Index

A

A (rmgpy.kinetics.Arrhenius attribute) (rmgpy.kinetics.StickingCoefficient attribute) (rmgpy.kinetics.SurfaceArrhenius attribute) a0 (rmgpy.thermo.Wilhoit attribute) a1 (rmgpy.thermo.Wilhoit attribute) a2 (rmgpy.thermo.Wilhoit attribute) a3 (rmgpy.thermo.Wilhoit attribute) ActionError add_action() (rmgpy.data.kinetics.ReactionRecipe method) add_allyls() (in module rmgpy.molecule.pathfinder) add_atom() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) add_atom_labels_for_reaction() (rmgpy.data.kinetics.KineticsFamily method) add_bond() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) add_edge() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) add_entry() (rmgpy.data.kinetics.KineticsFamily method) add_explicit_ligands() (rmgpy.molecule.Group method) add_implicit_atoms_from_atomtype() (rmgpy.molecule.Group method) add_implicit_benzene() (rmgpy.molecule.Group method) add_inverse_allyls() (in module rmgpy.molecule.pathfinder) add_new_surface_objects() (rmgpy.rmg.model.CoreEdgeReactionModel method) add_path_reaction() (rmgpy.rmg.pdep.PDepNetwork method) add_reaction_library_to_edge() (rmgpy.rmg.model.CoreEdgeReactionModel method) add_reaction_library_to_output() (rmgpy.rmg.model.CoreEdgeReactionModel method) add_reaction_to_core() (rmgpy.rmg.model.CoreEdgeReactionModel method) add_reaction_to_edge() (rmgpy.rmg.model.CoreEdgeReactionModel method) add_reaction_to_unimolecular_networks() (rmgpy.rmg.model.CoreEdgeReactionModel method) add_reactions_to_surface() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) add_reverse_attribute() (rmgpy.data.kinetics.KineticsFamily method) add_rules_from_training() (rmgpy.data.kinetics.KineticsFamily method) add_seed_mechanism_to_core() (rmgpy.rmg.model.CoreEdgeReactionModel method) add_species_to_core() (rmgpy.rmg.model.CoreEdgeReactionModel method) add_species_to_edge() (rmgpy.rmg.model.CoreEdgeReactionModel method) add_unsaturated_bonds() (in module rmgpy.molecule.pathfinder) add_vertex() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) adjust_surface() (rmgpy.rmg.model.CoreEdgeReactionModel method) advance() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) alpha (rmgpy.kinetics.Troe attribute) alpha0 (rmgpy.pdep.SingleExponentialDown attribute) analyze_molecule() (in module rmgpy.molecule.resonance) ancestors() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) apply_action() (rmgpy.molecule.Atom method) (rmgpy.molecule.Bond method) (rmgpy.molecule.GroupAtom method) (rmgpy.molecule.GroupBond method) apply_chemically_significant_eigenvalues_method() (in module rmgpy.pdep.cse) (rmgpy.pdep.Network method) (rmgpy.rmg.pdep.PDepNetwork method)

apply_forward() (rmgpy.data.kinetics.ReactionRecipe method) apply_inverse_laplace_transform_method() (in module rmgpy.pdep.reaction) apply_kinetics_to_reaction() (rmgpy.rmg.model.CoreEdgeReactionModel method) apply_modified_strong_collision_method() (in module rmgpy.pdep.msc) (rmgpy.pdep.Network method) (rmgpy.rmg.pdep.PDepNetwork method) apply_recipe() (rmgpy.data.kinetics.KineticsFamily method) apply_reservoir_state_method() (in module rmgpy.pdep.rs) (rmgpy.pdep.Network method) (rmgpy.rmg.pdep.PDepNetwork method) apply_reverse() (rmgpy.data.kinetics.ReactionRecipe method) apply_rrkm_theory() (in module rmgpy.pdep.reaction) apply_thermo_to_species() (rmgpy.rmg.model.CoreEdgeReactionModel method) are_siblings() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) arkane module Arkane (class in arkane) arkane.common module arkane.output module arkane.sensitivity module ArkaneSpecies (class in arkane.common) AromaticBond (class in rmgpy.molecule.kekulize) aromaticity_filtration() (in module rmgpy.molecule.filtration) AromaticRing (class in rmgpy.molecule.kekulize) ArrayQuantity (class in rmgpy.quantity) Arrhenius (class in rmgpy.kinetics) arrhenius (rmgpy.kinetics.MultiArrhenius attribute) (rmgpy.kinetics.MultiPDepArrhenius attribute) (rmgpy.kinetics.PDepArrhenius attribute) arrheniusHigh (rmgpy.kinetics.Lindemann attribute) (rmgpy.kinetics.Troe attribute) arrheniusLow (rmgpy.kinetics.Lindemann attribute) (rmgpy.kinetics.ThirdBody attribute) (rmgpy.kinetics.Troe attribute) as_dict() (arkane.common.ArkaneSpecies method) (rmgpy.pdep.SingleExponentialDown method) (rmgpy.quantity.ArrayQuantity method) (rmgpy.quantity.ScalarQuantity method) (rmgpy.statmech.Conformer method) (rmgpy.statmech.HarmonicOscillator method) (rmgpy.statmech.HinderedRotor method) (rmgpy.statmech.IdealGasTranslation method) (rmgpy.statmech.KRotor method) (rmgpy.statmech.LinearRotor method) (rmgpy.statmech.NonlinearRotor method) (rmgpy.statmech.SphericalTopRotor method) (rmgpy.thermo.NASA method) (rmgpy.thermo.NASAPolynomial method) (rmgpy.thermo.ThermoData method) (rmgpy.thermo.Wilhoit method) assign_atom_ids() (rmgpy.molecule.Molecule method) Atom (class in rmgpy.molecule) atom_ids_valid() (rmgpy.molecule.Molecule method) atoms (rmgpy.molecule.Group attribute) (rmgpy.molecule.Molecule attribute) AtomType (class in rmgpy.molecule) AtomTypeError

B

B (rmgpy.thermo.Wilhoit attribute) badness() (rmgpy.exceptions.InvalidMicrocanonicalRateError method)

barrier (rmgpy.statmech.HinderedRotor attribute) Bond (class in rmgpy.molecule)

C

c0 (rmgpy.thermo.NASAPolynomial attribute) c1 (rmgpy.thermo.NASAPolynomial attribute) c2 (rmgpy.thermo.NASAPolynomial attribute) c3 (rmgpy.thermo.NASAPolynomial attribute) c4 (rmgpy.thermo.NASAPolynomial attribute) c5 (rmgpy.thermo.NASAPolynomial attribute) c6 (rmgpy.thermo.NASAPolynomial attribute) calculate() (rmgpy.qm.symmetry.SymmetryJob method) calculate_atom_symmetry_number() (in module rmgpy.molecule.symmetry) calculate_axis_symmetry_number() (in module rmgpy.molecule.symmetry) calculate_bond_symmetry_number() (in module rmgpy.molecule.symmetry) calculate_chirality_correction() (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.molecule.QMMolecule method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) calculate_coll_limit() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) calculate_collision_efficiency() (rmgpy.pdep.SingleExponentialDown method) calculate_collision_frequency() (rmgpy.pdep.Configuration method) calculate_collision_model() (rmgpy.pdep.Network method) (rmgpy.rmg.pdep.PDepNetwork method) calculate_cp0() (rmgpy.molecule.Molecule method) (rmgpy.species.Species method) calculate_cpinf() (rmgpy.molecule.Molecule method) (rmgpy.species.Species method) calculate_cyclic_symmetry_number() (in module rmgpy.molecule.symmetry) calculate_degeneracy() (rmgpy.data.kinetics.KineticsFamily method) calculate_densities_of_states() (rmgpy.pdep.Network method) (rmgpy.rmg.pdep.PDepNetwork method) calculate_density_of_states() (rmgpy.pdep.Configuration method) calculate_effective_pressure() (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.SimpleReactor method) calculate_equilibrium_ratios() (rmgpy.pdep.Network method) (rmgpy.rmg.pdep.PDepNetwork method) calculate_microcanonical_rate_coefficient() (in module rmgpy.pdep.reaction) (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) calculate_microcanonical_rates() (rmgpy.pdep.Network method) (rmgpy.rmg.pdep.PDepNetwork method) calculate_symmetry_number() (in module rmgpy.molecule.symmetry) (rmgpy.molecule.Molecule method) calculate_thermo_data() (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.molecule.QMMolecule method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) calculate_tst_rate_coefficient() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) calculate_tunneling_factor() (rmgpy.kinetics.Eckart method) (rmgpy.kinetics.Wigner method) (rmgpy.species.TransitionState method) calculate_tunneling_function() (rmgpy.kinetics.Eckart method) (rmgpy.kinetics.Wigner method) (rmgpy.species.TransitionState method) can_tst() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) change_base_enthalpy() (rmgpy.thermo.NASA method) (rmgpy.thermo.NASAPolynomial method) change_base_entropy() (rmgpy.thermo.NASA method) (rmgpy.thermo.NASAPolynomial method) change_rate() (rmgpy.kinetics.Arrhenius method) (rmgpy.kinetics.Chebyshev method) (rmgpy.kinetics.Lindemann method) (rmgpy.kinetics.MultiArrhenius method) (rmgpy.kinetics.MultiPDepArrhenius method) (rmgpy.kinetics.PDepArrhenius method) (rmgpy.kinetics.StickingCoefficient method) (rmgpy.kinetics.SurfaceArrhenius method) (rmgpy.kinetics.ThirdBody method) (rmgpy.kinetics.Troe method) change_t0() (rmgpy.kinetics.Arrhenius method) (rmgpy.kinetics.StickingCoefficient method) (rmgpy.kinetics.SurfaceArrhenius method) charge_filtration() (in module rmgpy.molecule.filtration) Chebyshev (class in rmgpy.kinetics) chebyshev() (rmgpy.kinetics.Chebyshev method) check_all_set() (rmgpy.qm.main.QMSettings method) check_collision_limit_violation() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) check_conformer_energy() (in module arkane.common) check_for_duplicates() (rmgpy.data.kinetics.KineticsLibrary method) check_for_errors() (arkane.ess.ESSAdapter method) (arkane.ess.GaussianLog method) (arkane.ess.MolproLog method) (arkane.ess.OrcaLog method) (arkane.ess.QChemLog method) (arkane.ess.TeraChemLog method) check_for_existing_reaction() (rmgpy.rmg.model.CoreEdgeReactionModel method) check_for_existing_species() (rmgpy.rmg.model.CoreEdgeReactionModel method) check_for_inchi_key_collision() (rmgpy.qm.qmverifier.QMVerifier method) check_input() (rmgpy.rmg.main.RMG method) check_libraries() (rmgpy.rmg.main.RMG method) check_model() (rmgpy.rmg.main.RMG method) check_paths() (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.main.QMCalculator method) (rmgpy.qm.molecule.QMMolecule method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) check_reactive() (in module rmgpy.molecule.filtration)

