Index

_

__call__() (autode.neb.idpp.IDPP method) __eq__() (autode.bond_rearrangement.BondRearrangement method) (autode.solvent.explicit_solvent.ExplicitSolvent method) (autode.solvent.solvents.Solvent method) __init__() (autode.atoms.Atom method) (autode.atoms.AtomCollection method) (autode.atoms.DummyAtom method) (autode.bond_rearrangement.BondRearrangement method) (autode.bonds.BreakingBond method) (autode.bonds.FormingBond method) (autode.bonds.ScannedBond method) (autode.conformers.conformer.Conformer method) (autode.exceptions.CouldNotGetProperty method) (autode.exceptions.UnsupportedCalculationInput method) (autode.hessians.HybridHessianCalculator method) (autode.hessians.NumericalHessianCalculator method) (autode.neb.ci.CImage method) (autode.neb.ci.CImages method) (autode.neb.ci.CINEB method) (autode.neb.idpp.IDPP method) (autode.neb.original.Image method) (autode.neb.original.Images method) (autode.neb.original.NEB method) (autode.opt.coordinates.primitives.CompositeBonds method) (autode.opt.coordinates.primitives.ConstrainedCompositeBonds method) (autode.opt.coordinates.primitives.ConstrainedPrimitiveBondAngle method) (autode.opt.coordinates.primitives.ConstrainedPrimitiveDistance method) (autode.opt.coordinates.primitives.LinearAngleBase method) (autode.opt.coordinates.primitives.Primitive method) (autode.opt.coordinates.primitives.PrimitiveBondAngle method) (autode.opt.coordinates.primitives.PrimitiveDihedralAngle method) (autode.opt.coordinates.primitives.PrimitiveDummyLinearAngle method) (autode.opt.optimisers.base.ConvergenceParams method) (autode.opt.optimisers.base.NDOptimiser method) (autode.opt.optimisers.base.Optimiser method) (autode.opt.optimisers.base.OptimiserHistory method) (autode.opt.optimisers.dimer.Dimer method) (autode.opt.optimisers.hessian_update.BFGSPDUpdate method) (autode.opt.optimisers.hessian_update.HessianUpdater method) (autode.opt.optimisers.prfo.PRFOptimiser method) (autode.opt.optimisers.rfo.RFOptimiser method) (autode.pes.pes_nd.PESnD method) (autode.pes.reactive.ReactivePESnD method) (autode.point_charges.PointCharge method) (autode.reactions.multistep.MultiStepReaction method) (autode.reactions.reaction.Reaction method) (autode.reactions.reaction_types.ReactionType method) (autode.smiles.angles.SAngle method) (autode.smiles.angles.SDihedral method) (autode.smiles.atom_types.AtomType method) (autode.smiles.atom_types.BentAtom method) (autode.smiles.atom_types.LinearAtom method) (autode.smiles.atom_types.OctahedralAtom method) (autode.smiles.atom_types.PentagonalBipyramidalAtom method) (autode.smiles.atom_types.SquareAntiprismAtom method) (autode.smiles.atom_types.SquarePlanarAtom method) (autode.smiles.atom_types.TerminalAtom method) (autode.smiles.atom_types.TetrahedralAtom method) (autode.smiles.atom_types.TetrahedralIAtom method) (autode.smiles.atom_types.TetrahedralNAtom method) (autode.smiles.atom_types.TrigonalAtom method) (autode.smiles.atom_types.TrigonalBipyramidalAtom method) (autode.smiles.atom_types.TrigonalPyramidalAtom method) (autode.smiles.base.RingBond method) (autode.smiles.base.SMILESAtom method) (autode.smiles.base.SMILESBond method) (autode.smiles.builder.Builder method) (autode.smiles.parser.Parser method) (autode.solvent.explicit_solvent.ExplicitSolvent method) (autode.solvent.solvents.Solvent method) (autode.species.complex.Complex method) (autode.species.complex.ProductComplex method) (autode.species.complex.ReactantComplex method) (autode.species.molecule.Molecule method) (autode.species.species.Species method) (autode.substitution.SubstitutionCentre method) (autode.transition_states.base.TSbase method) (autode.transition_states.templates.TStemplate method) (autode.transition_states.transition_state.TransitionState method) (autode.units.BaseUnit method) (autode.units.Unit method) (autode.utils.StringDict method) (autode.values.Allocation method) (autode.values.Angle method) (autode.values.Distance method) (autode.values.Energies method) (autode.values.Energy method) (autode.values.ForceConstant method) (autode.values.Frequency method) (autode.values.GradientRMS method) (autode.values.Mass method) (autode.values.MWDistance method) (autode.values.Temperature method) (autode.values.Value method) (autode.wrappers.G09.G09 method) (autode.wrappers.G09.G09Optimiser method) (autode.wrappers.keywords.ECP method) (autode.wrappers.keywords.Functional method) (autode.wrappers.keywords.Keyword method) (autode.wrappers.keywords.Keywords method) (autode.wrappers.keywords.KeywordsSet method) (autode.wrappers.keywords.MaxOptCycles method) (autode.wrappers.MOPAC.MOPAC method) (autode.wrappers.MOPAC.MOPACOptimiser method) (autode.wrappers.NWChem.NWChem method) (autode.wrappers.ORCA.ORCA method) (autode.wrappers.ORCA.ORCAOptimiser method) (autode.wrappers.XTB.XTB method) (autode.wrappers.XTB.XTBOptimiser method)

__str__() (autode.bond_rearrangement.BondRearrangement method) (autode.solvent.solvents.Solvent method) _set_distance_matrices() (autode.neb.idpp.IDPP method) _set_gradients() (autode.pes.reactive.ReactivePESnD method) _step() (autode.opt.optimisers.base.Optimiser method) (autode.opt.optimisers.dimer.Dimer method) (autode.opt.optimisers.prfo.PRFOptimiser method) (autode.opt.optimisers.rfo.RFOptimiser method) _updated_h (autode.opt.optimisers.hessian_update.BFGSDampedUpdate property) (autode.opt.optimisers.hessian_update.BFGSSR1Update property) (autode.opt.optimisers.hessian_update.BFGSUpdate property) (autode.opt.optimisers.hessian_update.BofillUpdate property) (autode.opt.optimisers.hessian_update.FlowchartUpdate property) (autode.opt.optimisers.hessian_update.HessianUpdater property) (autode.opt.optimisers.hessian_update.NullUpdate property) (autode.opt.optimisers.hessian_update.SR1Update property) _updated_h_inv (autode.opt.optimisers.hessian_update.BFGSSR1Update property) (autode.opt.optimisers.hessian_update.BFGSUpdate property) (autode.opt.optimisers.hessian_update.BofillUpdate property) (autode.opt.optimisers.hessian_update.FlowchartUpdate property) (autode.opt.optimisers.hessian_update.HessianUpdater property) (autode.opt.optimisers.hessian_update.NullUpdate property) (autode.opt.optimisers.hessian_update.SR1Update property)

