Chemoton
2.2.0
Introduction
License and Copyright Information
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Tutorial
How to Cite
Support and Contact
Chemoton API
Changelog
Chemoton
Docs
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Index
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
_
__call__() (scine_chemoton.gears.Gear method)
A
add_reaction() (scine_chemoton.gears.pathfinder.Pathfinder.BasicHandler method)
assemble_reactive_complex() (in module scine_chemoton.utilities.reactive_complexes.inter_reactive_complexes)
Associative (scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer.ReactionType attribute)
atom_threshold (scine_chemoton.gears.elementary_steps.reactive_site_filters.SimpleRankingFilter attribute)
AtomNumberFilter (class in scine_chemoton.gears.elementary_steps.compound_filters)
AtomRuleBasedFilter (class in scine_chemoton.gears.elementary_steps.reactive_site_filters)
AtomRuleBasedFilter.FunctionalGroupRule (class in scine_chemoton.gears.elementary_steps.reactive_site_filters)
AtomRuleBasedFilter.ReactiveRuleFilterAndArray (class in scine_chemoton.gears.elementary_steps.reactive_site_filters)
AtomRuleBasedFilter.ReactiveRuleFilterOrArray (class in scine_chemoton.gears.elementary_steps.reactive_site_filters)
B
barrierless_weight (scine_chemoton.gears.pathfinder.Pathfinder.Options attribute)
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 (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options attribute)
bimolecular_association (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options attribute)
bimolecular_reactions() (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased method)
(scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased method)
(scine_chemoton.gears.elementary_steps.trial_generator.TrialGenerator method)
bond_order_job (scine_chemoton.gears.compound.BasicAggregateHousekeeping.Options attribute)
bond_order_settings (scine_chemoton.gears.compound.BasicAggregateHousekeeping.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)
build_graph() (scine_chemoton.gears.pathfinder.Pathfinder method)
C
caching_file_name (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
calculate_compound_costs() (scine_chemoton.gears.pathfinder.Pathfinder method)
calculation_exists_in_structure() (in module scine_chemoton.utilities.queries)
calculation_model (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
CatalystFilter (class in scine_chemoton.gears.elementary_steps.compound_filters)
central_atom (scine_chemoton.gears.elementary_steps.reactive_site_filters.AtomRuleBasedFilter.FunctionalGroupRule attribute)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter.FunctionalGroupRule attribute)
character (scine_chemoton.gears.elementary_steps.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter.FunctionalGroupRule attribute)
complex_generator (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.BimolOptions attribute)
(scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.BimolAssociationOptions attribute)
ComponentDistanceTuple (class in scine_chemoton.utilities.masm)
components (scine_chemoton.utilities.masm.ComponentDistanceTuple property)
CompoundFilter (class in scine_chemoton.gears.elementary_steps.compound_filters)
CompoundFilterAndArray (class in scine_chemoton.gears.elementary_steps.compound_filters)
CompoundFilterOrArray (class in scine_chemoton.gears.elementary_steps.compound_filters)
conformer_job (scine_chemoton.gears.conformers.brute_force.BruteForceConformers.Options attribute)
conformer_settings (scine_chemoton.gears.conformers.brute_force.BruteForceConformers.Options attribute)
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)
coordinate_threshold (scine_chemoton.gears.elementary_steps.reactive_site_filters.SimpleRankingFilter attribute)
cycle_time (scine_chemoton.gears.compound.BasicAggregateHousekeeping.Options attribute)
(scine_chemoton.gears.conformers.brute_force.BruteForceConformers.Options attribute)
(scine_chemoton.gears.elementary_steps.ElementaryStepGear.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.reaction.BasicReactionHousekeeping.Options attribute)
(scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
(scine_chemoton.gears.scheduler.Scheduler.Options attribute)
(scine_chemoton.gears.thermo.BasicThermoDataCompletion.Options attribute)
D
deserialize_molecules() (in module scine_chemoton.utilities.masm)
Disconnective (scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer.ReactionType attribute)
Dissociative (scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer.ReactionType attribute)
distance (scine_chemoton.gears.elementary_steps.reactive_site_filters.AtomRuleBasedFilter.FunctionalGroupRule attribute)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter.FunctionalGroupRule attribute)
(scine_chemoton.utilities.masm.ComponentDistanceTuple property)
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.refinement.NetworkRefinement.Options attribute)