check_ready() (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.main.QMCalculator method) (rmgpy.qm.molecule.QMMolecule method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) ChemicallySignificantEigenvaluesError ChemkinError classify_benzene_carbons() (rmgpy.molecule.Group method) clean_dir() (in module arkane.common) clean_tree_groups() (rmgpy.data.kinetics.KineticsFamily method) cleanup() (rmgpy.pdep.Configuration method) (rmgpy.rmg.pdep.PDepNetwork method) clear() (rmgpy.rmg.main.RMG method) clear_labeled_atoms() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) clear_reg_dims() (rmgpy.molecule.Group method) clear_surface_adjustments() (rmgpy.rmg.model.CoreEdgeReactionModel method) cm1 (rmgpy.thermo.NASAPolynomial attribute) cm2 (rmgpy.thermo.NASAPolynomial attribute) coeffs (rmgpy.kinetics.Chebyshev attribute) (rmgpy.thermo.NASAPolynomial attribute) CollisionError comment (rmgpy.kinetics.Arrhenius attribute) (rmgpy.kinetics.Chebyshev attribute) (rmgpy.kinetics.KineticsData attribute) (rmgpy.kinetics.Lindemann attribute) (rmgpy.kinetics.MultiArrhenius attribute) (rmgpy.kinetics.MultiPDepArrhenius attribute) (rmgpy.kinetics.PDepArrhenius attribute) (rmgpy.kinetics.PDepKineticsData attribute) (rmgpy.kinetics.StickingCoefficient attribute) (rmgpy.kinetics.SurfaceArrhenius attribute) (rmgpy.kinetics.ThirdBody attribute) (rmgpy.kinetics.Troe attribute) (rmgpy.thermo.NASA attribute) (rmgpy.thermo.NASAPolynomial attribute) (rmgpy.thermo.ThermoData attribute) (rmgpy.thermo.Wilhoit attribute) compute_atom_distance() (in module rmgpy.molecule.pathfinder) compute_group_additivity_thermo() (rmgpy.data.thermo.ThermoDatabase method) compute_network_variables() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) compute_rate_derivative() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) Configuration (class in rmgpy.pdep) Conformer (class in rmgpy.statmech) connect_the_dots() (rmgpy.molecule.Molecule method) contains_labeled_atom() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) contains_surface_site() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) (rmgpy.species.Species method) convert_duplicates_to_multi() (rmgpy.data.kinetics.KineticsLibrary method) convert_imaginary_freq_to_negative_float() (in module arkane.common) convert_initial_keys_to_species_objects() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) convolve() (in module rmgpy.statmech.schrodinger) convolve_bs() (in module rmgpy.statmech.schrodinger) convolve_bssr() (in module rmgpy.statmech.schrodinger) coordinates (rmgpy.statmech.Conformer attribute) copy() (arkane.ExplorerJob method) (arkane.PressureDependenceJob method) (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.molecule.Atom method) (rmgpy.molecule.Bond method) (rmgpy.molecule.graph.Edge method) (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.graph.Vertex method) (rmgpy.molecule.Group method) (rmgpy.molecule.GroupAtom method) (rmgpy.molecule.GroupBond method) (rmgpy.molecule.Molecule method) (rmgpy.quantity.ArrayQuantity method) (rmgpy.quantity.ScalarQuantity method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) (rmgpy.species.Species method) (rmgpy.thermo.Wilhoit method) copy_and_map() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) copy_data() (rmgpy.data.thermo.ThermoGroups method) CoreEdgeReactionModel (class in rmgpy.rmg.model) CoreError correct_binding_energy() (rmgpy.data.thermo.ThermoDatabase method) count_aromatic_rings() (rmgpy.molecule.Molecule method) count_bonds() (rmgpy.molecule.GroupAtom method) count_internal_rotors() (rmgpy.molecule.Molecule method) coverage_dependence (rmgpy.kinetics.StickingCoefficient attribute) (rmgpy.kinetics.SurfaceArrhenius attribute) Cp0 (rmgpy.thermo.NASA attribute) (rmgpy.thermo.NASAPolynomial attribute) (rmgpy.thermo.ThermoData attribute) (rmgpy.thermo.Wilhoit attribute) Cpdata (rmgpy.thermo.ThermoData attribute) CpInf (rmgpy.thermo.NASA attribute) (rmgpy.thermo.NASAPolynomial attribute) (rmgpy.thermo.ThermoData attribute) (rmgpy.thermo.Wilhoit attribute) create_and_connect_atom() (rmgpy.molecule.Group method) create_geometry() (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.molecule.QMMolecule method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) create_hindered_rotor_figure() (arkane.StatMechJob method) cross_validate() (rmgpy.data.kinetics.KineticsFamily method) cross_validate_old() (rmgpy.data.kinetics.KineticsFamily method)

D

Database (class in rmgpy.data.base) DatabaseError debug_rdkit_mol() (in module rmgpy.molecule.converter) decrement_lone_pairs() (rmgpy.molecule.Atom method) decrement_order() (rmgpy.molecule.Bond method) decrement_radical() (rmgpy.molecule.Atom method) degeneracy (rmgpy.data.kinetics.DepositoryReaction attribute) (rmgpy.data.kinetics.LibraryReaction attribute) (rmgpy.data.kinetics.TemplateReaction attribute) (rmgpy.reaction.Reaction attribute) (rmgpy.rmg.pdep.PDepReaction attribute) degreeP (rmgpy.kinetics.Chebyshev attribute) degreeT (rmgpy.kinetics.Chebyshev attribute) delete_hydrogens() (rmgpy.molecule.Molecule method) DependencyError DepositoryReaction (class in rmgpy.data.kinetics) descend_tree() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) descendants() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method)

determine_point_group() (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.molecule.QMMolecule method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) DirectFit (class in rmgpy.data.statmechfit) discrepancy() (rmgpy.kinetics.Arrhenius method) (rmgpy.kinetics.Chebyshev method) (rmgpy.kinetics.KineticsData method) (rmgpy.kinetics.Lindemann method) (rmgpy.kinetics.MultiArrhenius method) (rmgpy.kinetics.MultiPDepArrhenius method) (rmgpy.kinetics.PDepArrhenius method) (rmgpy.kinetics.PDepKineticsData method) (rmgpy.kinetics.StickingCoefficient method) (rmgpy.kinetics.SurfaceArrhenius method) (rmgpy.kinetics.ThirdBody method) (rmgpy.kinetics.Troe method) (rmgpy.thermo.NASA method) (rmgpy.thermo.NASAPolynomial method) (rmgpy.thermo.ThermoData method) (rmgpy.thermo.Wilhoit method) distribute_tree_distances() (rmgpy.data.kinetics.KineticsFamily method) draw() (arkane.KineticsJob method) (arkane.PressureDependenceJob method) (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.molecule.draw.MoleculeDrawer method) (rmgpy.molecule.draw.ReactionDrawer method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method)

E

E0 (rmgpy.pdep.Configuration attribute) (rmgpy.statmech.Conformer attribute) (rmgpy.thermo.NASA attribute) (rmgpy.thermo.NASAPolynomial attribute) (rmgpy.thermo.ThermoData attribute) (rmgpy.thermo.Wilhoit attribute) E0_prod (rmgpy.kinetics.Eckart attribute) E0_reac (rmgpy.kinetics.Eckart attribute) E0_TS (rmgpy.kinetics.Eckart attribute) Ea (rmgpy.kinetics.Arrhenius attribute) (rmgpy.kinetics.StickingCoefficient attribute) (rmgpy.kinetics.SurfaceArrhenius attribute) Eckart (class in rmgpy.kinetics) Edge (class in rmgpy.molecule.graph) efficiencies (rmgpy.kinetics.Chebyshev attribute) (rmgpy.kinetics.Lindemann attribute) (rmgpy.kinetics.MultiPDepArrhenius attribute) (rmgpy.kinetics.PDepArrhenius attribute) (rmgpy.kinetics.PDepKineticsData attribute) (rmgpy.kinetics.ThirdBody attribute) (rmgpy.kinetics.Troe attribute) Element (class in rmgpy.molecule) element_count_from_conformer() (arkane.ThermoJob method) ElementError energies (rmgpy.statmech.HinderedRotor attribute) enlarge() (rmgpy.rmg.model.CoreEdgeReactionModel method) ensure_species() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) Entry (class in rmgpy.data.base) enumerate_bonds() (rmgpy.molecule.Molecule method)

equals() (rmgpy.quantity.ArrayQuantity method) (rmgpy.quantity.ScalarQuantity method) equivalent() (rmgpy.molecule.Atom method) (rmgpy.molecule.AtomType method) (rmgpy.molecule.Bond method) (rmgpy.molecule.graph.Edge method) (rmgpy.molecule.graph.Vertex method) (rmgpy.molecule.GroupAtom method) (rmgpy.molecule.GroupBond method) ess_factory() (in module arkane.ess.factory) ESSAdapter (class in arkane.ess) estimate_kinetics() (rmgpy.data.kinetics.KineticsRules method) estimate_kinetics_using_rate_rules() (rmgpy.data.kinetics.KineticsFamily method) estimate_radical_thermo_via_hbi() (rmgpy.data.thermo.ThermoDatabase method) estimate_thermo_via_group_additivity() (rmgpy.data.thermo.ThermoDatabase method) eval_ext() (rmgpy.data.kinetics.KineticsFamily method) evaluate() (rmgpy.data.statmechfit.DirectFit method) (rmgpy.data.statmechfit.PseudoFit method) (rmgpy.data.statmechfit.PseudoRotorFit method) execute() (arkane.Arkane method) (arkane.ExplorerJob method) (arkane.KineticsJob method) (arkane.PressureDependenceJob method) (arkane.sensitivity.KineticsSensitivity method) (arkane.sensitivity.PDepSensitivity method) (arkane.StatMechJob method) (arkane.ThermoJob method) (rmgpy.rmg.main.RMG method) explore_isomer() (rmgpy.rmg.pdep.PDepNetwork method) ExplorerJob (class in arkane) extend_node() (rmgpy.data.kinetics.KineticsFamily method) extract_source_from_comments() (rmgpy.data.kinetics.KineticsDatabase method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.thermo.ThermoDatabase method)

F

failure_keys (rmgpy.qm.gaussian.Gaussian attribute) (rmgpy.qm.gaussian.GaussianMol attribute) (rmgpy.qm.gaussian.GaussianMolPM3 attribute) (rmgpy.qm.gaussian.GaussianMolPM6 attribute) (rmgpy.qm.mopac.Mopac attribute) (rmgpy.qm.mopac.MopacMol attribute) (rmgpy.qm.mopac.MopacMolPM3 attribute) (rmgpy.qm.mopac.MopacMolPM6 attribute) (rmgpy.qm.mopac.MopacMolPM7 attribute) feasible() (rmgpy.molecule.vf2.VF2 method) fill_rules_by_averaging_up() (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsRules method) filter_structures() (in module rmgpy.molecule.filtration) find_adj_lone_pair_multiple_bond_delocalization_paths() (in module rmgpy.molecule.pathfinder) find_adj_lone_pair_radical_delocalization_paths() (in module rmgpy.molecule.pathfinder) find_adj_lone_pair_radical_multiple_bond_delocalization_paths() (in module rmgpy.molecule.pathfinder) find_allyl_delocalization_paths() (in module rmgpy.molecule.pathfinder) find_allyl_end_with_charge() (in module rmgpy.molecule.pathfinder) find_butadiene() (in module rmgpy.molecule.pathfinder) find_butadiene_end_with_charge() (in module rmgpy.molecule.pathfinder) find_h_bonds() (rmgpy.molecule.Molecule method) find_isomorphism() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) (rmgpy.molecule.vf2.VF2 method) find_lone_pair_multiple_bond_paths() (in module rmgpy.molecule.pathfinder) find_N5dc_radical_delocalization_paths() (in module rmgpy.molecule.pathfinder) find_subgraph_isomorphisms() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) (rmgpy.molecule.vf2.VF2 method) find_unique_sites_in_charged_list() (in module rmgpy.molecule.filtration) fingerprint (rmgpy.molecule.Molecule attribute) (rmgpy.species.Species attribute) finish() (rmgpy.rmg.main.RMG method) fit_cosine_potential_to_data() (rmgpy.statmech.HinderedRotor method) fit_fourier_potential_to_data() (rmgpy.statmech.HinderedRotor method) fit_interpolation_model() (arkane.PressureDependenceJob method) fit_interpolation_models() (arkane.PressureDependenceJob method) fit_statmech_direct() (in module rmgpy.data.statmechfit) fit_statmech_pseudo() (in module rmgpy.data.statmechfit)

fit_statmech_pseudo_rotors() (in module rmgpy.data.statmechfit) fit_statmech_to_heat_capacity() (in module rmgpy.data.statmechfit) fit_to_data() (rmgpy.kinetics.Arrhenius method) (rmgpy.kinetics.Chebyshev method) (rmgpy.kinetics.PDepArrhenius method) (rmgpy.kinetics.StickingCoefficient method) (rmgpy.kinetics.SurfaceArrhenius method) (rmgpy.thermo.Wilhoit method) fit_to_data_for_constant_b() (rmgpy.thermo.Wilhoit method) fix_barrier_height() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) fix_diffusion_limited_a_factor() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) ForbiddenStructureException fourier (rmgpy.statmech.HinderedRotor attribute) frequencies (rmgpy.statmech.HarmonicOscillator attribute) frequency (rmgpy.kinetics.Eckart attribute) (rmgpy.kinetics.Wigner attribute) (rmgpy.species.TransitionState attribute) (rmgpy.statmech.HinderedRotor attribute) from_adjacency_list() (in module rmgpy.molecule.adjlist) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) (rmgpy.species.Species method) from_augmented_inchi() (in module rmgpy.molecule.translator) (rmgpy.molecule.Molecule method) from_inchi() (in module rmgpy.molecule.translator) (rmgpy.molecule.Molecule method) from_ob_mol() (in module rmgpy.molecule.converter) from_rdkit_mol() (in module rmgpy.molecule.converter) from_smarts() (in module rmgpy.molecule.translator) (rmgpy.molecule.Molecule method) from_smiles() (in module rmgpy.molecule.translator) (rmgpy.molecule.Molecule method) (rmgpy.species.Species method) from_xyz() (rmgpy.molecule.Molecule method)