A

a0 (in module autode.units) a02ang (autode.constants.Constants attribute) a0_to_ang (autode.constants.Constants attribute) a0_to_m (autode.constants.Constants attribute) abs_d_e (autode.opt.optimisers.base.ConvergenceParams attribute) actinides (autode.atoms.PeriodicTable attribute) actinoids (autode.atoms.PeriodicTable attribute) active_atoms (autode.bond_rearrangement.BondRearrangement property) active_bond_constraints (autode.transition_states.base.TSbase property) active_bonds (autode.mol_graphs.MolecularGraph property) active_indexes (autode.opt.coordinates.base.OptCoordinates property) (autode.opt.coordinates.cartesian.CartesianCoordinates property) (autode.opt.coordinates.dic.DIC property) (autode.opt.coordinates.dic.DICWithConstraints property) active_mol_indexes (autode.opt.coordinates.base.OptCoordinates property) add() (autode.opt.optimisers.base.OptimiserHistory method) add_active_edge() (autode.mol_graphs.MolecularGraph method) add_bond_rearrangment() (in module autode.bond_rearrangement) add_capping_atom() (in module autode.transition_states.truncation) add_capping_atoms() (in module autode.transition_states.truncation) add_core_pi_bonds() (in module autode.transition_states.truncation) add_dummy_atom() (in module autode.substitution) add_remaining_atoms() (in module autode.transition_states.truncation) add_remaining_bonds() (in module autode.transition_states.truncation) add_solvent_keyword() (autode.wrappers.ORCA.ORCA method) ALKENE_DOWN (autode.smiles.base.SMILESStereoChem attribute) ALKENE_UP (autode.smiles.base.SMILESStereoChem attribute) Allocation (class in autode.values) amu (in module autode.units) amu_ang_sq (in module autode.units) amu_to_kg (autode.constants.Constants attribute) amu_to_me (autode.constants.Constants attribute) ang (in module autode.units) ang2a0 (autode.constants.Constants attribute) ang_to_a0 (autode.constants.Constants attribute) ang_to_m (autode.constants.Constants attribute) ang_to_nm (autode.constants.Constants attribute) ang_to_pm (autode.constants.Constants attribute) Angle (class in autode.values) angle() (autode.atoms.AtomCollection method) append() (autode.smiles.base.SMILESBonds method) (autode.values.Energies method) (autode.wrappers.keywords.Keywords method) append_species() (autode.neb.original.Images method) are_coords_reasonable() (in module autode.geom) are_linear() (autode.atoms.Atoms method) are_planar() (autode.atoms.Atoms method) are_satisfied() (autode.opt.optimisers.base.ConvergenceParams method) atm_to_pa (autode.constants.Constants attribute) Atom (class in autode.atoms) atom_indexes (autode.smiles.base.SMILESBond property) atom_indexes() (autode.species.complex.Complex method) AtomCollection (class in autode.atoms) atomic_charge() (in module autode.smiles.parser) atomic_class() (in module autode.smiles.parser) atomic_masses (autode.species.species.Species property) atomic_n_hydrogens() (in module autode.smiles.parser) atomic_number (autode.atoms.Atom property) (autode.atoms.DummyAtom property) atomic_sterochem() (in module autode.smiles.parser) atomic_symbol (autode.atoms.Atom property) atomic_symbols (autode.reactions.reaction.Reaction property) (autode.species.species.Species property) atoms (autode.atoms.AtomCollection property) (autode.conformers.conformer.Conformer property) (autode.solvent.solvents.ImplicitSolvent property) (autode.solvent.solvents.Solvent property) (autode.species.complex.Complex property) (autode.species.species.Species property) Atoms (class in autode.atoms) atoms_from_rdkit_mol() (in module autode.conformers.conformers) atoms_to_xyz_file() (in module autode.input_output) AtomsNotFound AtomType (class in autode.smiles.atom_types) attack_cost() (in module autode.substitution) attrs_from_xyz_title_line() (in module autode.input_output) autode.atoms module autode.bond_rearrangement module autode.bonds module autode.config module autode.conformers.conf_gen module autode.conformers.conformer module autode.conformers.conformers module autode.constants module autode.exceptions module autode.geom module autode.hessians module autode.input_output module autode.log module autode.methods module autode.mol_graphs module autode.neb.ci module

autode.neb.idpp module autode.neb.neb module autode.neb.original module autode.opt.coordinates.base module autode.opt.coordinates.cartesian module autode.opt.coordinates.dic module autode.opt.coordinates.dimer module autode.opt.coordinates.primitives module autode.opt.optimisers.base module autode.opt.optimisers.dimer module autode.opt.optimisers.hessian_update module autode.opt.optimisers.prfo module autode.opt.optimisers.rfo module autode.pes.mep module autode.pes.pes_nd module autode.pes.reactive module autode.pes.relaxed module autode.pes.unrelaxed module autode.plotting module autode.point_charges module autode.reactions.multistep module autode.reactions.reaction module autode.reactions.reaction_types module autode.smiles.angles module autode.smiles.atom_types module autode.smiles.base module autode.smiles.builder module autode.smiles.parser module autode.smiles.smiles module autode.solvent.explicit_solvent module autode.solvent.solvents module autode.species.complex module autode.species.molecule module autode.species.species module autode.substitution module autode.thermochemistry.igm module autode.thermochemistry.symmetry module autode.transition_states.base module autode.transition_states.locate_tss module autode.transition_states.templates module autode.transition_states.transition_state module autode.transition_states.truncation module autode.transition_states.ts_guess module autode.units module autode.utils module autode.values module autode.wrappers.G09 module autode.wrappers.keywords module autode.wrappers.MOPAC module autode.wrappers.NWChem module autode.wrappers.ORCA module autode.wrappers.XTB module AutodeException axes (autode.smiles.angles.SAngles property) (autode.smiles.angles.SDihedrals property)

B

BaseOptimiser (class in autode.opt.optimisers.base) BaseUnit (class in autode.units) basis_set (autode.wrappers.keywords.Keywords property) BasisSet (class in autode.wrappers.keywords) batoms (autode.bond_rearrangement.BondRearrangement property) BEND (autode.opt.coordinates.primitives.LinearBendType attribute) BentAtom (class in autode.smiles.atom_types) BFGSDampedUpdate (class in autode.opt.optimisers.hessian_update) BFGSPDUpdate (class in autode.opt.optimisers.hessian_update) BFGSSR1Update (class in autode.opt.optimisers.hessian_update)

BFGSUpdate (class in autode.opt.optimisers.hessian_update) BofillUpdate (class in autode.opt.optimisers.hessian_update) bond_matrix (autode.species.species.Species property) BondRearrangement (class in autode.bond_rearrangement) BondsInSMILESAndGraphDontMatch BreakingBond (class in autode.bonds) bstring (autode.wrappers.keywords.Keywords property) build() (autode.smiles.builder.Builder method) Builder (class in autode.smiles.builder) built (autode.smiles.builder.Builder property) built_atom_idxs (autode.smiles.builder.Builder property)

C

c (autode.thermochemistry.igm.SIConstants attribute) c_in_cm (autode.constants.Constants attribute) calc_g_cont() (autode.species.species.Species method) calc_h_cont() (autode.species.species.Species method) calc_heavy_atom_rmsd() (in module autode.geom) calc_hessian() (autode.species.species.Species method) calc_multiplicity() (in module autode.smiles.smiles) calc_repulsion() (autode.species.complex.Complex method) calc_rmsd() (in module autode.geom) calc_thermo() (autode.species.species.Species method) calculate() (autode.hessians.HybridHessianCalculator method) (autode.hessians.NumericalHessianCalculator method) (autode.neb.original.NEB method) (autode.pes.pes_nd.PESnD method) calculate_complexes() (autode.reactions.reaction.Reaction method) calculate_reaction_profile() (autode.reactions.multistep.MultiStepReaction method) (autode.reactions.reaction.Reaction method) calculate_reaction_profile_energies() (in module autode.plotting) calculate_single_points() (autode.reactions.reaction.Reaction method) calculate_thermo_cont() (in module autode.thermochemistry.igm) calculate_thermochemical_cont() (autode.reactions.reaction.Reaction method) CalculationException CannotSplitAcrossBond canonical_atoms (autode.smiles.builder.Builder property) canonical_atoms_at_origin (autode.smiles.builder.Builder property) cart_proj_g (autode.opt.coordinates.base.OptCoordinates property) (autode.opt.coordinates.cartesian.CartesianCoordinates property) (autode.opt.coordinates.dic.DIC property) (autode.opt.coordinates.dic.DICWithConstraints property) CartesianCoordinates (class in autode.opt.coordinates.cartesian) centre() (autode.species.species.Species method) charge (autode.smiles.parser.Parser property) (autode.species.species.Species property) check_bonds() (in module autode.smiles.smiles) check_sufficient_memory() (in module autode.utils) checkpoint_rxn_profile_step() (in module autode.utils) CImage (class in autode.neb.ci) CImages (class in autode.neb.ci) CINEB (class in autode.neb.ci) classify() (in module autode.reactions.reaction_types) clean_up() (autode.opt.optimisers.base.NDOptimiser method) (autode.opt.optimisers.base.OptimiserHistory method) cleanup_after_timeout() (in module autode.utils) clear() (autode.pes.pes_nd.PESnD method) clear_tensors() (autode.opt.coordinates.base.OptCoordinates method) close() (autode.opt.optimisers.base.OptimiserHistory method) (autode.smiles.base.RingBond method) cn_and_axes() (in module autode.thermochemistry.symmetry) com (autode.atoms.AtomCollection property) (autode.atoms.Atoms property) COMPLEMENT (autode.opt.coordinates.primitives.LinearBendType attribute) Complex (class in autode.species.complex) CompositeBonds (class in autode.opt.coordinates.primitives) conditions_met (autode.opt.optimisers.hessian_update.BFGSPDUpdate property) (autode.opt.optimisers.hessian_update.BFGSSR1Update property) (autode.opt.optimisers.hessian_update.BFGSUpdate property) (autode.opt.optimisers.hessian_update.BofillUpdate property) (autode.opt.optimisers.hessian_update.FlowchartUpdate property) (autode.opt.optimisers.hessian_update.HessianUpdater property) (autode.opt.optimisers.hessian_update.NullUpdate property) (autode.opt.optimisers.hessian_update.SR1Update property)

