Index _ | A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | R | S | T | U | V | W _ __init__() (AaronTools.atoms.Atom method) (AaronTools.comp_output.CompOutput method) (AaronTools.component.Component method) (AaronTools.fileIO.FileReader method) (AaronTools.geometry.Geometry method) (AaronTools.job_control.SubmitProcess method) (AaronTools.orbitals.Orbitals method) (AaronTools.ring.Ring method) (AaronTools.substituent.Substituent method) (AaronTools.symmetry.PointGroup method) (AaronTools.theory.Basis method) (AaronTools.theory.BasisSet method) (AaronTools.theory.ECP method) (AaronTools.theory.EmpiricalDispersion method) (AaronTools.theory.ImplicitSolvent method) (AaronTools.theory.IntegrationGrid method) (AaronTools.theory.job_types.ConformerSearchJob method) (AaronTools.theory.job_types.ForceJob method) (AaronTools.theory.job_types.FrequencyJob method) (AaronTools.theory.job_types.JobType method) (AaronTools.theory.job_types.OptimizationJob method) (AaronTools.theory.job_types.TDDFTJob method) (AaronTools.theory.Method method) (AaronTools.theory.SAPTMethod method) (AaronTools.theory.Theory method) A AaronTools.finders module AaronTools.json_extension module AaronTools.spectra module AaronTools.theory module AaronTools.theory.job_types module add_basis() (AaronTools.theory.BasisSet method) add_bond_to() (AaronTools.atoms.Atom method) add_ecp() (AaronTools.theory.BasisSet method) add_kwargs() (AaronTools.theory.Theory method) add_links() (AaronTools.geometry.Geometry method) align_to_bond() (AaronTools.substituent.Substituent method) AmideCarbon (class in AaronTools.finders) angle() (AaronTools.atoms.Atom method) (AaronTools.geometry.Geometry method) AnharmonicVibration (class in AaronTools.spectra) AnyNonTransitionMetal (class in AaronTools.finders) AnyTransitionMetal (class in AaronTools.finders) Aromatics (class in AaronTools.finders) ATDecoder (class in AaronTools.json_extension) ATEncoder (class in AaronTools.json_extension) Atom (class in AaronTools.atoms) atoms_in_basis (AaronTools.theory.BasisSet property) B Basis (class in AaronTools.theory) BasisSet (class in AaronTools.theory) boltzmann_weights() (AaronTools.comp_output.CompOutput static method) bond() (AaronTools.atoms.Atom method) (AaronTools.geometry.Geometry method) BondedElements (class in AaronTools.finders) BondedTo (class in AaronTools.finders) BondsFrom (class in AaronTools.finders) Bridgehead (class in AaronTools.finders) C c2_symmetric() (AaronTools.component.Component method) calc_G_corr() (AaronTools.comp_output.CompOutput method) calc_Grimme_G() (AaronTools.comp_output.CompOutput method) calc_zpe() (AaronTools.comp_output.CompOutput method) canonical_rank() (AaronTools.geometry.Geometry method) change_angle() (AaronTools.geometry.Geometry method) change_chirality() (AaronTools.geometry.Geometry method) change_dihedral() (AaronTools.geometry.Geometry method) change_distance() (AaronTools.geometry.Geometry method) change_element() (AaronTools.geometry.Geometry method) check_for_elements() (AaronTools.theory.BasisSet method) ChiralCenters (in module AaronTools.finders) ChiralCentres (class in AaronTools.finders) CloserTo (class in AaronTools.finders) COM() (AaronTools.geometry.Geometry method) compare_connectivity() (AaronTools.geometry.Geometry method) Component (class in AaronTools.component) CompOutput (class in AaronTools.comp_output) compute_rot_temps() (AaronTools.comp_output.CompOutput method) condensed_fukui_acceptor_values() (AaronTools.orbitals.Orbitals method) condensed_fukui_donor_values() (AaronTools.orbitals.Orbitals method) condensed_fukui_dual_values() (AaronTools.orbitals.Orbitals method) cone_angle() (AaronTools.component.Component method) ConformerSearchJob (class in AaronTools.theory.job_types) coord_shift() (AaronTools.geometry.Geometry method) coordinates() (AaronTools.geometry.Geometry method) coords (AaronTools.geometry.Geometry property) copy() (AaronTools.component.Component method) (AaronTools.geometry.Geometry method) (AaronTools.ring.Ring