound.ThermoAggregateHousekeeping.Options attribute)

values() (scine_chemoton.reaction_rules.distance_rules.DistanceRuleSet method) (scine_chemoton.reaction_rules.element_rules.ElementRuleSet method) (scine_chemoton.reaction_rules.polarization_rules.PolarizationRuleSet method) (scine_chemoton.reaction_rules.reaction_rule_library.DefaultOrganicChemistry method) (scine_chemoton.reaction_rules.RuleSet method) (scine_chemoton.steering_wheel.datastructures.GearOptions method) variance_label (scine_chemoton.gears.kinetics.MaximumFluxKinetics.Options attribute)

W

wait_for_calculation_finish (scine_chemoton.steering_wheel.datastructures.ProtocolEntry attribute) wait_for_stop_signal() (scine_chemoton.engine.EngineHandler method)

WAITING (scine_chemoton.steering_wheel.datastructures.Status attribute) was_stopped (scine_chemoton.steering_wheel.datastructures.ProtocolEntry attribute) with_traceback() (scine_chemoton.gears.pathfinder.DifferentSubgraphsError method)

Z

ZeroEnergyReference (class in scine_chemoton.gears.kinetic_modeling.atomization)