G

Gaussian (class in rmgpy.qm.gaussian) GaussianLog (class in arkane.ess) GaussianMol (class in rmgpy.qm.gaussian) GaussianMolPM3 (class in rmgpy.qm.gaussian) GaussianMolPM6 (class in rmgpy.qm.gaussian) generate_3d_ts() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) generate_adj_lone_pair_multiple_bond_resonance_structures() (in module rmgpy.molecule.resonance) generate_adj_lone_pair_radical_multiple_bond_resonance_structures() (in module rmgpy.molecule.resonance) generate_adj_lone_pair_radical_resonance_structures() (in module rmgpy.molecule.resonance) generate_allyl_delocalization_resonance_structures() (in module rmgpy.molecule.resonance) generate_aromatic_resonance_structure() (in module rmgpy.molecule.resonance) generate_aryne_resonance_structures() (in module rmgpy.molecule.resonance) generate_cantera_files() (rmgpy.rmg.main.RMG method) generate_clar_structures() (in module rmgpy.molecule.resonance) generate_collision_matrix() (rmgpy.pdep.Configuration method) (rmgpy.pdep.SingleExponentialDown method) generate_energy_transfer_model() (rmgpy.species.Species method) generate_frequencies() (rmgpy.data.statmech.GroupFrequencies method) generate_full_me_matrix() (in module rmgpy.pdep.me) generate_h_bonded_structures() (rmgpy.molecule.Molecule method) generate_high_p_limit_kinetics() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) generate_isomorphic_resonance_structures() (in module rmgpy.molecule.resonance) generate_kekule_structure() (in module rmgpy.molecule.resonance) generate_kinetics() (arkane.KineticsJob method) (rmgpy.rmg.model.CoreEdgeReactionModel method) generate_lone_pair_multiple_bond_resonance_structures() (in module rmgpy.molecule.resonance) generate_N5dc_radical_resonance_structures() (in module rmgpy.molecule.resonance) generate_old_library_entry() (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) generate_old_tree() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) generate_optimal_aromatic_resonance_structures() (in module rmgpy.molecule.resonance) generate_P_list() (arkane.PressureDependenceJob method) generate_pairs() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) generate_product_template() (rmgpy.data.kinetics.KineticsFamily method) generate_qm_data() (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.molecule.QMMolecule method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) generate_rate_coefficients() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) generate_rdkit_geometries() (rmgpy.qm.molecule.Geometry method) generate_reactant_product_indices() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) generate_reaction_indices() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) generate_reactions() (rmgpy.data.kinetics.KineticsDatabase method) (rmgpy.data.kinetics.KineticsFamily method) generate_reactions_from_families() (rmgpy.data.kinetics.KineticsDatabase method) generate_reactions_from_libraries() (rmgpy.data.kinetics.KineticsDatabase method) generate_reactions_from_library() (rmgpy.data.kinetics.KineticsDatabase method) generate_resonance_structures() (in module rmgpy.molecule.resonance) (rmgpy.molecule.Molecule method) (rmgpy.species.Species method) generate_reverse_rate_coefficient() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) generate_species_indices() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) generate_statmech() (rmgpy.species.Species method) generate_T_list() (arkane.PressureDependenceJob method) generate_thermo() (arkane.ThermoJob method) (rmgpy.rmg.model.CoreEdgeReactionModel method) generate_thermo_data() (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.molecule.QMMolecule method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) generate_transport_data() (rmgpy.species.Species method) generate_tree() (rmgpy.data.kinetics.KineticsFamily method) generic_visit() (arkane.output.PrettifyVisitor method) Geometry (class in rmgpy.qm.molecule) get_active_modes() (rmgpy.statmech.Conformer method) get_adatoms() (rmgpy.molecule.Molecule method) get_all_cycles() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_all_cycles_of_size() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_all_cyclic_vertices() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_all_descendants() (rmgpy.data.base.Entry method) get_all_edges() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_all_labeled_atoms() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_all_polycyclic_vertices() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_all_rules() (rmgpy.data.kinetics.KineticsRules method) get_all_simple_cycles_of_size() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_all_species() (rmgpy.pdep.Network method) (rmgpy.rmg.pdep.PDepNetwork method) get_all_thermo_data() (rmgpy.data.thermo.ThermoDatabase method) get_alpha() (rmgpy.pdep.SingleExponentialDown method) get_aromatic_rings() (rmgpy.molecule.Molecule method) get_atomtype() (in module rmgpy.molecule) get_augmented_inchi_key() (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.molecule.QMMolecule method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) get_backbone_roots() (rmgpy.data.kinetics.KineticsFamily method) get_bde() (rmgpy.molecule.Bond method) get_bond() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_bond_string() (rmgpy.molecule.Bond method) get_bonds() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_cantera_efficiencies() (rmgpy.kinetics.Chebyshev method) (rmgpy.kinetics.Lindemann method) (rmgpy.kinetics.MultiPDepArrhenius method) (rmgpy.kinetics.PDepArrhenius method) (rmgpy.kinetics.PDepKineticsData method) (rmgpy.kinetics.ThirdBody method) (rmgpy.kinetics.Troe method) get_center_of_mass() (in module arkane.common) (rmgpy.statmech.Conformer method) get_charge_span() (rmgpy.molecule.Molecule method) get_charge_span_list() (in module rmgpy.molecule.filtration) get_const_spc_indices() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.SimpleReactor method) get_conversion_factor_from_si() (rmgpy.quantity.ArrayQuantity method) (rmgpy.quantity.ScalarQuantity method) get_conversion_factor_from_si_to_cm_mol_s() (rmgpy.quantity.ArrayQuantity method) (rmgpy.quantity.ScalarQuantity method) get_conversion_factor_to_si() (rmgpy.quantity.ArrayQuantity method) (rmgpy.quantity.ScalarQuantity method) get_crude_mol_file_path() (rmgpy.qm.molecule.Geometry method) get_D1_diagnostic() (arkane.ess.ESSAdapter method) (arkane.ess.GaussianLog method) (arkane.ess.MolproLog method) (arkane.ess.OrcaLog method) (arkane.ess.QChemLog method) (arkane.ess.TeraChemLog method) get_density_of_states() (in module rmgpy.statmech.schrodinger) (rmgpy.species.Species method) (rmgpy.species.TransitionState method) (rmgpy.statmech.Conformer method) (rmgpy.statmech.HarmonicOscillator method) (rmgpy.statmech.HinderedRotor method) (rmgpy.statmech.IdealGasTranslation method) (rmgpy.statmech.KRotor method) (rmgpy.statmech.LinearRotor method) (rmgpy.statmech.NonlinearRotor method) (rmgpy.statmech.SphericalTopRotor method) get_desorbed_molecules() (rmgpy.molecule.Molecule method) get_deterministic_sssr() (rmgpy.molecule.Molecule method) get_disparate_cycles() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_edge() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_edges() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_edges_in_cycle() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_effective_collider_efficiencies() (rmgpy.kinetics.Chebyshev method) (rmgpy.kinetics.Lindemann method) (rmgpy.kinetics.MultiPDepArrhenius method) (rmgpy.kinetics.PDepArrhenius method) (rmgpy.kinetics.PDepKineticsData method) (rmgpy.kinetics.ThirdBody method) (rmgpy.kinetics.Troe method) get_effective_pressure() (rmgpy.kinetics.Chebyshev method) (rmgpy.kinetics.Lindemann method) (rmgpy.kinetics.MultiPDepArrhenius method) (rmgpy.kinetics.PDepArrhenius method) (rmgpy.kinetics.PDepKineticsData method) (rmgpy.kinetics.ThirdBody method) (rmgpy.kinetics.Troe method) get_element() (in module rmgpy.molecule) get_element_count() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_element_mass() (in module arkane.common) get_end_roots() (rmgpy.data.kinetics.KineticsFamily method) get_energy_filtered_reactions() (rmgpy.rmg.pdep.PDepNetwork method) get_enthalpies_of_reaction() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) get_enthalpy() (in module rmgpy.statmech.schrodinger) (rmgpy.pdep.Configuration method) (rmgpy.species.Species method) (rmgpy.species.TransitionState method) (rmgpy.statmech.Conformer method) (rmgpy.statmech.HarmonicOscillator method) (rmgpy.statmech.HinderedRotor method) (rmgpy.statmech.IdealGasTranslation method) (rmgpy.statmech.KRotor method) (rmgpy.statmech.LinearRotor method) (rmgpy.statmech.NonlinearRotor method) (rmgpy.statmech.SphericalTopRotor method) (rmgpy.thermo.NASA method) (rmgpy.thermo.NASAPolynomial method) (rmgpy.thermo.ThermoData method) (rmgpy.thermo.Wilhoit method) get_enthalpy_of_reaction() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) get_entries() (rmgpy.data.kinetics.KineticsRules method) get_entries_to_save() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) get_entropies_of_reaction() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) get_entropy() (in module rmgpy.statmech.schrodinger) (rmgpy.pdep.Configuration method) (rmgpy.species.Species method) (rmgpy.species.TransitionState method) (rmgpy.statmech.Conformer method) (rmgpy.statmech.HarmonicOscillator method) (rmgpy.statmech.HinderedRotor method) (rmgpy.statmech.IdealGasTranslation method) (rmgpy.statmech.KRotor method) (rmgpy.statmech.LinearRotor method) (rmgpy.statmech.NonlinearRotor method) (rmgpy.statmech.SphericalTopRotor method) (rmgpy.thermo.NASA method) (rmgpy.thermo.NASAPolynomial method) (rmgpy.thermo.ThermoData method) (rmgpy.thermo.Wilhoit method) get_entropy_of_reaction() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) get_equilibrium_constant() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) get_equilibrium_constants() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) get_extension_edge() (rmgpy.data.kinetics.KineticsFamily method)