Conformer (class in autode.conformers.conformer) conformers (autode.species.species.Species property) Conformers (class in autode.conformers.conformers) connected_components() (autode.mol_graphs.MolecularGraph method) (in module autode.mol_graphs) Constants (class in autode.constants) ConstrainedCompositeBonds (class in autode.opt.coordinates.primitives) ConstrainedPrimitive (class in autode.opt.coordinates.primitives) ConstrainedPrimitiveBondAngle (class in autode.opt.coordinates.primitives) ConstrainedPrimitiveDistance (class in autode.opt.coordinates.primitives) contain_any_of() (autode.wrappers.keywords.Keywords method) contain_metals (autode.atoms.Atoms property) conv_params() (autode.opt.optimisers.base.OptimiserHistory method) conv_tol (autode.opt.optimisers.base.NDOptimiser property) converged (autode.opt.optimisers.base.BaseOptimiser property) (autode.opt.optimisers.base.ExternalOptimiser property) (autode.opt.optimisers.base.NDOptimiser property) (autode.opt.optimisers.base.NullOptimiser property) (autode.opt.optimisers.base.Optimiser property) (autode.opt.optimisers.dimer.Dimer property) (autode.wrappers.G09.G09Optimiser property) (autode.wrappers.MOPAC.MOPACOptimiser property) (autode.wrappers.ORCA.ORCAOptimiser property) (autode.wrappers.XTB.XTBOptimiser property) converged_line_in_output() (autode.wrappers.XTB.XTB static method) ConvergenceParams (class in autode.opt.optimisers.base) coord (autode.atoms.Atom property) Coordinate (class in autode.values) coordinates (autode.atoms.AtomCollection property) (autode.atoms.Atoms property) (autode.conformers.conformer.Conformer property) (autode.species.species.Species property) Coordinates (class in autode.values) coordinates_from() (autode.wrappers.G09.G09 method) (autode.wrappers.MOPAC.MOPAC method) (autode.wrappers.NWChem.NWChem method) (autode.wrappers.ORCA.ORCA method) (autode.wrappers.XTB.XTB method) CoordinateTransformFailed coords() (autode.neb.original.Images method) copy() (autode.atoms.Atom method) (autode.atoms.Atoms method) (autode.conformers.conformers.Conformers method) (autode.hessians.Hessian method) (autode.neb.original.Images method) (autode.opt.coordinates.base.OptCoordinates method) (autode.solvent.solvents.Solvent method) (autode.species.species.Species method) (autode.values.Energies method) (autode.values.Value method) (autode.wrappers.keywords.Keywords method) (autode.wrappers.keywords.KeywordsSet method) could_have_correct_imag_mode (autode.transition_states.base.TSbase property) CouldNotGetProperty CouldNotPlotSmoothProfile covalent_radius (autode.atoms.Atom property) (autode.atoms.DummyAtom property) create_pcoords() (in module autode.thermochemistry.symmetry)

D

deg (in module autode.units) delta (autode.opt.coordinates.dimer.DimerCoordinates property) delta() (autode.opt.coordinates.primitives.ConstrainedPrimitive method) (autode.reactions.reaction.Reaction method) deprecated() (in module autode.utils) derivative() (autode.opt.coordinates.primitives.Primitive method) (in module autode.neb.original) DIC (class in autode.opt.coordinates.dic) DICWithConstraints (class in autode.opt.coordinates.dic) did_rotation (autode.opt.coordinates.dimer.DimerCoordinates property) did_translation (autode.opt.coordinates.dimer.DimerCoordinates property) dielectric (autode.solvent.solvents.Solvent property) dihedral() (autode.atoms.AtomCollection method) Dimer (class in autode.opt.optimisers.dimer) DimerCoordinates (class in autode.opt.coordinates.dimer)

DimerPoint (class in autode.opt.coordinates.dimer) dispersion (autode.wrappers.keywords.Keywords property) DispersionCorrection (class in autode.wrappers.keywords) displaced_species_along_mode() (in module autode.transition_states.base) dist (autode.opt.coordinates.dimer.DimerCoordinates property) Distance (class in autode.values) distance() (autode.atoms.AtomCollection method) (autode.atoms.Atoms method) (autode.smiles.base.SMILESBond method) dm_to_m (autode.constants.Constants attribute) doi_str (autode.wrappers.keywords.Keyword property) dphi() (autode.smiles.angles.SDihedral method) dr (autode.bonds.ScannedBond property) DummyAtom (class in autode.atoms) dvalues() (autode.smiles.angles.SAngles method)

E

e (autode.opt.coordinates.base.OptCoordinates property) ecp (autode.wrappers.keywords.Keywords property) ECP (class in autode.wrappers.keywords) ecp_block() (in module autode.wrappers.NWChem) element() (autode.atoms.PeriodicTable class method) empty_site() (autode.smiles.atom_types.AtomType method) (autode.smiles.atom_types.TetrahedralIAtom method) empty_site_mr() (autode.smiles.atom_types.AtomType method) end_idxs (autode.smiles.angles.SDihedral property) energies (autode.species.species.Species attribute) Energies (class in autode.values) energy (autode.species.species.Species property) Energy (class in autode.values) energy_gradient() (in module autode.neb.original) energy_unit_from_name() (in module autode.units) EnergyArray (class in autode.values) enthalpy (autode.species.species.Species property) Enthalpy (class in autode.values)

EnthalpyCont (class in autode.values) eqm_bond_distance() (autode.atoms.AtomCollection method) (autode.atoms.Atoms method) eqm_bond_distance_matrix (autode.mol_graphs.MolecularGraph property) error_on_stationary_points() (in module autode.plotting) ev (in module autode.units) eV2ha (autode.constants.Constants attribute) ev_per_ang (in module autode.units) eV_to_ha (autode.constants.Constants attribute) execute() (autode.wrappers.G09.G09 method) (autode.wrappers.MOPAC.MOPAC method) (autode.wrappers.NWChem.NWChem method) (autode.wrappers.ORCA.ORCA method) (autode.wrappers.XTB.XTB method) expected_number_of_dof (autode.opt.coordinates.cartesian.CartesianCoordinates property) expected_planar_geometry (autode.mol_graphs.MolecularGraph property) explicitly_solvate() (autode.species.species.Species method) ExplicitSolvent (class in autode.solvent.explicit_solvent) ExternalOptimiser (class in autode.opt.optimisers.base)