method) (AaronTools.substituent.Substituent method) D default() (AaronTools.json_extension.ATEncoder method) define_layer() (AaronTools.geometry.Geometry method) density_value() (AaronTools.orbitals.Orbitals method) detect_backbone() (AaronTools.component.Component method) detect_fragments() (AaronTools.geometry.Geometry method) detect_solvent() (AaronTools.geometry.Geometry method) detect_sub() (AaronTools.substituent.Substituent method) detect_substituents() (AaronTools.geometry.Geometry method) determine_point_group() (AaronTools.symmetry.PointGroup method) dihedral() (AaronTools.geometry.Geometry method) dist() (AaronTools.atoms.Atom method) dist_is_connected() (AaronTools.atoms.Atom method) E ECP (class in AaronTools.theory) element_counts() (AaronTools.geometry.Geometry method) elements (AaronTools.geometry.Geometry property) elements_in_basis (AaronTools.theory.BasisSet property) EmpiricalDispersion (class in AaronTools.theory) equivalent_positions() (AaronTools.symmetry.PointGroup method) ev_to_nm() (AaronTools.spectra.ValenceExcitations static method) examine_constraints() (AaronTools.geometry.Geometry method) F FileReader (class in AaronTools.fileIO) FileWriter (class in AaronTools.fileIO) filter_data() (AaronTools.spectra.Frequency method) (AaronTools.spectra.Signals method) find() (AaronTools.geometry.Geometry method) find_end() (AaronTools.ring.Ring method) find_exact() (AaronTools.geometry.Geometry method) find_substituent() (AaronTools.geometry.Geometry method) fix_comment() (AaronTools.geometry.Geometry method) FlaggedAtoms (class in AaronTools.finders) follow() (AaronTools.comp_output.CompOutput method) ForceJob (class in AaronTools.theory.job_types) freeze() (AaronTools.geometry.Geometry method) Frequency (class in AaronTools.spectra) FrequencyJob (class in AaronTools.theory.job_types) from_string() (AaronTools.geometry.Geometry class method) (AaronTools.ring.Ring class method) (AaronTools.substituent.Substituent class method) fukui_acceptor_value() (AaronTools.orbitals.Orbitals method) fukui_donor_value() (AaronTools.orbitals.Orbitals method) G Geometry (class in AaronTools.geometry) get_all_connected() (AaronTools.geometry.Geometry method) get_aromatic_atoms() (AaronTools.geometry.Geometry method) get_class() (in module AaronTools.finders) get_connectivity() (AaronTools.geometry.Geometry method) get_constraints() (AaronTools.geometry.Geometry method) get_coordination_complexes() (AaronTools.geometry.Geometry class method) get_cube_array() (AaronTools.orbitals.Orbitals static method) get_cube_points() (AaronTools.orbitals.Orbitals static method) get_diastereomers() (AaronTools.geometry.Geometry class method) get_frag_list() (AaronTools.component.Component method) (AaronTools.geometry.Geometry method) get_fragment() (AaronTools.geometry.Geometry method) get_gaff_geom() (AaronTools.geometry.Geometry method) get_gaussian() (AaronTools.theory.Basis static method) (AaronTools.theory.EmpiricalDispersion method) (AaronTools.theory.ImplicitSolvent method) (AaronTools.theory.IntegrationGrid method) (AaronTools.theory.job_types.ForceJob method) (AaronTools.theory.job_types.FrequencyJob method) (AaronTools.theory.job_types.JobType method) (AaronTools.theory.job_types.OptimizationJob method) (AaronTools.theory.job_types.SinglePointJob method) (AaronTools.theory.job_types.TDDFTJob method) (AaronTools.theory.Method method) get_gaussian_basis_info() (AaronTools.theory.BasisSet method) get_gaussian_footer() (AaronTools.theory.Theory method) get_gaussian_header() (AaronTools.theory.Theory method) get_gaussian_molecule() (AaronTools.theory.Theory method) get_invariant() (AaronTools.atoms.Atom method) get_invariants() (AaronTools.geometry.Geometry method) get_mixed_signals() (AaronTools.spectra.Signals class method) get_monomers() (AaronTools.geometry.Geometry method) get_near() (AaronTools.geometry.Geometry method) get_neighbor_id() (AaronTools.atoms.Atom method) get_orca() (AaronTools.theory.Basis static method) (AaronTools.theory.EmpiricalDispersion