double_ended_job_settings (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
E
ElementaryStepGear (class in scine_chemoton.gears.elementary_steps)
ElementaryStepGear.Options (class in scine_chemoton.gears.elementary_steps)
ElementCountFilter (class in scine_chemoton.gears.elementary_steps.compound_filters)
ElementSumCountFilter (class in scine_chemoton.gears.elementary_steps.compound_filters)
ElementWiseReactionCoordinateFilter (class in scine_chemoton.gears.elementary_steps.reactive_site_filters)
enable_bimolecular_trials (scine_chemoton.gears.elementary_steps.ElementaryStepGear.Options attribute)
enable_unimolecular_trials (scine_chemoton.gears.elementary_steps.ElementaryStepGear.Options attribute)
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)
energy_threshold (scine_chemoton.gears.pathfinder.Pathfinder.Options attribute)
energy_tolerance (scine_chemoton.gears.reaction.BasicReactionHousekeeping.Options attribute)
enforce_free_energies (scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics.Options attribute)
(scine_chemoton.gears.kinetics.MaximumFluxKinetics.Options attribute)
Engine (class in scine_chemoton.engine)
estimate_n_bimolecular_trials() (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased method)
estimate_n_unimolecular_trials() (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased method)
exclude_barrierless (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
exclude_misguided_conformer_optimizations (scine_chemoton.gears.compound.BasicAggregateHousekeeping.Options attribute)
F
filter() (scine_chemoton.gears.elementary_steps.compound_filters.AtomNumberFilter method)
(scine_chemoton.gears.elementary_steps.compound_filters.CatalystFilter method)
(scine_chemoton.gears.elementary_steps.compound_filters.CompoundFilter method)
(scine_chemoton.gears.elementary_steps.compound_filters.CompoundFilterAndArray method)
(scine_chemoton.gears.elementary_steps.compound_filters.CompoundFilterOrArray method)
(scine_chemoton.gears.elementary_steps.compound_filters.ElementCountFilter method)
(scine_chemoton.gears.elementary_steps.compound_filters.ElementSumCountFilter method)
(scine_chemoton.gears.elementary_steps.compound_filters.IDFilter method)
(scine_chemoton.gears.elementary_steps.compound_filters.MolecularWeightFilter method)
(scine_chemoton.gears.elementary_steps.compound_filters.OneCompoundIDFilter method)
(scine_chemoton.gears.elementary_steps.compound_filters.SelectedCompoundIDFilter method)
(scine_chemoton.gears.elementary_steps.compound_filters.SelfReactionFilter method)
(scine_chemoton.gears.elementary_steps.compound_filters.TrueMinimumFilter method)
filter_atom_pairs() (scine_chemoton.gears.elementary_steps.reactive_site_filters.ReactiveSiteFilter method)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.ReactiveSiteFilterAndArray method)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.ReactiveSiteFilterOrArray method)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.SimpleRankingFilter method)
filter_atoms() (scine_chemoton.gears.elementary_steps.reactive_site_filters.AtomRuleBasedFilter method)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.MasmChemicalRankingFilter method)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.ReactiveSiteFilter method)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.ReactiveSiteFilterAndArray method)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.ReactiveSiteFilterOrArray method)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.SimpleRankingFilter method)
filter_by_rule() (scine_chemoton.gears.elementary_steps.reactive_site_filters.AtomRuleBasedFilter.FunctionalGroupRule method)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.AtomRuleBasedFilter.ReactiveRuleFilterAndArray method)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.AtomRuleBasedFilter.ReactiveRuleFilterOrArray method)
filter_reaction_coordinates() (scine_chemoton.gears.elementary_steps.reactive_site_filters.ElementWiseReactionCoordinateFilter method)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter method)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.ReactiveSiteFilter method)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.ReactiveSiteFilterAndArray method)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.ReactiveSiteFilterOrArray method)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.SimpleRankingFilter method)
filters (scine_chemoton.gears.elementary_steps.reactive_site_filters.ReactiveSiteFilterAndArray attribute)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.ReactiveSiteFilterOrArray attribute)
find_paths() (scine_chemoton.gears.pathfinder.Pathfinder method)
find_unique_paths() (scine_chemoton.gears.pathfinder.Pathfinder method)
flux_property_label (scine_chemoton.gears.kinetics.MaximumFluxKinetics.Options 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)
G
Gear (class in scine_chemoton.gears)