F

f_r (autode.opt.coordinates.dimer.DimerCoordinates property) f_t (autode.opt.coordinates.dimer.DimerCoordinates property) FailedToAdjustAngles FailedToSetRotationIdxs fatoms (autode.bond_rearrangement.BondRearrangement property) filename (autode.transition_states.templates.TStemplate property) final (autode.opt.optimisers.base.OptimiserHistory property) final_coordinates (autode.opt.optimisers.base.BaseOptimiser property) (autode.opt.optimisers.base.NullOptimiser property) (autode.opt.optimisers.base.Optimiser property) find_cycles() (in module autode.mol_graphs) find_lowest_energy_conformer() (autode.species.species.Species method) find_lowest_energy_conformers() (autode.reactions.reaction.Reaction method) find_lowest_energy_ts_conformer() (autode.reactions.reaction.Reaction method) (autode.transition_states.transition_state.TransitionState method) find_rot_idxs() (autode.smiles.angles.SAngle method) (autode.smiles.angles.SDihedral method) find_tss() (in module autode.transition_states.locate_tss) first() (autode.values.Energies method) first_involving() (autode.smiles.base.SMILESBonds method) first_potential (autode.values.Energies property) FlowchartUpdate (class in autode.opt.optimisers.hessian_update) ForceConstant (class in autode.values)

FormingBond (class in autode.bonds) formula (autode.species.species.Species property) forward_backward_isomorphic_to_reactant_product() (in module autode.transition_states.base) free_energy (autode.species.species.Species property) FreeEnergy (class in autode.values) FreeEnergyCont (class in autode.values) frequencies (autode.hessians.Hessian property) (autode.species.species.Species property) frequencies_proj (autode.hessians.Hessian property) Frequency (class in autode.values) from_cartesian() (autode.opt.coordinates.dic.DIC class method) (autode.opt.coordinates.dic.DICWithConstraints class method) from_checkpoint() (autode.reactions.reaction.Reaction class method) from_end_points() (autode.neb.original.NEB class method) from_file() (autode.neb.original.NEB class method) (autode.opt.optimisers.base.NDOptimiser class method) (autode.pes.pes_nd.PESnD class method) from_list() (autode.neb.original.NEB class method) from_preset() (autode.opt.optimisers.base.ConvergenceParams class method) from_species() (autode.opt.coordinates.dimer.DimerCoordinates class method) (autode.transition_states.transition_state.TransitionState class method) (autode.transition_states.ts_guess.TSguess class method) functional (autode.wrappers.keywords.Keywords property) Functional (class in autode.wrappers.keywords)

G

g (autode.opt.coordinates.base.OptCoordinates property) (autode.opt.coordinates.dic.DICWithConstraints property) g0 (autode.opt.coordinates.dimer.DimerCoordinates property) G09 (class in autode.wrappers.G09) G09Optimiser (class in autode.wrappers.G09) g1 (autode.opt.coordinates.dimer.DimerCoordinates property) g2 (autode.opt.coordinates.dimer.DimerCoordinates property) g_at() (autode.opt.coordinates.dimer.DimerCoordinates method) g_cont (autode.species.species.Species property) GB (in module autode.units) generate_input_for() (autode.wrappers.G09.G09 method) (autode.wrappers.MOPAC.MOPAC method) (autode.wrappers.NWChem.NWChem method) (autode.wrappers.ORCA.ORCA method) (autode.wrappers.XTB.XTB method) generate_rearranged_graph() (in module autode.bond_rearrangement) get() (autode.utils.StringDict method) get_active_atom_neighbour_lists() (autode.bond_rearrangement.BondRearrangement method) get_atoms_and_fixed_atom_indexes() (in module autode.wrappers.MOPAC) get_bond_rearrangs() (in module autode.bond_rearrangement) get_bond_rearrangs_from_file() (in module autode.bond_rearrangement) get_bond_type_list() (in module autode.mol_graphs) get_complex_conformer_atoms() (in module autode.species.complex) get_cost_rotate_translate() (in module autode.substitution) get_defined_method() (in module autode.methods) get_fbonds() (in module autode.mol_graphs) get_fbonds_bbonds_1b() (in module autode.bond_rearrangement) get_fbonds_bbonds_1b1f() (in module autode.bond_rearrangement) get_fbonds_bbonds_2b() (in module autode.bond_rearrangement) get_fbonds_bbonds_2b1f() (in module autode.bond_rearrangement) get_fbonds_bbonds_2b2f() (in module autode.bond_rearrangement) get_first_available_method() (in module autode.methods) get_force() (autode.neb.ci.CImage method) (autode.neb.original.Image method) get_graph_no_active_edges() (in module autode.mol_graphs) get_graphs_ignoring_active_edges() (in module autode.mol_graphs) get_hmethod() (in module autode.methods) get_keywords() (autode.wrappers.ORCA.ORCA method) (in module autode.wrappers.MOPAC) (in module autode.wrappers.NWChem) get_lmethod() (in module autode.methods) get_mapping() (in module autode.mol_graphs) get_mapping_ts_template() (in module autode.mol_graphs)

get_neighbour_list() (in module autode.geom) get_opt_params() (autode.opt.optimisers.base.OptimiserHistory method) get_points_on_sphere() (in module autode.geom) get_possible_axes() (in module autode.thermochemistry.symmetry) get_reaction_profile_warnings() (in module autode.plotting) get_rot_mat_euler() (in module autode.geom) get_rot_mat_euler_from_terms() (in module autode.geom) get_rot_mat_kabsch() (in module autode.geom) get_separate_subgraphs() (in module autode.mol_graphs) get_simanl_atoms() (in module autode.conformers.conf_gen) get_simanl_conformer() (in module autode.conformers.conf_gen) get_solvent() (in module autode.solvent.solvents) get_stationary_points() (in module autode.plotting) get_substc_and_add_dummy_atoms() (in module autode.substitution) get_template_ts_guess() (in module autode.transition_states.ts_guess) get_total_memory() (in module autode.utils) get_truncated_active_mol_graph() (in module autode.mol_graphs) get_truncated_species() (in module autode.transition_states.truncation) get_truncated_ts() (in module autode.transition_states.locate_tss) get_ts() (in module autode.transition_states.locate_tss) get_ts_guess_neb() (in module autode.neb.neb) get_ts_template_folder_path() (in module autode.transition_states.templates) get_ts_templates() (in module autode.transition_states.templates) get_value_from_file() (in module autode.transition_states.templates) get_values_dict_from_file() (in module autode.transition_states.templates) gm_is_isomorphic() (in module autode.mol_graphs) grad (autode.wrappers.keywords.KeywordsSet property) grad() (autode.neb.idpp.IDPP method) gradient (autode.neb.original.Image property) (autode.species.species.Species property) Gradient (class in autode.values) gradient_from() (autode.wrappers.G09.G09 method) (autode.wrappers.MOPAC.MOPAC method) (autode.wrappers.NWChem.NWChem method) (autode.wrappers.ORCA.ORCA method) (autode.wrappers.XTB.XTB method) GradientKeywords (class in autode.wrappers.keywords) GradientRMS (class in autode.values) graph (autode.species.species.Species property) graph_has_correct_structure() (autode.transition_states.templates.TStemplate method) graph_matcher() (in module autode.mol_graphs) grimme (autode.thermochemistry.igm.LFMethod attribute) group (autode.atoms.Atom property) group() (autode.atoms.PeriodicTable class method)