method) (AaronTools.theory.ImplicitSolvent method) (AaronTools.theory.IntegrationGrid method) (AaronTools.theory.job_types.ForceJob method) (AaronTools.theory.job_types.FrequencyJob method) (AaronTools.theory.job_types.JobType method) (AaronTools.theory.job_types.OptimizationJob method) (AaronTools.theory.job_types.SinglePointJob method) (AaronTools.theory.job_types.TDDFTJob method) (AaronTools.theory.Method method) get_orca_basis_info() (AaronTools.theory.BasisSet method) get_orca_footer() (AaronTools.theory.Theory method) get_orca_header() (AaronTools.theory.Theory method) get_plot_data() (AaronTools.spectra.Signals static method) get_principle_axes() (AaronTools.geometry.Geometry method) get_psi4() (AaronTools.theory.Basis static method) (AaronTools.theory.EmpiricalDispersion method) (AaronTools.theory.ImplicitSolvent method) (AaronTools.theory.IntegrationGrid method) (AaronTools.theory.job_types.ForceJob method) (AaronTools.theory.job_types.FrequencyJob method) (AaronTools.theory.job_types.JobType method) (AaronTools.theory.job_types.OptimizationJob method) (AaronTools.theory.job_types.SinglePointJob method) (AaronTools.theory.job_types.TDDFTJob method) (AaronTools.theory.Method method) get_psi4_basis_info() (AaronTools.theory.BasisSet method) get_psi4_footer() (AaronTools.theory.Theory method) get_psi4_header() (AaronTools.theory.Theory method) get_psi4_molecule() (AaronTools.theory.Theory method) get_qchem() (AaronTools.theory.Basis static method) (AaronTools.theory.EmpiricalDispersion method) (AaronTools.theory.ImplicitSolvent method) (AaronTools.theory.job_types.ForceJob method) (AaronTools.theory.job_types.FrequencyJob method) (AaronTools.theory.job_types.JobType method) (AaronTools.theory.job_types.OptimizationJob method) (AaronTools.theory.job_types.SinglePointJob method) (AaronTools.theory.job_types.TDDFTJob method) (AaronTools.theory.Method method) get_qchem_basis_info() (AaronTools.theory.BasisSet method) get_qchem_header() (AaronTools.theory.Theory method) get_shape() (AaronTools.atoms.Atom class method) get_spectrum_functions() (AaronTools.spectra.Signals method) get_sqm() (AaronTools.theory.job_types.FrequencyJob method) (AaronTools.theory.job_types.JobType method) (AaronTools.theory.job_types.OptimizationJob method) (AaronTools.theory.job_types.SinglePointJob method) (AaronTools.theory.Method method) get_sqm_header() (AaronTools.theory.Theory method) get_sqm_molecule() (AaronTools.theory.Theory method) get_substituents() (AaronTools.geometry.Geometry method) get_symmetry_elements() (AaronTools.symmetry.PointGroup method) get_vsepr() (AaronTools.atoms.Atom method) get_xtb() (AaronTools.theory.job_types.ForceJob method) (AaronTools.theory.job_types.FrequencyJob method) (AaronTools.theory.job_types.JobType method) (AaronTools.theory.job_types.OptimizationJob method) get_xtb_cmdline() (AaronTools.theory.Theory method) H HarmonicVibration (class in AaronTools.spectra) HasAttribute (class in AaronTools.finders) I idealize_geometry() (AaronTools.symmetry.PointGroup method) ImplicitSolvent (class in AaronTools.theory) IntegrationGrid (class in AaronTools.theory) invert() (AaronTools.geometry.Geometry method) is_connected() (AaronTools.atoms.Atom method) IsElement (class in AaronTools.finders) iupac2smiles() (AaronTools.geometry.Geometry static method) J job_from_string() (in module AaronTools.theory.job_types) JobType (class in AaronTools.theory.job_types) L linear_shape() (AaronTools.atoms.Atom class method) list() (AaronTools.component.Component class method) (AaronTools.ring.Ring class method) (AaronTools.substituent.Substituent class method) LJ_energy() (AaronTools.geometry.Geometry method) M make_conformer() (AaronTools.geometry.Geometry method) make_footer() (AaronTools.theory.Theory method) make_header() (AaronTools.theory.Theory method) make_molecule() (AaronTools.theory.Theory method) make_oniom() (AaronTools.geometry.Geometry method) map_ligand() (AaronTools.geometry.Geometry method) mass (AaronTools.atoms.Atom