get_extensions() (rmgpy.molecule.Group method) get_features() (rmgpy.molecule.AtomType method) get_file_path() (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.molecule.Geometry method) (rmgpy.qm.molecule.QMMolecule method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) get_formula() (rmgpy.molecule.Molecule method) get_forward_reaction_for_family_entry() (rmgpy.data.kinetics.KineticsDatabase method) get_free_energies_of_reaction() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) get_free_energy() (rmgpy.pdep.Configuration method) (rmgpy.species.Species method) (rmgpy.species.TransitionState method) (rmgpy.statmech.Conformer method) (rmgpy.thermo.NASA method) (rmgpy.thermo.NASAPolynomial method) (rmgpy.thermo.ThermoData method) (rmgpy.thermo.Wilhoit method) get_free_energy_of_reaction() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) get_frequency() (rmgpy.statmech.HinderedRotor method) get_frequency_groups() (rmgpy.data.statmech.StatmechGroups method) get_hamiltonian() (rmgpy.statmech.HinderedRotor method) get_heat_capacity() (in module rmgpy.statmech.schrodinger) (rmgpy.pdep.Configuration method) (rmgpy.species.Species method) (rmgpy.species.TransitionState method) (rmgpy.statmech.Conformer method) (rmgpy.statmech.HarmonicOscillator method) (rmgpy.statmech.HinderedRotor method) (rmgpy.statmech.IdealGasTranslation method) (rmgpy.statmech.KRotor method) (rmgpy.statmech.LinearRotor method) (rmgpy.statmech.NonlinearRotor method) (rmgpy.statmech.SphericalTopRotor method) (rmgpy.thermo.NASA method) (rmgpy.thermo.NASAPolynomial method) (rmgpy.thermo.ThermoData method) (rmgpy.thermo.Wilhoit method) get_internal_reduced_moment_of_inertia() (rmgpy.statmech.Conformer method) get_kinetics() (rmgpy.data.kinetics.KineticsFamily method) get_kinetics_for_template() (rmgpy.data.kinetics.KineticsFamily method) get_kinetics_from_depository() (rmgpy.data.kinetics.KineticsFamily method) get_labeled_atoms() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_labeled_reactants_and_products() (rmgpy.data.kinetics.KineticsFamily method) get_largest_ring() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_layering_indices() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) get_leak_branching_ratios() (rmgpy.rmg.pdep.PDepNetwork method) get_leak_coefficient() (rmgpy.rmg.pdep.PDepNetwork method) get_level_degeneracy() (rmgpy.statmech.HinderedRotor method) (rmgpy.statmech.KRotor method) (rmgpy.statmech.LinearRotor method) (rmgpy.statmech.SphericalTopRotor method) get_level_energy() (rmgpy.statmech.HinderedRotor method) (rmgpy.statmech.KRotor method) (rmgpy.statmech.LinearRotor method) (rmgpy.statmech.SphericalTopRotor method) get_libraries() (arkane.Arkane method) get_library_reactions() (rmgpy.data.kinetics.KineticsLibrary method) get_max_cycle_overlap() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_maximum_leak_species() (rmgpy.rmg.pdep.PDepNetwork method) get_mean_sigma_and_epsilon() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) get_model_size() (rmgpy.rmg.model.CoreEdgeReactionModel method) get_mol_file_path_for_calculation() (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.molecule.QMMolecule method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) get_molecular_weight() (rmgpy.molecule.Molecule method) get_moment_of_inertia_tensor() (in module arkane.common) (rmgpy.statmech.Conformer method) get_monocycles() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_net_charge() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_nth_neighbor() (rmgpy.molecule.Molecule method) get_num_atoms() (rmgpy.molecule.Molecule method) get_number_degrees_of_freedom() (rmgpy.statmech.Conformer method) get_number_of_atoms() (arkane.ess.ESSAdapter method) (arkane.ess.GaussianLog method) (arkane.ess.MolproLog method) (arkane.ess.OrcaLog method) (arkane.ess.QChemLog method) (arkane.ess.TeraChemLog method) get_octet_deviation() (in module rmgpy.molecule.filtration) get_octet_deviation_list() (in module rmgpy.molecule.filtration) get_order_num() (rmgpy.molecule.Bond method) (rmgpy.molecule.GroupBond method) get_order_str() (rmgpy.molecule.Bond method) (rmgpy.molecule.GroupBond method) get_other_vertex() (rmgpy.molecule.Bond method) (rmgpy.molecule.graph.Edge method) (rmgpy.molecule.GroupBond method) get_parser() (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.mopac.Mopac method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) get_partition_function() (in module rmgpy.statmech.schrodinger) (rmgpy.species.Species method) (rmgpy.species.TransitionState method) (rmgpy.statmech.Conformer method) (rmgpy.statmech.HarmonicOscillator method) (rmgpy.statmech.HinderedRotor method) (rmgpy.statmech.IdealGasTranslation method) (rmgpy.statmech.KRotor method) (rmgpy.statmech.LinearRotor method) (rmgpy.statmech.NonlinearRotor method) (rmgpy.statmech.SphericalTopRotor method) get_polycycles() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_possible_structures() (rmgpy.data.base.LogicOr method) get_potential() (rmgpy.statmech.HinderedRotor method) get_principal_moments_of_inertia() (in module arkane.common) (rmgpy.statmech.Conformer method) get_radical_atoms() (rmgpy.molecule.Molecule method) get_radical_count() (rmgpy.molecule.Molecule method) get_rate_coefficient() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.kinetics.Arrhenius method) (rmgpy.kinetics.Chebyshev method) (rmgpy.kinetics.KineticsData method) (rmgpy.kinetics.Lindemann method) (rmgpy.kinetics.MultiArrhenius method) (rmgpy.kinetics.MultiPDepArrhenius method) (rmgpy.kinetics.PDepArrhenius method) (rmgpy.kinetics.PDepKineticsData method) (rmgpy.kinetics.StickingCoefficient method) (rmgpy.kinetics.SurfaceArrhenius method) (rmgpy.kinetics.ThirdBody method) (rmgpy.kinetics.Troe method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) get_rate_filtered_products() (rmgpy.rmg.pdep.PDepNetwork method) get_rate_rule() (rmgpy.data.kinetics.KineticsFamily method) get_reaction_matches() (rmgpy.data.kinetics.KineticsFamily method) get_reaction_pairs() (rmgpy.data.kinetics.KineticsFamily method) get_reaction_template() (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) get_reaction_template_labels() (rmgpy.data.kinetics.KineticsFamily method) get_reduced_mass() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) get_reduced_pressure() (rmgpy.kinetics.Chebyshev method) get_reduced_temperature() (rmgpy.kinetics.Chebyshev method) get_refined_mol_file_path() (rmgpy.qm.molecule.Geometry method) get_relevant_cycles() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_resonance_hybrid() (rmgpy.species.Species method) get_reverse() (rmgpy.data.kinetics.ReactionRecipe method) get_ring_groups_from_comments() (rmgpy.data.thermo.ThermoDatabase method) get_root_template() (rmgpy.data.kinetics.KineticsFamily method) get_rule() (rmgpy.data.kinetics.KineticsRules method) get_rxn_batches() (rmgpy.data.kinetics.KineticsFamily method) get_singlet_carbene_count() (rmgpy.molecule.Molecule method) get_smallest_set_of_smallest_rings() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_software() (arkane.ess.ESSAdapter method) (arkane.ess.GaussianLog method) (arkane.ess.MolproLog method) (arkane.ess.OrcaLog method) (arkane.ess.QChemLog method) (arkane.ess.TeraChemLog method) get_source() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.rmg.pdep.PDepReaction method) get_sources_for_template() (rmgpy.data.kinetics.KineticsFamily method) get_species() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) get_species_identifier() (in module rmgpy.chemkin) get_species_index() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) get_species_reaction_lists() (rmgpy.rmg.model.CoreEdgeReactionModel method) get_statmech_data() (rmgpy.data.statmech.StatmechDatabase method) (rmgpy.data.statmech.StatmechGroups method) get_statmech_data_from_depository() (rmgpy.data.statmech.StatmechDatabase method) get_statmech_data_from_groups() (rmgpy.data.statmech.StatmechDatabase method) get_statmech_data_from_library() (rmgpy.data.statmech.StatmechDatabase method) get_sticking_coefficient() (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.kinetics.StickingCoefficient method) get_stoichiometric_coefficient() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) get_stoichiometry_matrix() (rmgpy.rmg.model.CoreEdgeReactionModel method) get_str_xyz() (in module arkane.output) get_sum_of_states() (in module rmgpy.statmech.schrodinger) (rmgpy.species.Species method) (rmgpy.species.TransitionState method) (rmgpy.statmech.Conformer method) (rmgpy.statmech.HarmonicOscillator method) (rmgpy.statmech.HinderedRotor method) (rmgpy.statmech.IdealGasTranslation method) (rmgpy.statmech.KRotor method) (rmgpy.statmech.LinearRotor method) (rmgpy.statmech.NonlinearRotor method) (rmgpy.statmech.SphericalTopRotor method) get_surface_rate_coefficient() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) get_surface_sites() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) get_symmetric_top_rotors() (rmgpy.statmech.Conformer method) get_symmetry_number() (rmgpy.molecule.Molecule method) (rmgpy.species.Species method) get_symmetry_properties() (arkane.ess.ESSAdapter method) (arkane.ess.GaussianLog method) (arkane.ess.MolproLog method) (arkane.ess.OrcaLog method) (arkane.ess.QChemLog method) (arkane.ess.TeraChemLog method) get_T1_diagnostic() (arkane.ess.ESSAdapter method) (arkane.ess.GaussianLog method) (arkane.ess.MolproLog method) (arkane.ess.OrcaLog method) (arkane.ess.QChemLog method) (arkane.ess.TeraChemLog method) get_thermo_data() (rmgpy.data.thermo.ThermoDatabase method) (rmgpy.qm.main.QMCalculator method) (rmgpy.species.Species method) get_thermo_data_for_surface_species() (rmgpy.data.thermo.ThermoDatabase method) get_thermo_data_from_depository() (rmgpy.data.thermo.ThermoDatabase method) get_thermo_data_from_groups() (rmgpy.data.thermo.ThermoDatabase method) get_thermo_data_from_libraries() (rmgpy.data.thermo.ThermoDatabase method) get_thermo_data_from_library() (rmgpy.data.thermo.ThermoDatabase method) get_thermo_data_from_ml() (rmgpy.data.thermo.ThermoDatabase method) get_thermo_file_path() (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.molecule.QMMolecule method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) get_threshold_rate_constants() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) get_top_level_groups() (rmgpy.data.kinetics.KineticsFamily method) get_total_bond_order() (rmgpy.molecule.Atom method) get_total_mass() (rmgpy.statmech.Conformer method) get_training_depository() (rmgpy.data.kinetics.KineticsFamily method) get_training_set() (rmgpy.data.kinetics.KineticsFamily method) get_transport_data() (rmgpy.species.Species method) get_url() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.molecule.Molecule method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) Graph (class in rmgpy.molecule.graph) groundStateDegeneracy (rmgpy.qm.qmdata.QMData attribute) Group (class in rmgpy.molecule) GroupAtom (class in rmgpy.molecule) GroupBond (class in rmgpy.molecule) GroupFrequencies (class in rmgpy.data.statmech)

H

H0 (rmgpy.thermo.Wilhoit attribute) H298 (rmgpy.thermo.ThermoData attribute) harmonic_oscillator_d_heat_capacity_d_freq() (in module rmgpy.data.statmechfit) harmonic_oscillator_heat_capacity() (in module rmgpy.data.statmechfit) HarmonicOscillator (class in rmgpy.statmech) has_atom() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) has_bond() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) has_edge() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) has_halogen() (rmgpy.molecule.Molecule method) has_lone_pairs() (rmgpy.molecule.Molecule method) has_rate_rule() (rmgpy.data.kinetics.KineticsFamily method) has_reactive_molecule() (rmgpy.species.Species method) has_rule() (rmgpy.data.kinetics.KineticsRules method) has_statmech() (rmgpy.pdep.Configuration method) (rmgpy.species.Species method) has_template() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method)

has_thermo() (rmgpy.pdep.Configuration method) (rmgpy.species.Species method) has_vertex() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) has_wildcards() (rmgpy.molecule.Group method) (rmgpy.molecule.GroupAtom method) highPlimit (rmgpy.kinetics.Chebyshev attribute) (rmgpy.kinetics.Lindemann attribute) (rmgpy.kinetics.MultiPDepArrhenius attribute) (rmgpy.kinetics.PDepArrhenius attribute) (rmgpy.kinetics.PDepKineticsData attribute) (rmgpy.kinetics.ThirdBody attribute) (rmgpy.kinetics.Troe attribute) hindered_rotor_d_heat_capacity_d_barr() (in module rmgpy.data.statmechfit) hindered_rotor_d_heat_capacity_d_freq() (in module rmgpy.data.statmechfit) hindered_rotor_heat_capacity() (in module rmgpy.data.statmechfit) HinderedRotor (class in rmgpy.statmech)