generate_reactive_complexes() (scine_chemoton.utilities.reactive_complexes.inter_reactive_complexes.InterReactiveComplexes method)
get_adjacency_matrix() (scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer.ConnectivityAnalyzer method)
get_atom_pairs() (in module scine_chemoton.utilities.masm)
get_calculation_id() (in module scine_chemoton.utilities.queries)
get_calculation_id_from_structure() (in module scine_chemoton.utilities.queries)
get_elementary_step_sequence() (scine_chemoton.gears.pathfinder.Pathfinder method)
get_graph_distance() (scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer.ConnectivityAnalyzer method)
get_n_atoms() (scine_chemoton.gears.compound.BasicAggregateHousekeeping static method)
get_reaction_type() (scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer.ConnectivityAnalyzer method)
get_temperature() (scine_chemoton.gears.pathfinder.Pathfinder.BarrierBasedHandler method)
get_valid_graph_handler_options() (scine_chemoton.gears.pathfinder.Pathfinder static method)
get_valid_reaction_ids() (scine_chemoton.gears.pathfinder.Pathfinder.BasicHandler method)
graph_handler (scine_chemoton.gears.pathfinder.Pathfinder attribute)
(scine_chemoton.gears.pathfinder.Pathfinder.Options attribute)
graph_job (scine_chemoton.gears.compound.BasicAggregateHousekeeping.Options attribute)
graph_settings (scine_chemoton.gears.compound.BasicAggregateHousekeeping.Options attribute)
H
hetero_atoms (scine_chemoton.gears.elementary_steps.reactive_site_filters.AtomRuleBasedFilter.FunctionalGroupRule attribute)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter.FunctionalGroupRule attribute)
HeuristicPolarizationReactionCoordinateFilter (class in scine_chemoton.gears.elementary_steps.reactive_site_filters)
HeuristicPolarizationReactionCoordinateFilter.FunctionalGroupRule (class in scine_chemoton.gears.elementary_steps.reactive_site_filters)
HeuristicPolarizationReactionCoordinateFilter.PaulingElectronegativityRule (class in scine_chemoton.gears.elementary_steps.reactive_site_filters)
I
identical_reaction() (in module scine_chemoton.utilities.queries)
IDFilter (class in scine_chemoton.gears.elementary_steps.compound_filters)
insert_initial_structure() (in module scine_chemoton.utilities.insert_initial_structure)
InterReactiveComplexes (class in scine_chemoton.utilities.reactive_complexes.inter_reactive_complexes)
InterReactiveComplexes.Options (class in scine_chemoton.utilities.reactive_complexes.inter_reactive_complexes)
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.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.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.fragment_based.FragmentBased.Options.BimolAssociationOptions attribute)
(scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.UnimolAssociationOptions attribute)
job_settings_associative (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.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.fragment_based.FragmentBased.Options.UnimolDissociationOptions attribute)
job_settings_dissociative (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.UnimolOptions attribute)
(scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.UnimolDissociationOptions attribute)
jobs_to_wait_for (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
K
KineticsBase (class in scine_chemoton.gears.kinetics)
KineticsBase.Options (class in scine_chemoton.gears.kinetics)
L
LebedevSphere (class in scine_chemoton.utilities.reactive_complexes.lebedev_sphere)
M
make_sorted_pair() (in module scine_chemoton.utilities.masm)
MasmChemicalRankingFilter (class in scine_chemoton.gears.elementary_steps.reactive_site_filters)
max_allowed_barrier (scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics.Options attribute)
(scine_chemoton.gears.kinetics.MaximumFluxKinetics.Options attribute)
max_barrier (scine_chemoton.gears.refinement.NetworkRefinement.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)
max_bond_formations (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.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)
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)
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)
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)
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)
min_bond_formations (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.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)
min_concentration_flux (scine_chemoton.gears.kinetics.MaximumFluxKinetics.Options attribute)
min_difference (scine_chemoton.gears.elementary_steps.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter.PaulingElectronegativityRule attribute)
min_inter_bond_formations (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.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)
minimal_spin_multiplicity (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options.BimolOptions attribute)
(scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options.BimolAssociationOptions 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)
minimization_job (scine_chemoton.gears.conformers.brute_force.BruteForceConformers.Options attribute)
minimization_settings (scine_chemoton.gears.conformers.brute_force.BruteForceConformers.Options attribute)
Mixed (scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer.ReactionType attribute)
model (scine_chemoton.gears.compound.BasicAggregateHousekeeping.Options attribute)
(scine_chemoton.gears.conformers.brute_force.BruteForceConformers.Options attribute)
(scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options attribute)
(scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options attribute)
(scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics.Options attribute)
(scine_chemoton.gears.kinetics.MaximumFluxKinetics.Options attribute)
(scine_chemoton.gears.pathfinder.Pathfinder.Options attribute)
(scine_chemoton.gears.thermo.BasicThermoDataCompletion.Options attribute)
model_query() (in module scine_chemoton.utilities.queries)
module
queries
scine_chemoton.engine
scine_chemoton.gears.compound
scine_chemoton.gears.conformers.brute_force
scine_chemoton.gears.elementary_steps.brute_force
scine_chemoton.gears.elementary_steps.compound_filters
scine_chemoton.gears.elementary_steps.minimal
scine_chemoton.gears.elementary_steps.reactive_site_filters
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.fragment_based
scine_chemoton.gears.kinetics
scine_chemoton.gears.pathfinder
scine_chemoton.gears.reaction
scine_chemoton.gears.refinement
scine_chemoton.gears.scheduler
scine_chemoton.gears.thermo
scine_chemoton.utilities.insert_initial_structure
scine_chemoton.utilities.masm
scine_chemoton.utilities.queries
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 property)
mol_to_cbor() (in module scine_chemoton.utilities.masm)
MolecularWeightFilter (class in scine_chemoton.gears.elementary_steps.compound_filters)
multiple_attack_points (scine_chemoton.utilities.reactive_complexes.inter_reactive_complexes.InterReactiveComplexes.Options attribute)
N
n_bonds (scine_chemoton.gears.elementary_steps.reactive_site_filters.AtomRuleBasedFilter.FunctionalGroupRule attribute)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter.FunctionalGroupRule attribute)
n_hetero_atoms (scine_chemoton.gears.elementary_steps.reactive_site_filters.AtomRuleBasedFilter.FunctionalGroupRule attribute)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter.FunctionalGroupRule attribute)
nearest_neighbors (scine_chemoton.utilities.reactive_complexes.lebedev_sphere.LebedevSphere property)
(scine_chemoton.utilities.reactive_complexes.unit_circle.UnitCircle property)
NetworkRefinement (class in scine_chemoton.gears.refinement)
NetworkRefinement.Options (class in scine_chemoton.gears.refinement)
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
OneCompoundIDFilter (class in scine_chemoton.gears.elementary_steps.compound_filters)
opt_job (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
opt_job_settings (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
options (scine_chemoton.gears.compound.BasicAggregateHousekeeping attribute)
(scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased attribute)
(scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased attribute)
P
pair_is_bound() (scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer.ConnectivityAnalyzer method)
pair_threshold (scine_chemoton.gears.elementary_steps.reactive_site_filters.SimpleRankingFilter attribute)
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)
points (scine_chemoton.utilities.reactive_complexes.lebedev_sphere.LebedevSphere property)
(scine_chemoton.utilities.reactive_complexes.unit_circle.UnitCircle property)
post_refine_model (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
pre_refine_model (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
primitive_rules (scine_chemoton.gears.elementary_steps.reactive_site_filters.AtomRuleBasedFilter.ReactiveRuleFilterAndArray attribute)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.AtomRuleBasedFilter.ReactiveRuleFilterOrArray attribute)
property_label (scine_chemoton.gears.kinetics.MaximumFluxKinetics.Options attribute)
prune (scine_chemoton.gears.elementary_steps.reactive_site_filters.MasmChemicalRankingFilter attribute)
pruned_atom_pairs() (in module scine_chemoton.utilities.masm)
Q
queries
module
R
reaction_based_loop (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
ReactionType (class in scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer)
reactive_if_rules_apply (scine_chemoton.gears.elementary_steps.reactive_site_filters.ElementWiseReactionCoordinateFilter attribute)
reactive_site_filter (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased attribute)
(scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased attribute)
ReactiveComplexes (class in scine_chemoton.utilities.reactive_complexes)