H

h (autode.opt.coordinates.base.OptCoordinates property) (autode.opt.coordinates.dic.DICWithConstraints property) (autode.thermochemistry.igm.SIConstants attribute) h_cont (autode.species.species.Species property) h_inv (autode.opt.coordinates.base.OptCoordinates property) h_or_h_inv_has_correct_shape() (autode.opt.coordinates.base.OptCoordinates method) ha (in module autode.units) ha2eV (autode.constants.Constants attribute) ha2kcalmol (autode.constants.Constants attribute) ha2kJmol (autode.constants.Constants attribute) ha_per_a0 (in module autode.units) ha_per_a0_sq (in module autode.units) ha_per_ang_sq (in module autode.units) ha_to_eV (autode.constants.Constants attribute) ha_to_J (autode.constants.Constants attribute) ha_to_kcalmol (autode.constants.Constants attribute) ha_to_kJmol (autode.constants.Constants attribute) has_correct_imag_mode (autode.transition_states.base.TSbase property) has_identical_composition_as() (autode.reactions.reaction.Reaction method) (autode.species.species.Species method)

has_imaginary_frequencies (autode.transition_states.base.TSbase property) has_matching_ts_templates() (in module autode.transition_states.ts_guess) has_only_name (autode.wrappers.keywords.Keyword property) has_reasonable_coordinates (autode.species.species.Species property) has_same_connectivity_as() (autode.species.species.Species method) has_stereochem (autode.smiles.base.SMILESAtom property) has_valid_spin_state (autode.species.species.Species property) hashable() (in module autode.utils) hess (autode.wrappers.keywords.KeywordsSet property) hessian (autode.hessians.NumericalHessianCalculator property) (autode.species.species.Species property) Hessian (class in autode.hessians) hessian_from() (autode.wrappers.G09.G09 method) (autode.wrappers.NWChem.NWChem method) (autode.wrappers.ORCA.ORCA method) HessianKeywords (class in autode.wrappers.keywords) HessianUpdater (class in autode.opt.optimisers.hessian_update) HybridHessianCalculator (class in autode.hessians) hz (in module autode.units)

I

iadd() (autode.opt.coordinates.base.OptCoordinates method) (autode.opt.coordinates.cartesian.CartesianCoordinates method) (autode.opt.coordinates.dic.DIC method) (autode.opt.coordinates.dic.DICWithConstraints method) (autode.opt.coordinates.dimer.DimerCoordinates method) ideal_angles (autode.smiles.angles.SAngles property) IDPP (class in autode.neb.idpp) idpp_relax() (autode.neb.original.NEB method) idxs_are_present() (autode.atoms.Atoms method) igm (autode.thermochemistry.igm.LFMethod attribute) imag_mode_generates_other_bonds() (in module autode.transition_states.base) imag_mode_has_correct_displacement() (autode.transition_states.base.TSbase method) imag_mode_links_reactant_products() (autode.transition_states.base.TSbase method) Image (class in autode.neb.original) Images (class in autode.neb.original) imaginary_frequencies (autode.species.species.Species property) implemented_units (autode.hessians.Hessian attribute) (autode.opt.coordinates.base.OptCoordinates attribute) (autode.opt.coordinates.dimer.DimerCoordinates attribute) (autode.values.Allocation attribute) (autode.values.Angle attribute) (autode.values.Coordinate attribute) (autode.values.Coordinates attribute) (autode.values.Distance attribute) (autode.values.Energy attribute) (autode.values.EnergyArray attribute) (autode.values.ForceConstant attribute) (autode.values.Frequency attribute) (autode.values.Gradient attribute) (autode.values.GradientRMS attribute) (autode.values.Mass attribute) (autode.values.MomentOfInertia attribute) (autode.values.MWDistance attribute) (autode.values.Temperature attribute) (autode.values.Value attribute) (autode.values.ValueArray attribute) ImplicitSolvent (class in autode.solvent.solvents) ImplicitSolventType (class in autode.wrappers.keywords) in_ring() (autode.smiles.base.RingBond method) (autode.smiles.base.SMILESBond method) inactive_indexes (autode.opt.coordinates.base.OptCoordinates property) (autode.opt.coordinates.cartesian.CartesianCoordinates property) (autode.opt.coordinates.dic.DIC property) (autode.opt.coordinates.dic.DICWithConstraints property)

increment() (autode.neb.ci.CImages method) (autode.neb.original.Images method) indexes (autode.opt.coordinates.base.OptCoordinates property) init_k (autode.neb.original.NEB property) init_organic_smiles() (in module autode.smiles.smiles) init_smiles() (in module autode.smiles.smiles) input_filename_for() (autode.wrappers.G09.G09 static method) (autode.wrappers.MOPAC.MOPAC static method) (autode.wrappers.NWChem.NWChem static method) (autode.wrappers.ORCA.ORCA static method) (autode.wrappers.XTB.XTB static method) insert() (autode.smiles.base.SMILESBonds method) InvalidSmilesString inverse_rot_idxs() (autode.smiles.angles.SAngle method) invert_stereochem() (autode.smiles.base.SMILESAtom method) involving() (autode.smiles.base.SMILESBonds method) is_aromatic (autode.smiles.base.SMILESAtom property) is_barrierless (autode.reactions.reaction.Reaction property) is_cis() (autode.smiles.base.SMILESBond method) is_connected (autode.mol_graphs.MolecularGraph property) is_constrained (autode.opt.coordinates.primitives.ConstrainedPrimitive attribute) (autode.opt.coordinates.primitives.Primitive attribute) is_explicit (autode.solvent.solvents.Solvent property) is_explicitly_solvated (autode.species.species.Species property) is_imaginary (autode.values.Frequency property) is_implicit (autode.solvent.explicit_solvent.ExplicitSolvent property) (autode.solvent.solvents.ImplicitSolvent property) (autode.solvent.solvents.Solvent property) is_implicitly_solvated (autode.species.species.Species property) is_isomorphic_to() (autode.mol_graphs.MolecularGraph method) is_linear() (autode.species.species.Species method) is_metal (autode.atoms.Atom property) is_pi() (autode.atoms.Atom method) (autode.smiles.base.SMILESAtom method) is_planar() (autode.species.species.Species method) is_same_under_n_fold() (in module autode.thermochemistry.symmetry) is_satisfied() (autode.opt.coordinates.primitives.ConstrainedPrimitive method) is_shifted (autode.smiles.base.SMILESAtom property) is_subgraph_isomorphic() (in module autode.mol_graphs) is_trans() (autode.smiles.base.SMILESBond method) is_true_ts (autode.transition_states.transition_state.TransitionState property) is_v5 (autode.wrappers.ORCA.ORCA property) is_worth_truncating() (in module autode.transition_states.truncation) iteration (autode.neb.original.Image attribute) (autode.opt.optimisers.base.Optimiser property)

J

J (in module autode.units) J_per_ang_sq (in module autode.units)

J_per_ang_sq_kg (in module autode.units) J_per_m_sq (in module autode.units) J_to_ha (autode.constants.Constants attribute)

K

k_b (autode.thermochemistry.igm.SIConstants attribute) kcal2kJ (autode.constants.Constants attribute) kcal_to_kJ (autode.constants.Constants attribute) kcalmol (in module autode.units)

Keyword (class in autode.wrappers.keywords) Keywords (class in autode.wrappers.keywords) KeywordsSet (class in autode.wrappers.keywords) kg (in module autode.units) kjmol (in module autode.units)

L

lanthanides (autode.atoms.PeriodicTable attribute) lanthanoids (autode.atoms.PeriodicTable attribute) last() (autode.values.Energies method) last_energy_change (autode.opt.optimisers.base.BaseOptimiser property) (autode.opt.optimisers.base.ExternalOptimiser property) (autode.opt.optimisers.base.NullOptimiser property) (autode.opt.optimisers.base.Optimiser property) (autode.wrappers.G09.G09Optimiser property) (autode.wrappers.MOPAC.MOPACOptimiser property) (autode.wrappers.ORCA.ORCAOptimiser property) (autode.wrappers.XTB.XTBOptimiser property) last_potential (autode.values.Energies property) left (autode.opt.coordinates.dimer.DimerPoint attribute) LFMethod (class in autode.thermochemistry.igm)

LinearAngleBase (class in autode.opt.coordinates.primitives) LinearAtom (class in autode.smiles.atom_types) LinearBendType (class in autode.opt.coordinates.primitives) load() (autode.opt.optimisers.base.OptimiserHistory class method) (autode.pes.pes_nd.PESnD method) (autode.reactions.reaction.Reaction method) (autode.transition_states.templates.TStemplate method) locate_transition_state() (autode.reactions.reaction.Reaction method) log_time() (in module autode.utils) low_opt (autode.wrappers.keywords.KeywordsSet property) low_sp (autode.wrappers.keywords.KeywordsSet property) lower() (autode.units.Unit method) (autode.wrappers.keywords.Keyword method) lowest_energy (autode.conformers.conformers.Conformers property)