I

IdealGasTranslation (class in rmgpy.statmech) identify_ring_membership() (rmgpy.molecule.Molecule method) ILPSolutionError ImplicitBenzeneError inchi (rmgpy.molecule.Molecule attribute) (rmgpy.species.Species attribute) InchiException increment_lone_pairs() (rmgpy.molecule.Atom method) increment_order() (rmgpy.molecule.Bond method) increment_radical() (rmgpy.molecule.Atom method) inertia (rmgpy.statmech.HinderedRotor attribute) (rmgpy.statmech.KRotor attribute) (rmgpy.statmech.LinearRotor attribute) (rmgpy.statmech.NonlinearRotor attribute) (rmgpy.statmech.SphericalTopRotor attribute) initialize() (arkane.PressureDependenceJob method) (rmgpy.data.statmechfit.DirectFit method) (rmgpy.data.statmechfit.PseudoFit method) (rmgpy.data.statmechfit.PseudoRotorFit method) (rmgpy.pdep.Network method) (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.main.QMCalculator method) (rmgpy.qm.molecule.QMMolecule method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) (rmgpy.rmg.main.RMG method) (rmgpy.rmg.pdep.PDepNetwork method) (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) initialize_index_species_dict() (rmgpy.rmg.model.CoreEdgeReactionModel method) initialize_log() (in module rmgpy.rmg.main) initialize_model() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) initialize_seed_mech() (rmgpy.rmg.main.RMG method) initialize_surface() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) initiate_tolerances() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) input_file_keywords() (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) input_file_path (rmgpy.qm.gaussian.GaussianMol property) (rmgpy.qm.gaussian.GaussianMolPM3 property) (rmgpy.qm.gaussian.GaussianMolPM6 property) (rmgpy.qm.molecule.QMMolecule property) (rmgpy.qm.mopac.MopacMol property) (rmgpy.qm.mopac.MopacMolPM3 property) (rmgpy.qm.mopac.MopacMolPM6 property) (rmgpy.qm.mopac.MopacMolPM7 property) (rmgpy.qm.symmetry.SymmetryJob property) InputError InvalidActionError InvalidAdjacencyListError invalidate() (rmgpy.pdep.Network method) (rmgpy.rmg.pdep.PDepNetwork method) InvalidMicrocanonicalRateError is_all_zeros() (rmgpy.thermo.ThermoData method) is_aromatic() (rmgpy.molecule.Molecule method) is_aromatic_ring() (rmgpy.molecule.Group method) is_aryl_radical() (rmgpy.molecule.Molecule method) is_association() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) is_atom_able_to_gain_lone_pair() (in module rmgpy.molecule.pathfinder) is_atom_able_to_lose_lone_pair() (in module rmgpy.molecule.pathfinder) is_atom_in_cycle() (rmgpy.molecule.Molecule method) is_balanced() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) is_benzene() (rmgpy.molecule.Bond method) (rmgpy.molecule.GroupBond method) is_benzene_explicit() (rmgpy.molecule.Group method) is_bimolecular() (rmgpy.pdep.Configuration method) is_bond_in_cycle() (rmgpy.molecule.Molecule method) is_bonded_to_halogen() (rmgpy.molecule.Atom method) is_bonded_to_surface() (rmgpy.molecule.Atom method) (rmgpy.molecule.GroupAtom method) is_bromine() (rmgpy.molecule.Atom method) (rmgpy.molecule.GroupAtom method) is_carbon() (rmgpy.molecule.Atom method) (rmgpy.molecule.GroupAtom method) is_chlorine() (rmgpy.molecule.Atom method) (rmgpy.molecule.GroupAtom method) is_cyclic() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) is_dissociation() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) is_double() (rmgpy.molecule.Bond method) (rmgpy.molecule.GroupBond method) is_edge_in_cycle() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) is_entry_match() (rmgpy.data.kinetics.KineticsFamily method) is_fluorine() (rmgpy.molecule.Atom method) (rmgpy.molecule.GroupAtom method) is_halogen() (rmgpy.molecule.Atom method) is_heterocyclic() (rmgpy.molecule.Molecule method) is_hydrogen() (rmgpy.molecule.Atom method) is_hydrogen_bond() (rmgpy.molecule.Bond method) (rmgpy.molecule.GroupBond method) is_identical() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) (rmgpy.species.Species method) is_identical_to() (rmgpy.kinetics.Arrhenius method) (rmgpy.kinetics.Chebyshev method) (rmgpy.kinetics.KineticsData method) (rmgpy.kinetics.Lindemann method) (rmgpy.kinetics.MultiArrhenius method) (rmgpy.kinetics.MultiPDepArrhenius method) (rmgpy.kinetics.PDepArrhenius method) (rmgpy.kinetics.PDepKineticsData method) (rmgpy.kinetics.StickingCoefficient method) (rmgpy.kinetics.SurfaceArrhenius method) (rmgpy.kinetics.ThirdBody method) (rmgpy.kinetics.Troe method) (rmgpy.thermo.NASA method) (rmgpy.thermo.NASAPolynomial method) (rmgpy.thermo.ThermoData method) (rmgpy.thermo.Wilhoit method)

is_iodine() (rmgpy.molecule.Atom method) is_isomerization() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) is_isomorphic() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) (rmgpy.molecule.vf2.VF2 method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) (rmgpy.species.Species method) is_linear() (rmgpy.molecule.Molecule method) is_mapping_valid() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) is_molecule_forbidden() (rmgpy.data.kinetics.KineticsFamily method) is_nitrogen() (rmgpy.molecule.Atom method) (rmgpy.molecule.GroupAtom method) is_non_hydrogen() (rmgpy.molecule.Atom method) is_nos() (rmgpy.molecule.Atom method) is_order() (rmgpy.molecule.Bond method) is_oxygen() (rmgpy.molecule.Atom method) (rmgpy.molecule.GroupAtom method) is_pdep() (in module arkane.common) is_phosphorus() (rmgpy.molecule.Atom method) is_pressure_dependent() (rmgpy.kinetics.Arrhenius method) (rmgpy.kinetics.Chebyshev method) (rmgpy.kinetics.KineticsData method) (rmgpy.kinetics.Lindemann method) (rmgpy.kinetics.MultiArrhenius method) (rmgpy.kinetics.MultiPDepArrhenius method) (rmgpy.kinetics.PDepArrhenius method) (rmgpy.kinetics.PDepKineticsData method) (rmgpy.kinetics.StickingCoefficient method) (rmgpy.kinetics.SurfaceArrhenius method) (rmgpy.kinetics.ThirdBody method) (rmgpy.kinetics.Troe method) is_pressure_valid() (rmgpy.kinetics.Chebyshev method) (rmgpy.kinetics.Lindemann method) (rmgpy.kinetics.MultiPDepArrhenius method) (rmgpy.kinetics.PDepArrhenius method) (rmgpy.kinetics.PDepKineticsData method) (rmgpy.kinetics.ThirdBody method) (rmgpy.kinetics.Troe method) is_quadruple() (rmgpy.molecule.Bond method) (rmgpy.molecule.GroupBond method) is_radical() (rmgpy.molecule.Molecule method) is_reaction_bond() (rmgpy.molecule.Bond method) (rmgpy.molecule.GroupBond method) is_silicon() (rmgpy.molecule.Atom method) is_similar_to() (rmgpy.kinetics.Arrhenius method) (rmgpy.kinetics.Chebyshev method) (rmgpy.kinetics.KineticsData method) (rmgpy.kinetics.Lindemann method) (rmgpy.kinetics.MultiArrhenius method) (rmgpy.kinetics.MultiPDepArrhenius method) (rmgpy.kinetics.PDepArrhenius method) (rmgpy.kinetics.PDepKineticsData method) (rmgpy.kinetics.StickingCoefficient method) (rmgpy.kinetics.SurfaceArrhenius method) (rmgpy.kinetics.ThirdBody method) (rmgpy.kinetics.Troe method) (rmgpy.thermo.NASA method) (rmgpy.thermo.NASAPolynomial method) (rmgpy.thermo.ThermoData method) (rmgpy.thermo.Wilhoit method) is_single() (rmgpy.molecule.Bond method) (rmgpy.molecule.GroupBond method) is_specific_case_of() (rmgpy.molecule.Atom method) (rmgpy.molecule.AtomType method) (rmgpy.molecule.Bond method) (rmgpy.molecule.graph.Edge method) (rmgpy.molecule.graph.Vertex method) (rmgpy.molecule.GroupAtom method) (rmgpy.molecule.GroupBond method) is_structure_in_list() (rmgpy.species.Species method) is_subgraph_isomorphic() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) (rmgpy.molecule.vf2.VF2 method) is_sulfur() (rmgpy.molecule.Atom method) (rmgpy.molecule.GroupAtom method) is_surface_reaction() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) is_surface_site() (rmgpy.molecule.Atom method) (rmgpy.molecule.Group method) (rmgpy.molecule.GroupAtom method) (rmgpy.molecule.Molecule method) (rmgpy.species.Species method) is_temperature_valid() (rmgpy.kinetics.Arrhenius method) (rmgpy.kinetics.Chebyshev method) (rmgpy.kinetics.KineticsData method) (rmgpy.kinetics.Lindemann method) (rmgpy.kinetics.MultiArrhenius method) (rmgpy.kinetics.MultiPDepArrhenius method) (rmgpy.kinetics.PDepArrhenius method) (rmgpy.kinetics.PDepKineticsData method) (rmgpy.kinetics.StickingCoefficient method) (rmgpy.kinetics.SurfaceArrhenius method) (rmgpy.kinetics.ThirdBody method) (rmgpy.kinetics.Troe method) (rmgpy.thermo.NASA method) (rmgpy.thermo.NASAPolynomial method) (rmgpy.thermo.ThermoData method) (rmgpy.thermo.Wilhoit method) is_termolecular() (rmgpy.pdep.Configuration method) is_transition_state() (rmgpy.pdep.Configuration method) is_triple() (rmgpy.molecule.Bond method) (rmgpy.molecule.GroupBond method) is_uncertainty_additive() (rmgpy.quantity.ArrayQuantity method) (rmgpy.quantity.ScalarQuantity method) is_uncertainty_multiplicative() (rmgpy.quantity.ArrayQuantity method) (rmgpy.quantity.ScalarQuantity method) is_unimolecular() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.pdep.Configuration method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) is_van_der_waals() (rmgpy.molecule.Bond method) (rmgpy.molecule.GroupBond method) is_vertex_in_cycle() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method)

J

jacobian() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.SimpleReactor method)

K

kdata (rmgpy.kinetics.KineticsData attribute) (rmgpy.kinetics.PDepKineticsData attribute) KekulizationError kekulize() (in module rmgpy.molecule.kekulize) (rmgpy.molecule.kekulize.AromaticRing method) (rmgpy.molecule.Molecule method) keywords (rmgpy.qm.gaussian.GaussianMolPM3 attribute) (rmgpy.qm.gaussian.GaussianMolPM6 attribute) (rmgpy.qm.mopac.MopacMol attribute) (rmgpy.qm.mopac.MopacMolPM3 attribute) (rmgpy.qm.mopac.MopacMolPM6 attribute) (rmgpy.qm.mopac.MopacMolPM7 attribute)

KineticsData (class in rmgpy.kinetics) KineticsDatabase (class in rmgpy.data.kinetics) KineticsDepository (class in rmgpy.data.kinetics) KineticsError KineticsFamily (class in rmgpy.data.kinetics) KineticsGroups (class in rmgpy.data.kinetics) KineticsJob (class in arkane) KineticsLibrary (class in rmgpy.data.kinetics) KineticsRules (class in rmgpy.data.kinetics) KineticsSensitivity (class in arkane.sensitivity) KRotor (class in rmgpy.statmech) kunits (rmgpy.kinetics.Chebyshev attribute)

L

label (rmgpy.thermo.NASA attribute) (rmgpy.thermo.NASAPolynomial attribute) (rmgpy.thermo.ThermoData attribute) (rmgpy.thermo.Wilhoit attribute) LibraryReaction (class in rmgpy.data.kinetics) Lindemann (class in rmgpy.kinetics) LinearRotor (class in rmgpy.statmech) LiquidReactor (class in rmgpy.solver) load() (arkane.StatMechJob method) (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDatabase method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDatabase method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDatabase method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) load_chemkin_file() (in module rmgpy.chemkin) load_conformer() (arkane.ess.ESSAdapter method) (arkane.ess.GaussianLog method) (arkane.ess.MolproLog method) (arkane.ess.OrcaLog method) (arkane.ess.QChemLog method) (arkane.ess.TeraChemLog method) load_depository() (rmgpy.data.statmech.StatmechDatabase method) (rmgpy.data.thermo.ThermoDatabase method) load_energy() (arkane.ess.ESSAdapter method) (arkane.ess.GaussianLog method) (arkane.ess.MolproLog method) (arkane.ess.OrcaLog method) (arkane.ess.QChemLog method) (arkane.ess.TeraChemLog method) load_entry() (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) load_families() (rmgpy.data.kinetics.KineticsDatabase method) load_forbidden() (rmgpy.data.kinetics.KineticsFamily method) load_force_constant_matrix() (arkane.ess.ESSAdapter method) (arkane.ess.GaussianLog method) (arkane.ess.MolproLog method) (arkane.ess.OrcaLog method) (arkane.ess.QChemLog method) (arkane.ess.TeraChemLog method) load_geometry() (arkane.ess.ESSAdapter method) (arkane.ess.GaussianLog method) (arkane.ess.MolproLog method) (arkane.ess.OrcaLog method) (arkane.ess.QChemLog method) (arkane.ess.TeraChemLog method) load_groups() (rmgpy.data.statmech.StatmechDatabase method) (rmgpy.data.thermo.ThermoDatabase method) load_input() (rmgpy.rmg.main.RMG method) load_input_file() (arkane.Arkane method) (in module arkane.input) load_libraries() (rmgpy.data.kinetics.KineticsDatabase method) (rmgpy.data.statmech.StatmechDatabase method) (rmgpy.data.thermo.ThermoDatabase method) load_negative_frequency() (arkane.ess.ESSAdapter method) (arkane.ess.GaussianLog method) (arkane.ess.MolproLog method) (arkane.ess.OrcaLog method) (arkane.ess.QChemLog method) (arkane.ess.TeraChemLog method) load_old() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDatabase method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDatabase method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDatabase method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) load_old_dictionary() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method)

load_old_library() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) load_old_tree() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) load_recipe() (rmgpy.data.kinetics.KineticsFamily method) load_recommended_families() (rmgpy.data.kinetics.KineticsDatabase method) load_scan_energies() (arkane.ess.ESSAdapter method) (arkane.ess.GaussianLog method) (arkane.ess.MolproLog method) (arkane.ess.OrcaLog method) (arkane.ess.QChemLog method) (arkane.ess.TeraChemLog method) load_scan_frozen_atoms() (arkane.ess.ESSAdapter method) (arkane.ess.GaussianLog method) (arkane.ess.MolproLog method) (arkane.ess.OrcaLog method) (arkane.ess.QChemLog method) (arkane.ess.TeraChemLog method) load_scan_pivot_atoms() (arkane.ess.ESSAdapter method) (arkane.ess.GaussianLog method) (arkane.ess.MolproLog method) (arkane.ess.OrcaLog method) (arkane.ess.QChemLog method) (arkane.ess.TeraChemLog method) load_species_dictionary() (in module rmgpy.chemkin) load_surface() (rmgpy.data.thermo.ThermoDatabase method) load_template() (rmgpy.data.kinetics.KineticsFamily method) load_thermo_data() (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.molecule.QMMolecule method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) load_thermo_input() (rmgpy.rmg.main.RMG method) load_transport_file() (in module rmgpy.chemkin) load_yaml() (arkane.common.ArkaneSpecies method) load_zero_point_energy() (arkane.ess.ESSAdapter method) (arkane.ess.GaussianLog method) (arkane.ess.MolproLog method) (arkane.ess.OrcaLog method) (arkane.ess.QChemLog method) (arkane.ess.TeraChemLog method) log_conversions() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) log_enlarge_summary() (rmgpy.rmg.model.CoreEdgeReactionModel method) log_header() (rmgpy.rmg.main.RMG method) log_initial_conditions() (rmgpy.solver.SurfaceReactor method) log_rates() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) log_summary() (rmgpy.pdep.Network method) (rmgpy.rmg.pdep.PDepNetwork method) LogicAnd (class in rmgpy.data.base) LogicNode (class in rmgpy.data.base) LogicOr (class in rmgpy.data.base)