ReactiveComplexes.Options (class in scine_chemoton.utilities.reactive_complexes)
ReactiveSiteFilter (class in scine_chemoton.gears.elementary_steps.reactive_site_filters)
ReactiveSiteFilterAndArray (class in scine_chemoton.gears.elementary_steps.reactive_site_filters)
ReactiveSiteFilterOrArray (class in scine_chemoton.gears.elementary_steps.reactive_site_filters)
refinements (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
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)
rmsd_tolerance (scine_chemoton.gears.reaction.BasicReactionHousekeeping.Options attribute)
rules (scine_chemoton.gears.elementary_steps.reactive_site_filters.AtomRuleBasedFilter attribute)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.ElementWiseReactionCoordinateFilter attribute)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter attribute)
run() (scine_chemoton.engine.Engine method)
S
Scheduler (class in scine_chemoton.gears.scheduler)
Scheduler.Options (class in scine_chemoton.gears.scheduler)
scine_chemoton.engine
module
scine_chemoton.gears.compound
module
scine_chemoton.gears.conformers.brute_force
module
scine_chemoton.gears.elementary_steps.brute_force
module
scine_chemoton.gears.elementary_steps.compound_filters
module
scine_chemoton.gears.elementary_steps.minimal
module
scine_chemoton.gears.elementary_steps.reactive_site_filters
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.fragment_based
module
scine_chemoton.gears.kinetics
module
scine_chemoton.gears.pathfinder
module
scine_chemoton.gears.reaction
module
scine_chemoton.gears.refinement
module
scine_chemoton.gears.scheduler
module
scine_chemoton.gears.thermo
module
scine_chemoton.utilities.insert_initial_structure
module
scine_chemoton.utilities.masm
module
scine_chemoton.utilities.queries
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
select_calculation_by_structures() (in module scine_chemoton.utilities.queries)
SelectedCompoundIDFilter (class in scine_chemoton.gears.elementary_steps.compound_filters)
SelfReactionFilter (class in scine_chemoton.gears.elementary_steps.compound_filters)
set_gear() (scine_chemoton.engine.Engine method)
set_options() (scine_chemoton.utilities.reactive_complexes.ReactiveComplexes method)
set_start_conditions() (scine_chemoton.gears.pathfinder.Pathfinder method)
set_temperature() (scine_chemoton.gears.pathfinder.Pathfinder.BarrierBasedHandler method)
settings (scine_chemoton.gears.thermo.BasicThermoDataCompletion.Options attribute)
SimpleRankingFilter (class in scine_chemoton.gears.elementary_steps.reactive_site_filters)
single_ended_job (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
single_ended_job_settings (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
single_ended_step_refinement_job (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
single_ended_step_refinement_settings (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
sp_job (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
sp_job_settings (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
stationary_points() (in module scine_chemoton.utilities.queries)
stop() (scine_chemoton.engine.Engine method)
stop_on_timeout (class in scine_chemoton.utilities.queries)
string_from_rule() (scine_chemoton.gears.elementary_steps.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter.FunctionalGroupRule method)
(scine_chemoton.gears.elementary_steps.reactive_site_filters.HeuristicPolarizationReactionCoordinateFilter.PaulingElectronegativityRule method)
T
temperature (scine_chemoton.gears.conformers.brute_force.BruteForceConformers.Options attribute)
transition_state_energy_window (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
TrialGenerator (class in scine_chemoton.gears.elementary_steps.trial_generator)
TrueMinimumFilter (class in scine_chemoton.gears.elementary_steps.compound_filters)
tsopt_job (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
tsopt_job_settings (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
U
unimolecular (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased.Options attribute)
unimolecular_association (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options attribute)
unimolecular_dissociation (scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased.Options attribute)
unimolecular_reactions() (scine_chemoton.gears.elementary_steps.trial_generator.bond_based.BondBased method)
(scine_chemoton.gears.elementary_steps.trial_generator.fragment_based.FragmentBased 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)
update_graph_compound_costs() (scine_chemoton.gears.pathfinder.Pathfinder method)
use_calculation_model (scine_chemoton.gears.refinement.NetworkRefinement.Options attribute)
use_energy_deduplication (scine_chemoton.gears.reaction.BasicReactionHousekeeping.Options attribute)
use_energy_threshold (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)
user_input_only (scine_chemoton.gears.kinetics.MinimalConnectivityKinetics.Options attribute)