M

m (in module autode.units) m_e (in module autode.units) make_graph() (in module autode.mol_graphs) make_hessian_positive_definite() (autode.opt.coordinates.base.OptCoordinates method) mass (autode.atoms.Atom property) (autode.atoms.AtomCollection property) (autode.atoms.DummyAtom property) Mass (class in autode.values) max_atom_distance_between_images (autode.neb.original.NEB property) max_g (autode.opt.optimisers.base.ConvergenceParams attribute) max_opt_cycles (autode.wrappers.keywords.OptKeywords property) max_ring_n (autode.smiles.builder.Builder property) max_s (autode.opt.optimisers.base.ConvergenceParams attribute) maximal_valance (autode.atoms.Atom property) MaxOptCycles (class in autode.wrappers.keywords) MB (in module autode.units) meets_criteria() (autode.opt.optimisers.base.ConvergenceParams method) method_or_default_hmethod() (in module autode.methods) method_or_default_lmethod() (in module autode.methods) method_string (autode.wrappers.keywords.Keywords property) method_string() (in module autode.values) MethodUnavailable midpoint (autode.opt.coordinates.dimer.DimerPoint attribute) min_eigval (autode.opt.coordinates.base.OptCoordinates property) min_update_tol (autode.opt.optimisers.hessian_update.BofillUpdate attribute) minenkov (autode.thermochemistry.igm.LFMethod attribute) module autode.atoms autode.bond_rearrangement autode.bonds autode.config autode.conformers.conf_gen autode.conformers.conformer autode.conformers.conformers autode.constants autode.exceptions autode.geom autode.hessians autode.input_output autode.log autode.methods autode.mol_graphs autode.neb.ci autode.neb.idpp autode.neb.neb autode.neb.original autode.opt.coordinates.base autode.opt.coordinates.cartesian autode.opt.coordinates.dic autode.opt.coordinates.dimer autode.opt.coordinates.primitives autode.opt.optimisers.base autode.opt.optimisers.dimer autode.opt.optimisers.hessian_update autode.opt.optimisers.prfo autode.opt.optimisers.rfo autode.pes.mep autode.pes.pes_nd autode.pes.reactive autode.pes.relaxed autode.pes.unrelaxed autode.plotting autode.point_charges autode.reactions.multistep autode.reactions.reaction autode.reactions.reaction_types autode.smiles.angles autode.smiles.atom_types autode.smiles.base autode.smiles.builder autode.smiles.parser autode.smiles.smiles autode.solvent.explicit_solvent autode.solvent.solvents autode.species.complex autode.species.molecule autode.species.species autode.substitution autode.thermochemistry.igm autode.thermochemistry.symmetry autode.transition_states.base autode.transition_states.locate_tss autode.transition_states.templates autode.transition_states.transition_state autode.transition_states.truncation autode.transition_states.ts_guess autode.units autode.utils autode.values autode.wrappers.G09 autode.wrappers.keywords autode.wrappers.MOPAC autode.wrappers.NWChem autode.wrappers.ORCA autode.wrappers.XTB

moi (autode.atoms.AtomCollection property) (autode.atoms.Atoms property) MolecularGraph (class in autode.mol_graphs) Molecule (class in autode.species.molecule) MomentOfInertia (class in autode.values) MOPAC (class in autode.wrappers.MOPAC) MOPACOptimiser (class in autode.wrappers.MOPAC) mult (autode.smiles.parser.Parser property) (autode.species.species.Species property) MultiStepReaction (class in autode.reactions.multistep) MWDistance (class in autode.values)

N

n_a (autode.constants.Constants attribute) n_atoms (autode.atoms.AtomCollection property) (autode.smiles.parser.Parser property) n_bbonds (autode.bond_rearrangement.BondRearrangement property) n_bonded (autode.smiles.base.SMILESAtom property) n_bonds (autode.smiles.parser.Parser property) n_conformers (autode.species.species.Species property) n_constraints (autode.opt.coordinates.base.OptCoordinates property) (autode.opt.coordinates.cartesian.CartesianCoordinates property) n_empty_sites (autode.smiles.atom_types.AtomType property) n_fbonds (autode.bond_rearrangement.BondRearrangement property) n_involving() (autode.smiles.base.SMILESBonds method) n_membered_rings() (autode.bond_rearrangement.BondRearrangement method) n_molecules (autode.species.complex.Complex property) n_satisfied_constraints (autode.opt.coordinates.base.OptCoordinates property) (autode.opt.coordinates.cartesian.CartesianCoordinates property) n_solvent_molecules (autode.solvent.explicit_solvent.ExplicitSolvent property) n_steps (autode.reactions.multistep.MultiStepReaction property) n_tr (autode.hessians.Hessian property) n_v (autode.hessians.Hessian property) NCIComplex (class in autode.species.complex) ndim (autode.pes.pes_nd.PESnD property) NDOptimiser (class in autode.opt.optimisers.base) NEB (class in autode.neb.original)

needs_forcing() (autode.smiles.angles.SDihedral method) new_species() (autode.species.species.Species method) next_char() (in module autode.smiles.parser) nm (in module autode.units) no_exceptions() (in module autode.utils) NoAtomsInMolecule NoCalculationOutput NoConformers node_matcher (autode.mol_graphs.MolecularGraph property) NoInputError NoMapping NoMolecularGraph non_bonded_idx_matrix (autode.smiles.builder.Builder property) NONE (autode.smiles.base.SMILESStereoChem attribute) normal_mode() (autode.species.species.Species method) normal_modes (autode.hessians.Hessian property) normal_modes_proj (autode.hessians.Hessian property) NotImplementedInMethod NullOptimiser (class in autode.opt.optimisers.base) NullUpdate (class in autode.opt.optimisers.hessian_update) NumericalHessianCalculator (class in autode.hessians) NumericStringDict (class in autode.utils) nvector() (autode.atoms.Atoms method) NWChem (class in autode.wrappers.NWChem)

O

OctahedralAtom (class in autode.smiles.atom_types) open() (autode.opt.optimisers.base.OptimiserHistory method) opt (autode.wrappers.keywords.KeywordsSet property) opt_ts (autode.wrappers.keywords.KeywordsSet property) OptCoordinates (class in autode.opt.coordinates.base) optimise() (autode.conformers.conformer.Conformer method) (autode.conformers.conformers.Conformers method) (autode.opt.optimisers.base.NDOptimiser class method) (autode.opt.optimisers.base.Optimiser class method) (autode.opt.optimisers.dimer.Dimer class method) (autode.species.species.Species method) (autode.transition_states.transition_state.TransitionState method) optimise_reacs_prods() (autode.reactions.reaction.Reaction method) Optimiser (class in autode.opt.optimisers.base) optimiser_from() (autode.wrappers.G09.G09 method) (autode.wrappers.MOPAC.MOPAC method) (autode.wrappers.ORCA.ORCA method) (autode.wrappers.XTB.XTB method)

optimiser_params (autode.opt.optimisers.base.NDOptimiser property) (autode.opt.optimisers.base.Optimiser property) OptimiserHistory (class in autode.opt.optimisers.base) OptimiserStepError OptKeywords (class in autode.wrappers.keywords) OptTSKeywords (class in autode.wrappers.keywords) ORCA (class in autode.wrappers.ORCA) ORCAOptimiser (class in autode.wrappers.ORCA) origin (autode.pes.pes_nd.PESnD property) origins (autode.smiles.angles.SAngles property) (autode.smiles.angles.SDihedrals property) output_filename_for() (autode.wrappers.G09.G09 static method) (autode.wrappers.MOPAC.MOPAC static method) (autode.wrappers.NWChem.NWChem static method) (autode.wrappers.ORCA.ORCA static method) (autode.wrappers.XTB.XTB static method)