M

make_bond() (rmgpy.molecule.GroupBond method) make_logic_node() (in module rmgpy.data.base) make_new_pdep_reaction() (rmgpy.rmg.model.CoreEdgeReactionModel method) make_new_reaction() (rmgpy.rmg.model.CoreEdgeReactionModel method) make_new_species() (rmgpy.rmg.model.CoreEdgeReactionModel method) make_object() (arkane.common.ArkaneSpecies method) (rmgpy.pdep.SingleExponentialDown method) (rmgpy.quantity.ArrayQuantity method) (rmgpy.quantity.ScalarQuantity method) (rmgpy.statmech.Conformer method) (rmgpy.statmech.HarmonicOscillator method) (rmgpy.statmech.HinderedRotor method) (rmgpy.statmech.IdealGasTranslation method) (rmgpy.statmech.KRotor method) (rmgpy.statmech.LinearRotor method) (rmgpy.statmech.NonlinearRotor method) (rmgpy.statmech.SphericalTopRotor method) (rmgpy.thermo.NASA method) (rmgpy.thermo.NASAPolynomial method) (rmgpy.thermo.ThermoData method) (rmgpy.thermo.Wilhoit method) make_profile_graph() (in module rmgpy.rmg.main) make_sample_atom() (rmgpy.molecule.GroupAtom method) make_sample_molecule() (rmgpy.molecule.Group method) make_seed_mech() (rmgpy.rmg.main.RMG method) make_species_labels_independent() (rmgpy.rmg.main.RMG method) make_tree() (rmgpy.data.kinetics.KineticsFamily method) map_densities_of_states() (rmgpy.pdep.Network method) (rmgpy.rmg.pdep.PDepNetwork method) map_density_of_states() (rmgpy.pdep.Configuration method) map_sum_of_states() (rmgpy.pdep.Configuration method) mark_chemkin_duplicates() (rmgpy.rmg.model.CoreEdgeReactionModel method) mark_duplicate_reactions() (in module rmgpy.chemkin) mark_unreactive_structures() (in module rmgpy.molecule.filtration) mark_valid_duplicates() (rmgpy.data.kinetics.KineticsLibrary method) mass (rmgpy.statmech.Conformer attribute) (rmgpy.statmech.IdealGasTranslation attribute) match_logic_or() (rmgpy.data.base.LogicOr method) match_node_to_child() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) match_node_to_node() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) match_node_to_structure() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method)

match_to_structure() (rmgpy.data.base.LogicAnd method) (rmgpy.data.base.LogicOr method) matches_species() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) max_attempts (rmgpy.qm.gaussian.GaussianMol property) (rmgpy.qm.gaussian.GaussianMolPM3 property) (rmgpy.qm.gaussian.GaussianMolPM6 property) (rmgpy.qm.molecule.QMMolecule property) (rmgpy.qm.mopac.MopacMol property) (rmgpy.qm.mopac.MopacMolPM3 property) (rmgpy.qm.mopac.MopacMolPM6 property) (rmgpy.qm.mopac.MopacMolPM7 property) maximum_grain_size (arkane.PressureDependenceJob property) MBSampledReactor (class in rmgpy.solver) merge() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) (rmgpy.rmg.model.ReactionModel method) (rmgpy.rmg.pdep.PDepNetwork method) merge_groups() (rmgpy.molecule.Group method) modes (rmgpy.statmech.Conformer attribute) ModifiedStrongCollisionError module arkane arkane.common arkane.output arkane.sensitivity rmgpy.chemkin rmgpy.constants rmgpy.data rmgpy.exceptions rmgpy.kinetics rmgpy.molecule rmgpy.molecule.adjlist rmgpy.molecule.converter rmgpy.molecule.filtration rmgpy.molecule.kekulize rmgpy.molecule.pathfinder rmgpy.molecule.resonance rmgpy.molecule.translator rmgpy.pdep rmgpy.qm rmgpy.quantity rmgpy.reaction rmgpy.rmg rmgpy.solver rmgpy.species rmgpy.statmech rmgpy.statmech.schrodinger rmgpy.thermo molecular_weight (rmgpy.species.Species attribute) Molecule (class in rmgpy.molecule) MoleculeDrawer (class in rmgpy.molecule.draw) MolproLog (class in arkane.ess) Mopac (class in rmgpy.qm.mopac) MopacMol (class in rmgpy.qm.mopac) MopacMolPM3 (class in rmgpy.qm.mopac) MopacMolPM6 (class in rmgpy.qm.mopac) MopacMolPM7 (class in rmgpy.qm.mopac) MultiArrhenius (class in rmgpy.kinetics) MultiPDepArrhenius (class in rmgpy.kinetics) multiplicity (rmgpy.species.Species attribute)

N

n (rmgpy.kinetics.Arrhenius attribute) (rmgpy.kinetics.StickingCoefficient attribute) (rmgpy.kinetics.SurfaceArrhenius attribute) (rmgpy.pdep.SingleExponentialDown attribute) NASA (class in rmgpy.thermo) NASAPolynomial (class in rmgpy.thermo) NegativeBarrierException

Network (class in rmgpy.pdep) NetworkError NonlinearRotor (class in rmgpy.statmech) number (rmgpy.statmech.Conformer attribute) number_of_surface_sites() (rmgpy.molecule.Molecule method) (rmgpy.species.Species method) numberOfAtoms (rmgpy.qm.qmdata.QMData attribute)

O

octet_filtration() (in module rmgpy.molecule.filtration) optical_isomers (rmgpy.statmech.Conformer attribute) OrcaLog (class in arkane.ess) output_file_path (rmgpy.qm.gaussian.GaussianMol property) (rmgpy.qm.gaussian.GaussianMolPM3 property) (rmgpy.qm.gaussian.GaussianMolPM6 property) (rmgpy.qm.molecule.QMMolecule property) (rmgpy.qm.mopac.MopacMol property) (rmgpy.qm.mopac.MopacMolPM3 property) (rmgpy.qm.mopac.MopacMolPM6 property) (rmgpy.qm.mopac.MopacMolPM7 property)

OutputError

P

parse() (rmgpy.qm.gaussian.Gaussian method) (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.molecule.QMMolecule method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) (rmgpy.qm.symmetry.SymmetryJob method) parse_command_line_arguments() (arkane.Arkane method) parse_old_library() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) Pdata (rmgpy.kinetics.PDepKineticsData attribute) PDepArrhenius (class in rmgpy.kinetics) PDepKineticsData (class in rmgpy.kinetics) PDepNetwork (class in rmgpy.rmg.pdep) PDepReaction (class in rmgpy.rmg.pdep) PDepSensitivity (class in arkane.sensitivity) perturb() (arkane.sensitivity.KineticsSensitivity method) (arkane.sensitivity.PDepSensitivity method) pick_wildcards() (rmgpy.molecule.Group method) Plist (arkane.PressureDependenceJob property) plot() (arkane.KineticsJob method) (arkane.PressureDependenceJob method) (arkane.sensitivity.KineticsSensitivity method) (arkane.sensitivity.PDepSensitivity method) (arkane.ThermoJob method) Pmax (arkane.PressureDependenceJob property) (rmgpy.kinetics.Arrhenius attribute) (rmgpy.kinetics.Chebyshev attribute) (rmgpy.kinetics.KineticsData attribute) (rmgpy.kinetics.Lindemann attribute) (rmgpy.kinetics.MultiArrhenius attribute) (rmgpy.kinetics.MultiPDepArrhenius attribute) (rmgpy.kinetics.PDepArrhenius attribute) (rmgpy.kinetics.PDepKineticsData attribute) (rmgpy.kinetics.StickingCoefficient attribute) (rmgpy.kinetics.SurfaceArrhenius attribute) (rmgpy.kinetics.ThirdBody attribute) (rmgpy.kinetics.Troe attribute)

Pmin (arkane.PressureDependenceJob property) (rmgpy.kinetics.Arrhenius attribute) (rmgpy.kinetics.Chebyshev attribute) (rmgpy.kinetics.KineticsData attribute) (rmgpy.kinetics.Lindemann attribute) (rmgpy.kinetics.MultiArrhenius attribute) (rmgpy.kinetics.MultiPDepArrhenius attribute) (rmgpy.kinetics.PDepArrhenius attribute) (rmgpy.kinetics.PDepKineticsData attribute) (rmgpy.kinetics.StickingCoefficient attribute) (rmgpy.kinetics.SurfaceArrhenius attribute) (rmgpy.kinetics.ThirdBody attribute) (rmgpy.kinetics.Troe attribute) PointGroup (class in rmgpy.qm.symmetry) PointGroupCalculator (class in rmgpy.qm.symmetry) poly1 (rmgpy.thermo.NASA attribute) poly2 (rmgpy.thermo.NASA attribute) poly3 (rmgpy.thermo.NASA attribute) polynomials (rmgpy.thermo.NASA attribute) populate_resonance_algorithms() (in module rmgpy.molecule.resonance) PressureDependenceError PressureDependenceJob (class in arkane) pressures (rmgpy.kinetics.PDepArrhenius attribute) prettify() (in module arkane.output) PrettifyVisitor (class in arkane.output) prioritize_thermo() (rmgpy.data.thermo.ThermoDatabase method) process_bonds() (rmgpy.molecule.kekulize.AromaticRing method) process_coverage_dependence() (rmgpy.rmg.model.CoreEdgeReactionModel method) process_new_reactions() (rmgpy.rmg.model.CoreEdgeReactionModel method) process_old_library_entry() (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) process_pdep_networks() (rmgpy.rmg.main.RMG method) process_profile_stats() (in module rmgpy.rmg.main) process_reactions_to_species() (rmgpy.rmg.main.RMG method) process_to_species_networks() (rmgpy.rmg.main.RMG method) prune() (rmgpy.rmg.model.CoreEdgeReactionModel method) prune_heteroatoms() (rmgpy.data.thermo.ThermoDatabase method) prune_tree() (rmgpy.data.kinetics.KineticsFamily method) PseudoFit (class in rmgpy.data.statmechfit) PseudoRotorFit (class in rmgpy.data.statmechfit)

Q

QChemLog (class in arkane.ess) QMCalculator (class in rmgpy.qm.main) QMData (class in rmgpy.qm.qmdata) QMMolecule (class in rmgpy.qm.molecule) QMSettings (class in rmgpy.qm.main) QMVerifier (class in rmgpy.qm.qmverifier) Quantity() (in module rmgpy.quantity)

QuantityError quantum (rmgpy.statmech.HarmonicOscillator attribute) (rmgpy.statmech.HinderedRotor attribute) (rmgpy.statmech.IdealGasTranslation attribute) (rmgpy.statmech.KRotor attribute) (rmgpy.statmech.LinearRotor attribute) (rmgpy.statmech.NonlinearRotor attribute) (rmgpy.statmech.SphericalTopRotor attribute)

R

rd_build() (rmgpy.qm.molecule.Geometry method) rd_embed() (rmgpy.qm.molecule.Geometry method) react_init_tuples() (rmgpy.rmg.main.RMG method) react_molecules() (rmgpy.data.kinetics.KineticsDatabase method) Reaction (class in rmgpy.reaction) ReactionDrawer (class in rmgpy.molecule.draw) ReactionError ReactionModel (class in rmgpy.rmg.model) ReactionPairsError ReactionRecipe (class in rmgpy.data.kinetics) ReactionSystem (class in rmgpy.solver) read_input_file() (in module rmgpy.rmg.input) read_kinetics_entry() (in module rmgpy.chemkin) read_reaction_comments() (in module rmgpy.chemkin) read_reactions_block() (in module rmgpy.chemkin) read_thermo_entry() (in module rmgpy.chemkin) reconstruct_kinetics_from_source() (rmgpy.data.kinetics.KineticsDatabase method) record_polycylic_generic_nodes() (rmgpy.data.thermo.ThermoDatabase method) record_ring_generic_nodes() (rmgpy.data.thermo.ThermoDatabase method) register_ess_adapter() (in module arkane.ess.factory) register_listeners() (rmgpy.rmg.main.RMG method) register_reaction() (rmgpy.rmg.model.CoreEdgeReactionModel method) regularize() (rmgpy.data.kinetics.KineticsFamily method) remove_atom() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) remove_bond() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) remove_comment_from_line() (in module rmgpy.chemkin) remove_disconnected_reactions() (rmgpy.rmg.pdep.PDepNetwork method) remove_edge() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) remove_empty_pdep_networks() (rmgpy.rmg.model.CoreEdgeReactionModel method) remove_group() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) remove_h_bonds() (rmgpy.molecule.Molecule method) remove_reactions() (rmgpy.rmg.pdep.PDepNetwork method) remove_species_from_edge() (rmgpy.rmg.model.CoreEdgeReactionModel method) remove_van_der_waals_bonds() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) remove_vertex() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) render() (rmgpy.molecule.draw.MoleculeDrawer method) replace_halogen_with_hydrogen() (rmgpy.molecule.Molecule method) replace_yaml_syntax() (in module arkane.common) ReservoirStateError reset_connectivity_values() (rmgpy.molecule.Atom method) (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.graph.Vertex method) (rmgpy.molecule.Group method) (rmgpy.molecule.GroupAtom method) (rmgpy.molecule.Molecule method) reset_max_edge_species_rate_ratios() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) reset_ring_membership() (rmgpy.molecule.Group method) residual() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) ResonanceError restore_vertex_order() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method)

retrieve() (rmgpy.rmg.model.CoreEdgeReactionModel method) retrieve_original_entry() (rmgpy.data.kinetics.KineticsFamily method) retrieve_template() (rmgpy.data.kinetics.KineticsFamily method) reverse_arrhenius_rate() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) reverse_sticking_coeff_rate() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) reverse_surface_arrhenius_rate() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) RMG (class in rmgpy.rmg.main) rmgpy.chemkin module rmgpy.constants module rmgpy.data module rmgpy.exceptions module rmgpy.kinetics module rmgpy.molecule module rmgpy.molecule.adjlist module rmgpy.molecule.converter module rmgpy.molecule.filtration module rmgpy.molecule.kekulize module rmgpy.molecule.pathfinder module rmgpy.molecule.resonance module rmgpy.molecule.translator module rmgpy.pdep module rmgpy.qm module rmgpy.quantity module rmgpy.reaction module rmgpy.rmg module rmgpy.solver module rmgpy.species module rmgpy.statmech module rmgpy.statmech.schrodinger module rmgpy.thermo module rotationalConstant (rmgpy.statmech.HinderedRotor attribute) (rmgpy.statmech.KRotor attribute) (rmgpy.statmech.LinearRotor attribute) (rmgpy.statmech.NonlinearRotor attribute) (rmgpy.statmech.SphericalTopRotor attribute) run() (rmgpy.qm.symmetry.SymmetryJob method) run_jobs() (rmgpy.qm.main.QMCalculator method) run_model_analysis() (rmgpy.rmg.main.RMG method) run_uncertainty_analysis() (rmgpy.rmg.main.RMG method)

S

S0 (rmgpy.thermo.Wilhoit attribute) S298 (rmgpy.thermo.ThermoData attribute) saturate_radicals() (rmgpy.molecule.Molecule method) saturate_unfilled_valence() (rmgpy.molecule.Molecule method) save() (arkane.PressureDependenceJob method) (arkane.sensitivity.KineticsSensitivity method) (arkane.sensitivity.PDepSensitivity method) (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDatabase method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDatabase method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDatabase method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) save_chemkin_file() (in module rmgpy.chemkin) save_coordinates_from_qm_data() (rmgpy.qm.molecule.Geometry method) save_depository() (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.statmech.StatmechDatabase method) (rmgpy.data.thermo.ThermoDatabase method) save_dictionary() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) save_diff_html() (in module rmgpy.rmg.output) save_entry() (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) save_everything() (rmgpy.rmg.main.RMG method) save_families() (rmgpy.data.kinetics.KineticsDatabase method) save_generated_tree() (rmgpy.data.kinetics.KineticsFamily method) save_groups() (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.statmech.StatmechDatabase method) (rmgpy.data.thermo.ThermoDatabase method) save_hindered_rotor_figures() (arkane.StatMechJob method) save_input() (rmgpy.rmg.main.RMG method) save_input_file() (arkane.PressureDependenceJob method) (in module rmgpy.rmg.input) save_kinetics_lib() (in module arkane.output) save_libraries() (rmgpy.data.kinetics.KineticsDatabase method) (rmgpy.data.statmech.StatmechDatabase method) (rmgpy.data.thermo.ThermoDatabase method) save_old() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDatabase method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDatabase method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDatabase method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) save_old_dictionary() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) save_old_library() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) save_old_tree() (rmgpy.data.base.Database method) (rmgpy.data.kinetics.KineticsDepository method) (rmgpy.data.kinetics.KineticsFamily method) (rmgpy.data.kinetics.KineticsGroups method) (rmgpy.data.kinetics.KineticsLibrary method) (rmgpy.data.kinetics.KineticsRules method) (rmgpy.data.statmech.StatmechDepository method) (rmgpy.data.statmech.StatmechGroups method) (rmgpy.data.statmech.StatmechLibrary method) (rmgpy.data.thermo.ThermoDepository method) (rmgpy.data.thermo.ThermoGroups method) (rmgpy.data.thermo.ThermoLibrary method) save_output_html() (in module rmgpy.rmg.output) save_recommended_families() (rmgpy.data.kinetics.KineticsDatabase method) save_species_dictionary() (in module rmgpy.chemkin) save_surface() (rmgpy.data.thermo.ThermoDatabase method) save_thermo_data() (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.molecule.QMMolecule method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) save_thermo_lib() (in module arkane.output) save_training_reactions() (rmgpy.data.kinetics.KineticsFamily method) save_transport_file() (in module rmgpy.chemkin) save_yaml() (arkane.common.ArkaneSpecies method) (arkane.KineticsJob method)

ScalarQuantity (class in rmgpy.quantity) script_attempts (rmgpy.qm.gaussian.GaussianMol property) (rmgpy.qm.gaussian.GaussianMolPM3 property) (rmgpy.qm.gaussian.GaussianMolPM6 property) (rmgpy.qm.molecule.QMMolecule property) (rmgpy.qm.mopac.MopacMol property) (rmgpy.qm.mopac.MopacMolPM3 property) (rmgpy.qm.mopac.MopacMolPM6 property) (rmgpy.qm.mopac.MopacMolPM7 property) search_retrieve_reactions() (rmgpy.rmg.model.CoreEdgeReactionModel method) select_energy_grains() (rmgpy.pdep.Network method) (rmgpy.rmg.pdep.PDepNetwork method) select_polynomial() (rmgpy.thermo.NASA method) semiclassical (rmgpy.statmech.HinderedRotor attribute) set_binding_energies() (rmgpy.data.thermo.ThermoDatabase method) set_cantera_kinetics() (rmgpy.kinetics.Arrhenius method) (rmgpy.kinetics.Chebyshev method) (rmgpy.kinetics.KineticsData method) (rmgpy.kinetics.Lindemann method) (rmgpy.kinetics.MultiArrhenius method) (rmgpy.kinetics.MultiPDepArrhenius method) (rmgpy.kinetics.PDepArrhenius method) (rmgpy.kinetics.PDepKineticsData method) (rmgpy.kinetics.StickingCoefficient method) (rmgpy.kinetics.SurfaceArrhenius method) (rmgpy.kinetics.ThirdBody method) (rmgpy.kinetics.Troe method) set_colliders() (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.SimpleReactor method) set_conditions() (rmgpy.pdep.Network method) (rmgpy.rmg.pdep.PDepNetwork method) set_default_output_directory() (rmgpy.qm.main.QMCalculator method) set_e0_with_thermo() (rmgpy.species.Species method) set_initial_conditions() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) set_initial_derivative() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) set_lone_pairs() (rmgpy.molecule.Atom method) set_order_num() (rmgpy.molecule.Bond method) (rmgpy.molecule.GroupBond method) set_order_str() (rmgpy.molecule.Bond method) (rmgpy.molecule.GroupBond method) set_structure() (rmgpy.species.Species method) set_thermodynamic_filtering_parameters() (rmgpy.rmg.model.CoreEdgeReactionModel method) SettingsError simple_regularization() (rmgpy.data.kinetics.KineticsFamily method) SimpleReactor (class in rmgpy.solver) simulate() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) SingleExponentialDown (class in rmgpy.pdep) smiles (rmgpy.molecule.Molecule attribute) (rmgpy.species.Species attribute) solve() (rmgpy.data.statmechfit.DirectFit method) (rmgpy.data.statmechfit.PseudoFit method) (rmgpy.data.statmechfit.PseudoRotorFit method) solve_full_me() (rmgpy.pdep.Network method) (rmgpy.rmg.pdep.PDepNetwork method) solve_reduced_me() (rmgpy.pdep.Network method) (rmgpy.rmg.pdep.PDepNetwork method) solve_schrodinger_equation() (rmgpy.statmech.HinderedRotor method) solve_ss_network() (rmgpy.rmg.pdep.PDepNetwork method) sort_atoms() (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) sort_by_connectivity() (rmgpy.molecule.Group method) sort_cyclic_vertices() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) sort_vertices() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) sorting_key (rmgpy.molecule.Atom attribute) (rmgpy.molecule.Bond attribute) (rmgpy.molecule.Molecule attribute) (rmgpy.species.Species attribute) Species (class in rmgpy.species) SpeciesError specify_atom_extensions() (rmgpy.molecule.Group method) specify_bond_extensions() (rmgpy.molecule.Group method) specify_external_new_bond_extensions() (rmgpy.molecule.Group method) specify_internal_new_bond_extensions() (rmgpy.molecule.Group method) specify_ring_extensions() (rmgpy.molecule.Group method) specify_unpaired_extensions() (rmgpy.molecule.Group method) SphericalTopRotor (class in rmgpy.statmech) spin_multiplicity (rmgpy.statmech.Conformer attribute) split() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) stabilize_charges_by_electronegativity() (in module rmgpy.molecule.filtration) stabilize_charges_by_proximity() (in module rmgpy.molecule.filtration) standardize_atomtype() (rmgpy.molecule.Group method) standardize_group() (rmgpy.molecule.Group method) StatmechDatabase (class in rmgpy.data.statmech) StatmechDepository (class in rmgpy.data.statmech) StatmechError StatmechFitError StatmechGroups (class in rmgpy.data.statmech) StatMechJob (class in arkane) StatmechLibrary (class in rmgpy.data.statmech) step() (rmgpy.solver.LiquidReactor method) (rmgpy.solver.MBSampledReactor method) (rmgpy.solver.ReactionSystem method) (rmgpy.solver.SimpleReactor method) (rmgpy.solver.SurfaceReactor method) StickingCoefficient (class in rmgpy.kinetics) str_repr() (in module arkane.common) succesful_job_exists() (rmgpy.qm.qmverifier.QMVerifier method) success_keys (rmgpy.qm.gaussian.Gaussian attribute) (rmgpy.qm.gaussian.GaussianMol attribute) (rmgpy.qm.gaussian.GaussianMolPM3 attribute) (rmgpy.qm.gaussian.GaussianMolPM6 attribute) (rmgpy.qm.mopac.Mopac attribute) (rmgpy.qm.mopac.MopacMol attribute) (rmgpy.qm.mopac.MopacMolPM3 attribute) (rmgpy.qm.mopac.MopacMolPM6 attribute) (rmgpy.qm.mopac.MopacMolPM7 attribute) SurfaceArrhenius (class in rmgpy.kinetics) SurfaceReactor (class in rmgpy.solver) symmetry (rmgpy.statmech.HinderedRotor attribute) (rmgpy.statmech.KRotor attribute) (rmgpy.statmech.LinearRotor attribute) (rmgpy.statmech.NonlinearRotor attribute) (rmgpy.statmech.SphericalTopRotor attribute) SymmetryJob (class in rmgpy.qm.symmetry)