P

parse() (autode.smiles.parser.Parser method) parsed (autode.smiles.parser.Parser property) Parser (class in autode.smiles.parser) partial_charges (autode.species.species.Species property) partial_charges_from() (autode.wrappers.G09.G09 method) (autode.wrappers.MOPAC.MOPAC method) (autode.wrappers.NWChem.NWChem method) (autode.wrappers.ORCA.ORCA method) (autode.wrappers.XTB.XTB method) partition() (autode.neb.original.NEB method) peak_point() (in module autode.pes.mep) peak_species (autode.neb.original.NEB property) PentagonalBipyramidalAtom (class in autode.smiles.atom_types) penultimate (autode.opt.optimisers.base.OptimiserHistory property) per_cm_to_hz (autode.constants.Constants attribute) period (autode.atoms.Atom property) period() (autode.atoms.PeriodicTable class method) PeriodicTable (class in autode.atoms) PESnD (class in autode.pes.pes_nd) phi (autode.opt.coordinates.dimer.DimerCoordinates property) phi0 (autode.smiles.angles.SAngle property) (autode.smiles.angles.SDihedral property) plot() (autode.pes.pes_nd.PESnD method) plot_bracket_method_energy_profile() (in module autode.plotting) plot_energies() (autode.neb.original.Images method) plot_optimisation() (autode.opt.optimisers.base.NDOptimiser method) plot_optimiser_profile() (in module autode.plotting) plot_points() (in module autode.plotting) plot_reaction_profile() (in module autode.plotting) plot_smooth_profile() (in module autode.plotting) pm (in module autode.units) PointCharge (class in autode.point_charges) populate_conformers() (autode.species.complex.Complex method) (autode.species.molecule.Molecule method) (autode.species.species.Species method) PotentialEnergy (class in autode.values) pred_quad_delta_e() (autode.opt.coordinates.base.OptCoordinates method)

PRFOptimiser (class in autode.opt.optimisers.prfo) Primitive (class in autode.opt.coordinates.primitives) PrimitiveBondAngle (class in autode.opt.coordinates.primitives) PrimitiveDihedralAngle (class in autode.opt.coordinates.primitives) PrimitiveDistance (class in autode.opt.coordinates.primitives) PrimitiveDummyLinearAngle (class in autode.opt.coordinates.primitives) PrimitiveImproperDihedral (class in autode.opt.coordinates.primitives) PrimitiveInverseDistance (class in autode.opt.coordinates.primitives) PrimitiveLinearAngle (class in autode.opt.coordinates.primitives) print_added_internals() (in module autode.wrappers.ORCA) print_atoms() (in module autode.wrappers.MOPAC) print_cartesian_constraints() (autode.wrappers.XTB.XTB method) (in module autode.wrappers.ORCA) print_coordinates() (in module autode.wrappers.ORCA) print_default_params() (in module autode.wrappers.ORCA) print_distance_constraints() (autode.wrappers.XTB.XTB method) (in module autode.wrappers.ORCA) print_geometries() (autode.neb.original.NEB method) (autode.opt.optimisers.base.NDOptimiser method) print_geometries_from() (in module autode.opt.optimisers.base) print_imag_vector() (autode.transition_states.transition_state.TransitionState method) print_num_optimisation_steps() (in module autode.wrappers.ORCA) print_output() (autode.reactions.reaction.Reaction method) print_point_charge_file() (autode.wrappers.XTB.XTB static method) print_point_charges() (in module autode.wrappers.MOPAC) (in module autode.wrappers.ORCA) print_solvent() (autode.wrappers.ORCA.ORCA method) print_xcontrol_file() (autode.wrappers.XTB.XTB method) print_xyz_file() (autode.species.species.Species method) product (autode.reactions.reaction.Reaction property) Product (class in autode.species.molecule) ProductComplex (class in autode.species.complex) proj() (in module autode.geom) prune() (autode.conformers.conformers.Conformers method) prune_diff_graph() (autode.conformers.conformers.Conformers method) prune_on_energy() (autode.conformers.conformers.Conformers method) prune_on_rmsd() (autode.conformers.conformers.Conformers method) prune_small_ring_rearrs() (in module autode.bond_rearrangement)

R

rad (in module autode.units) rad_to_deg (autode.constants.Constants attribute) radius (autode.species.species.Species property) randomise_around() (autode.solvent.explicit_solvent.ExplicitSolvent method) (autode.solvent.solvents.Solvent method) raw (autode.opt.coordinates.base.OptCoordinates property) (autode.opt.coordinates.dic.DICWithConstraints property) RDKitFailed reac_graph_to_prod_graph() (in module autode.mol_graphs) reactant (autode.reactions.reaction.Reaction property) Reactant (class in autode.species.molecule) ReactantComplex (class in autode.species.complex) Reaction (class in autode.reactions.reaction) ReactionFormationFailed ReactionType (class in autode.reactions.reaction_types) ReactivePESnD (class in autode.pes.reactive) real (autode.values.Frequency property) relative_energies (autode.pes.pes_nd.PESnD property) RelaxedPESnD (class in autode.pes.relaxed) remove() (autode.wrappers.keywords.Keywords method) remove_bonds_invalid_valancies() (in module autode.mol_graphs) remove_dummy() (autode.atoms.Atoms method) remove_no_energy() (autode.conformers.conformers.Conformers method) reorder_atoms() (autode.species.complex.Complex method) (autode.species.species.Species method) reorder_nodes() (in module autode.mol_graphs) requires_atoms() (in module autode.utils)

requires_conformers() (in module autode.utils) requires_graph() (in module autode.utils) requires_hl_level_methods() (in module autode.utils) requires_output() (in module autode.utils) requires_output_to_exist() (in module autode.utils) reset_graph() (autode.species.species.Species method) reset_onto() (autode.smiles.atom_types.AtomType method) rfo_shift (autode.opt.coordinates.base.OptCoordinates property) RFOptimiser (class in autode.opt.optimisers.rfo) RI (class in autode.wrappers.keywords) right (autode.opt.coordinates.dimer.DimerPoint attribute) RingBond (class in autode.smiles.base) rms_g (autode.opt.optimisers.base.ConvergenceParams attribute) rms_s (autode.opt.optimisers.base.ConvergenceParams attribute) rot_idxs (autode.smiles.angles.SAngles property) rotate() (autode.atoms.Atom method) (autode.species.species.Species method) rotate_empty_onto() (autode.smiles.atom_types.AtomType method) rotate_mol() (autode.species.complex.Complex method) rotate_onto() (autode.smiles.atom_types.AtomType method) rotate_randomly() (autode.smiles.atom_types.AtomType method) run() (autode.opt.optimisers.base.BaseOptimiser method) (autode.opt.optimisers.base.NullOptimiser method) (autode.opt.optimisers.base.Optimiser method) run_constrained_opt() (autode.transition_states.ts_guess.TSguess method) run_external() (in module autode.utils) run_external_monitored() (in module autode.utils) run_in_tmp_environment() (in module autode.utils)