T

T0 (rmgpy.kinetics.Arrhenius attribute) (rmgpy.kinetics.StickingCoefficient attribute) (rmgpy.kinetics.SurfaceArrhenius attribute) (rmgpy.pdep.SingleExponentialDown attribute) T1 (rmgpy.kinetics.Troe attribute) T2 (rmgpy.kinetics.Troe attribute) T3 (rmgpy.kinetics.Troe attribute) Tdata (rmgpy.kinetics.KineticsData attribute) (rmgpy.kinetics.PDepKineticsData attribute) (rmgpy.thermo.ThermoData attribute) TemplateReaction (class in rmgpy.data.kinetics) TeraChemLog (class in arkane.ess) TerminationConversion (class in rmgpy.solver) TerminationRateRatio (class in rmgpy.solver) TerminationTime (class in rmgpy.solver) thermo_filter_down() (rmgpy.rmg.model.CoreEdgeReactionModel method) thermo_filter_species() (rmgpy.rmg.model.CoreEdgeReactionModel method) ThermoData (class in rmgpy.thermo) ThermoDatabase (class in rmgpy.data.thermo) ThermoDepository (class in rmgpy.data.thermo) ThermoGroups (class in rmgpy.data.thermo) ThermoJob (class in arkane) ThermoLibrary (class in rmgpy.data.thermo) ThirdBody (class in rmgpy.kinetics) Tlist (arkane.KineticsJob property) (arkane.PressureDependenceJob property) Tmax (arkane.KineticsJob property) (arkane.PressureDependenceJob property) (rmgpy.kinetics.Arrhenius attribute) (rmgpy.kinetics.Chebyshev attribute) (rmgpy.kinetics.KineticsData attribute) (rmgpy.kinetics.Lindemann attribute) (rmgpy.kinetics.MultiArrhenius attribute) (rmgpy.kinetics.MultiPDepArrhenius attribute) (rmgpy.kinetics.PDepArrhenius attribute) (rmgpy.kinetics.PDepKineticsData attribute) (rmgpy.kinetics.StickingCoefficient attribute) (rmgpy.kinetics.SurfaceArrhenius attribute) (rmgpy.kinetics.ThirdBody attribute) (rmgpy.kinetics.Troe attribute) (rmgpy.thermo.NASA attribute) (rmgpy.thermo.NASAPolynomial attribute) (rmgpy.thermo.ThermoData attribute) (rmgpy.thermo.Wilhoit attribute) Tmin (arkane.KineticsJob property) (arkane.PressureDependenceJob property) (rmgpy.kinetics.Arrhenius attribute) (rmgpy.kinetics.Chebyshev attribute) (rmgpy.kinetics.KineticsData attribute) (rmgpy.kinetics.Lindemann attribute) (rmgpy.kinetics.MultiArrhenius attribute) (rmgpy.kinetics.MultiPDepArrhenius attribute) (rmgpy.kinetics.PDepArrhenius attribute) (rmgpy.kinetics.PDepKineticsData attribute) (rmgpy.kinetics.StickingCoefficient attribute) (rmgpy.kinetics.SurfaceArrhenius attribute) (rmgpy.kinetics.ThirdBody attribute) (rmgpy.kinetics.Troe attribute) (rmgpy.thermo.NASA attribute) (rmgpy.thermo.NASAPolynomial attribute) (rmgpy.thermo.ThermoData attribute) (rmgpy.thermo.Wilhoit attribute) to_adjacency_list() (in module rmgpy.molecule.adjlist) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) (rmgpy.species.Species method)

to_arrhenius() (rmgpy.kinetics.MultiArrhenius method) to_arrhenius_ep() (rmgpy.kinetics.Arrhenius method) (rmgpy.kinetics.SurfaceArrhenius method) to_augmented_inchi() (rmgpy.molecule.Molecule method) to_augmented_inchi_key() (rmgpy.molecule.Molecule method) to_cantera() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) (rmgpy.species.Species method) (rmgpy.thermo.NASA method) to_cantera_kinetics() (rmgpy.kinetics.Arrhenius method) (rmgpy.kinetics.Lindemann method) (rmgpy.kinetics.SurfaceArrhenius method) (rmgpy.kinetics.Troe method) to_chemkin() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) (rmgpy.species.Species method) to_group() (rmgpy.molecule.Molecule method) to_html() (rmgpy.kinetics.Arrhenius method) (rmgpy.kinetics.Chebyshev method) (rmgpy.kinetics.KineticsData method) (rmgpy.kinetics.Lindemann method) (rmgpy.kinetics.MultiArrhenius method) (rmgpy.kinetics.MultiPDepArrhenius method) (rmgpy.kinetics.PDepArrhenius method) (rmgpy.kinetics.PDepKineticsData method) (rmgpy.kinetics.StickingCoefficient method) (rmgpy.kinetics.SurfaceArrhenius method) (rmgpy.kinetics.ThirdBody method) (rmgpy.kinetics.Troe method) to_inchi() (in module rmgpy.molecule.translator) (rmgpy.molecule.Molecule method) to_inchi_key() (in module rmgpy.molecule.translator) (rmgpy.molecule.Molecule method) to_labeled_str() (rmgpy.data.kinetics.DepositoryReaction method) (rmgpy.data.kinetics.LibraryReaction method) (rmgpy.data.kinetics.TemplateReaction method) (rmgpy.reaction.Reaction method) (rmgpy.rmg.pdep.PDepReaction method) to_nasa() (rmgpy.thermo.ThermoData method) (rmgpy.thermo.Wilhoit method) to_ob_mol() (in module rmgpy.molecule.converter) to_rdkit_mol() (in module rmgpy.molecule.converter) (rmgpy.molecule.Molecule method) to_single_bonds() (rmgpy.molecule.Molecule method) to_smarts() (in module rmgpy.molecule.translator) (rmgpy.molecule.Molecule method) to_smiles() (in module rmgpy.molecule.translator) (rmgpy.molecule.Molecule method) to_thermo_data() (rmgpy.thermo.NASA method) (rmgpy.thermo.Wilhoit method) to_wilhoit() (rmgpy.thermo.NASA method) (rmgpy.thermo.ThermoData method) TransitionState (class in rmgpy.species) Troe (class in rmgpy.kinetics)

U

uncertainty (rmgpy.kinetics.Arrhenius attribute) (rmgpy.kinetics.Chebyshev attribute) (rmgpy.kinetics.KineticsData attribute) (rmgpy.kinetics.Lindemann attribute) (rmgpy.kinetics.MultiArrhenius attribute) (rmgpy.kinetics.MultiPDepArrhenius attribute) (rmgpy.kinetics.PDepArrhenius attribute) (rmgpy.kinetics.PDepKineticsData attribute) (rmgpy.kinetics.StickingCoefficient attribute) (rmgpy.kinetics.SurfaceArrhenius attribute) (rmgpy.kinetics.ThirdBody attribute) (rmgpy.kinetics.Troe attribute) (rmgpy.quantity.ArrayQuantity attribute) (rmgpy.quantity.ScalarQuantity attribute) uncertainty_type (rmgpy.quantity.ArrayQuantity attribute) (rmgpy.quantity.ScalarQuantity attribute) UndeterminableKineticsError UnexpectedChargeError unique_id (rmgpy.qm.molecule.Geometry attribute) (rmgpy.qm.symmetry.SymmetryJob attribute) unique_id_long (rmgpy.qm.molecule.Geometry attribute)

unit_degeneracy() (in module rmgpy.statmech.schrodinger) unperturb() (arkane.sensitivity.KineticsSensitivity method) (arkane.sensitivity.PDepSensitivity method) update() (rmgpy.molecule.kekulize.AromaticBond method) (rmgpy.molecule.kekulize.AromaticRing method) (rmgpy.molecule.Molecule method) (rmgpy.rmg.pdep.PDepNetwork method) update_atomtypes() (rmgpy.molecule.Molecule method) update_charge() (rmgpy.molecule.Atom method) (rmgpy.molecule.Group method) update_configurations() (rmgpy.rmg.pdep.PDepNetwork method) update_connectivity_values() (rmgpy.molecule.graph.Graph method) (rmgpy.molecule.Group method) (rmgpy.molecule.Molecule method) update_fingerprint() (rmgpy.molecule.Group method) update_lone_pairs() (rmgpy.molecule.Molecule method) update_multiplicity() (rmgpy.molecule.Molecule method) update_reaction_threshold_and_react_flags() (rmgpy.rmg.main.RMG method) update_species_attributes() (arkane.common.ArkaneSpecies method) update_unimolecular_reaction_networks() (rmgpy.rmg.model.CoreEdgeReactionModel method) update_xyz_string() (arkane.common.ArkaneSpecies method)

V

value (rmgpy.quantity.ArrayQuantity attribute) (rmgpy.quantity.ScalarQuantity attribute) verify_output_file() (rmgpy.qm.gaussian.Gaussian method) (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.mopac.Mopac method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method)

Vertex (class in rmgpy.molecule.graph) VF2 (class in rmgpy.molecule.vf2) VF2Error visit() (arkane.output.PrettifyVisitor method) visit_Call() (arkane.output.PrettifyVisitor method) visit_Dict() (arkane.output.PrettifyVisitor method) visit_List() (arkane.output.PrettifyVisitor method) visit_Num() (arkane.output.PrettifyVisitor method) visit_Str() (arkane.output.PrettifyVisitor method) visit_Tuple() (arkane.output.PrettifyVisitor method) visit_UnaryOp() (arkane.output.PrettifyVisitor method)

W

Wigner (class in rmgpy.kinetics) Wilhoit (class in rmgpy.thermo) with_traceback() (rmgpy.exceptions.ActionError method) (rmgpy.exceptions.AtomTypeError method) (rmgpy.exceptions.ChemicallySignificantEigenvaluesError method) (rmgpy.exceptions.ChemkinError method) (rmgpy.exceptions.CollisionError method) (rmgpy.exceptions.CoreError method) (rmgpy.exceptions.DatabaseError method) (rmgpy.exceptions.DependencyError method) (rmgpy.exceptions.ElementError method) (rmgpy.exceptions.ForbiddenStructureException method) (rmgpy.exceptions.ILPSolutionError method) (rmgpy.exceptions.ImplicitBenzeneError method) (rmgpy.exceptions.InchiException method) (rmgpy.exceptions.InputError method) (rmgpy.exceptions.InvalidActionError method) (rmgpy.exceptions.InvalidAdjacencyListError method) (rmgpy.exceptions.InvalidMicrocanonicalRateError method) (rmgpy.exceptions.KekulizationError method) (rmgpy.exceptions.KineticsError method) (rmgpy.exceptions.ModifiedStrongCollisionError method) (rmgpy.exceptions.NegativeBarrierException method) (rmgpy.exceptions.NetworkError method) (rmgpy.exceptions.OutputError method) (rmgpy.exceptions.PressureDependenceError method) (rmgpy.exceptions.QuantityError method) (rmgpy.exceptions.ReactionError method) (rmgpy.exceptions.ReactionPairsError method) (rmgpy.exceptions.ReservoirStateError method) (rmgpy.exceptions.ResonanceError method) (rmgpy.exceptions.SettingsError method) (rmgpy.exceptions.SpeciesError method) (rmgpy.exceptions.StatmechError method) (rmgpy.exceptions.StatmechFitError method) (rmgpy.exceptions.UndeterminableKineticsError method) (rmgpy.exceptions.UnexpectedChargeError method) (rmgpy.exceptions.VF2Error method)

write_chemkin() (arkane.KineticsJob method) (arkane.ThermoJob method) write_input_file() (rmgpy.qm.gaussian.GaussianMol method) (rmgpy.qm.gaussian.GaussianMolPM3 method) (rmgpy.qm.gaussian.GaussianMolPM6 method) (rmgpy.qm.mopac.MopacMol method) (rmgpy.qm.mopac.MopacMolPM3 method) (rmgpy.qm.mopac.MopacMolPM6 method) (rmgpy.qm.mopac.MopacMolPM7 method) (rmgpy.qm.symmetry.SymmetryJob method) write_kinetics_entry() (in module rmgpy.chemkin) write_output() (arkane.KineticsJob method) (arkane.StatMechJob method) (arkane.ThermoJob method) write_thermo_entry() (in module rmgpy.chemkin)