S

SAngle (class in autode.smiles.angles) SAngles (class in autode.smiles.angles) save() (autode.pes.pes_nd.PESnD method) (autode.reactions.reaction.Reaction method) (autode.transition_states.templates.TStemplate method) save_bond_rearrangs_to_file() (in module autode.bond_rearrangement) save_opt_params() (autode.opt.optimisers.base.OptimiserHistory method) save_plot() (in module autode.plotting) save_ts_template() (autode.transition_states.transition_state.TransitionState method) ScannedBond (class in autode.bonds) SDihedral (class in autode.smiles.angles) SDihedrals (class in autode.smiles.angles) second_derivative() (autode.opt.coordinates.primitives.Primitive method) set_atoms_bonds() (autode.smiles.builder.Builder method) set_attack_r0() (autode.substitution.SubstitutionCentre method) set_coords() (autode.neb.original.Images method) set_dispersion() (autode.wrappers.keywords.KeywordsSet method) set_ecp() (autode.wrappers.keywords.KeywordsSet method) set_functional() (autode.wrappers.keywords.KeywordsSet method) set_g_at() (autode.opt.coordinates.dimer.DimerCoordinates method) set_method_str() (autode.values.Energy method) set_opt_basis_set() (autode.wrappers.keywords.KeywordsSet method) set_opt_functional() (autode.wrappers.keywords.KeywordsSet method) shape (autode.pes.pes_nd.PESnD property) should_calculate_hessian (autode.opt.optimisers.prfo.PRFOptimiser property) SIConstants (class in autode.thermochemistry.igm) single_point() (autode.conformers.conformer.Conformer method) (autode.conformers.conformers.Conformers method) (autode.species.species.Species method) SinglePointKeywords (class in autode.wrappers.keywords) smiles (autode.smiles.parser.Parser property)

SMILESAtom (class in autode.smiles.base) SMILESBond (class in autode.smiles.base) SMILESBonds (class in autode.smiles.base) SMILESBuildFailed SMILESStereoChem (class in autode.smiles.base) sn (autode.species.species.Species property) solvent (autode.species.species.Species property) Solvent (class in autode.solvent.solvents) solvent_atom_idxs() (autode.solvent.explicit_solvent.ExplicitSolvent method) solvent_name (autode.species.species.Species property) SolventNotFound SolventsDontMatch SolventUnavailable sorted_atomic_symbols (autode.species.species.Species property) sp (autode.wrappers.keywords.KeywordsSet property) Species (class in autode.species.species) species_are_isomorphic() (in module autode.mol_graphs) split_mol_across_bond() (in module autode.mol_graphs) SquareAntiprismAtom (class in autode.smiles.atom_types) SquarePlanarAtom (class in autode.smiles.atom_types) SR1Update (class in autode.opt.optimisers.hessian_update) strict (autode.opt.optimisers.base.ConvergenceParams attribute) StringDict (class in autode.utils) strip_equiv_bond_rearrs() (in module autode.bond_rearrangement) strip_identical_and_inv_axes() (in module autode.thermochemistry.symmetry) SubstitutionCentre (class in autode.substitution) switch_reactants_products() (autode.reactions.reaction.Reaction method) symbol (autode.smiles.base.SMILESBond property) symm_matrix_from_ltril() (in module autode.geom) symmetry_number (autode.species.species.Species property) symmetry_number() (in module autode.thermochemistry.symmetry)

T

table (autode.atoms.PeriodicTable attribute) tau (autode.opt.coordinates.dimer.DimerCoordinates property) tau_hat (autode.opt.coordinates.dimer.DimerCoordinates property) TB (in module autode.units) Temperature (class in autode.values) template_matches() (in module autode.transition_states.templates) TemplateLoadingFailed temporary_config() (in module autode.utils) TerminalAtom (class in autode.smiles.atom_types) terminated_normally_in() (autode.wrappers.G09.G09 method) (autode.wrappers.MOPAC.MOPAC method) (autode.wrappers.NWChem.NWChem method) (autode.wrappers.ORCA.ORCA method) (autode.wrappers.XTB.XTB method) TET_INVERTED (autode.smiles.base.SMILESStereoChem attribute) TET_NORMAL (autode.smiles.base.SMILESStereoChem attribute) TetrahedralAtom (class in autode.smiles.atom_types) TetrahedralIAtom (class in autode.smiles.atom_types) TetrahedralNAtom (class in autode.smiles.atom_types) timeout() (in module autode.utils) tm_row (autode.atoms.Atom property) to() (autode.opt.coordinates.base.OptCoordinates method) (autode.opt.coordinates.cartesian.CartesianCoordinates method) (autode.opt.coordinates.dic.DIC method) (autode.opt.coordinates.dimer.DimerCoordinates method) (autode.values.Value method) (autode.values.ValueArray method)

to_() (autode.values.ValueArray method) to_explicit() (autode.solvent.solvents.ImplicitSolvent method) (autode.solvent.solvents.Solvent method) to_product() (autode.species.molecule.Molecule method) to_product_complex() (autode.species.complex.ReactantComplex method) to_reactant() (autode.species.molecule.Molecule method) to_reactant_complex() (autode.species.complex.ProductComplex method) tolist() (autode.wrappers.keywords.Keywords method) total_energy() (in module autode.neb.original) transition_metals() (autode.atoms.PeriodicTable class method) TransitionState (class in autode.transition_states.transition_state) translate() (autode.atoms.Atom method) (autode.species.species.Species method) translate_mol() (autode.species.complex.Complex method) translate_rotate_reactant() (in module autode.transition_states.locate_tss) TrigonalAtom (class in autode.smiles.atom_types) TrigonalBipyramidalAtom (class in autode.smiles.atom_types) TrigonalPyramidalAtom (class in autode.smiles.atom_types) truhlar (autode.thermochemistry.igm.LFMethod attribute) ts (autode.reactions.reaction.Reaction property) ts_guess_funcs_prms() (in module autode.transition_states.locate_tss) ts_guesses() (autode.pes.reactive.ReactivePESnD method) TSbase (class in autode.transition_states.base) TSguess (class in autode.transition_states.ts_guess) TStemplate (class in autode.transition_states.templates)

U

UnbalancedReaction union() (in module autode.mol_graphs) Unit (class in autode.units) UnRelaxedPES1D (class in autode.pes.unrelaxed) UnsupportedCalculationInput update_g_from_cart_g() (autode.opt.coordinates.base.OptCoordinates method)

update_h_from_cart_h() (autode.opt.coordinates.base.OptCoordinates method) update_h_from_old_h() (autode.opt.coordinates.base.OptCoordinates method) update_lagrange_multipliers() (autode.opt.coordinates.dic.DICWithConstraints method) updated_h (autode.opt.optimisers.hessian_update.HessianUpdater property) updated_h_inv (autode.opt.optimisers.hessian_update.HessianUpdater property) upper() (autode.wrappers.keywords.Keyword method) use_vdw_gaussian_solvent() (autode.wrappers.ORCA.ORCA method)

V

Value (class in autode.values) value() (autode.smiles.angles.SAngle method) (autode.smiles.angles.SDihedral method) ValueArray (class in autode.values) values() (autode.smiles.angles.SAngles method) vdw_radii (in module autode.atoms) vdw_radius (autode.atoms.Atom property) (autode.atoms.DummyAtom property)

vector() (autode.atoms.Atoms method) version_in() (autode.wrappers.G09.G09 method) (autode.wrappers.MOPAC.MOPAC method) (autode.wrappers.NWChem.NWChem method) (autode.wrappers.ORCA.ORCA method) (autode.wrappers.XTB.XTB method) vib_frequencies (autode.species.species.Species property) (autode.transition_states.transition_state.TransitionState property)

W

warnings (autode.transition_states.transition_state.TransitionState attribute) wavenumber (in module autode.units) weight (autode.atoms.Atom property) (autode.atoms.AtomCollection property) (autode.atoms.DummyAtom property)

wf_method (autode.wrappers.keywords.Keywords property) WFMethod (class in autode.wrappers.keywords) work_in() (in module autode.utils) work_in_tmp_dir() (in module autode.utils)

X

x (autode.values.Coordinate property) x0 (autode.opt.coordinates.dimer.DimerCoordinates property) x1 (autode.opt.coordinates.dimer.DimerCoordinates property) x2 (autode.opt.coordinates.dimer.DimerCoordinates property) x_at() (autode.opt.coordinates.dimer.DimerCoordinates method)

XTB (class in autode.wrappers.XTB) XTBOptimiser (class in autode.wrappers.XTB) xyz_file_to_atoms() (in module autode.input_output) xyz_file_to_molecules() (in module autode.input_output) XYZfileDidNotExist XYZfileWrongFormat

Y

y (autode.values.Coordinate property)

Z

z (autode.values.Coordinate property)

zpe (autode.species.species.Species property)