property) memory_estimate() (AaronTools.orbitals.Orbitals method) Method (class in AaronTools.theory) minimize() (AaronTools.geometry.Geometry method) minimize_sub_torsion() (AaronTools.component.Component method) (AaronTools.geometry.Geometry method) minimize_torsion() (AaronTools.geometry.Geometry method) mirror() (AaronTools.geometry.Geometry method) mo_value() (AaronTools.orbitals.Orbitals method) module AaronTools.finders AaronTools.json_extension AaronTools.spectra AaronTools.theory AaronTools.theory.job_types N new_shape() (AaronTools.atoms.Atom static method) next_conformer() (AaronTools.geometry.Geometry method) nm_to_ev() (AaronTools.spectra.ValenceExcitations static method) NotAny (class in AaronTools.finders) num_atoms (AaronTools.geometry.Geometry property) NumberOfBonds (class in AaronTools.finders) O octahedral_shape() (AaronTools.atoms.Atom class method) OfType (class in AaronTools.finders) oniom_layer() (AaronTools.geometry.Geometry method) ONIOMLayer (class in AaronTools.finders) optically_chiral (AaronTools.symmetry.PointGroup property) OptimizationJob (class in AaronTools.theory.job_types) Orbitals (class in AaronTools.orbitals) P parse_archive() (AaronTools.comp_output.CompOutput method) parse_basis_str() (AaronTools.theory.BasisSet static method) parse_comment() (AaronTools.geometry.Geometry method) parse_gaussian_lines() (AaronTools.spectra.Frequency method) (AaronTools.spectra.Signals method) (AaronTools.spectra.ValenceExcitations method) parse_orca_lines() (AaronTools.spectra.Frequency method) (AaronTools.spectra.Signals method) (AaronTools.spectra.ValenceExcitations method) parse_psi4_lines() (AaronTools.spectra.Frequency method) (AaronTools.spectra.Signals method) (AaronTools.spectra.ValenceExcitations method) parse_qchem_lines() (AaronTools.spectra.Frequency method) (AaronTools.spectra.Signals method) (AaronTools.spectra.ValenceExcitations method) percent_buried_volume() (AaronTools.geometry.Geometry method) plot_ir() (AaronTools.spectra.Frequency method) plot_spectrum() (AaronTools.spectra.Signals class method) plot_uv_vis() (AaronTools.spectra.ValenceExcitations method) PointGroup (class in AaronTools.symmetry) power_integral() (AaronTools.orbitals.Orbitals method) R read_com() (AaronTools.fileIO.FileReader method) read_crest() (AaronTools.fileIO.FileReader method) read_fchk() (AaronTools.fileIO.FileReader method) read_file() (AaronTools.fileIO.FileReader method) read_log() (AaronTools.fileIO.FileReader method) read_mmcif() (AaronTools.fileIO.FileReader method) read_mol2() (AaronTools.fileIO.FileReader method) read_nbo() (AaronTools.fileIO.FileReader method) read_nbo_31() (AaronTools.fileIO.FileReader method) read_nbo_47() (AaronTools.fileIO.FileReader method) read_orca_out() (AaronTools.fileIO.FileReader method) read_pdb() (AaronTools.fileIO.FileReader method) read_psi4_out() (AaronTools.fileIO.FileReader method) read_qchem_out() (AaronTools.fileIO.FileReader method) read_sd() (AaronTools.fileIO.FileReader method) read_sqm() (AaronTools.fileIO.FileReader method) read_xtb() (AaronTools.fileIO.FileReader method) read_xyz() (AaronTools.fileIO.FileReader method) refresh_atoms() (AaronTools.theory.Basis method) (AaronTools.theory.BasisSet method) refresh_connected() (AaronTools.geometry.Geometry method) refresh_elements() (AaronTools.theory.Basis method) (AaronTools.theory.BasisSet method) refresh_ranks() (AaronTools.geometry.Geometry method) relax() (AaronTools.geometry.Geometry method) remove_clash() (AaronTools.geometry.Geometry method) remove_fragment() (AaronTools.geometry.Geometry method) remove_kwargs() (AaronTools.theory.Theory method) reorder() (AaronTools.geometry.Geometry method) Resiude (class in AaronTools.finders) resolve_error() (AaronTools.theory.job_types.FrequencyJob static method) (AaronTools.theory.job_types.JobType static method) (AaronTools.theory.job_types.OptimizationJob static method) Ring (class in AaronTools.ring) ring_substitute() (AaronTools.geometry.Geometry method) RMSD() (AaronTools.geometry.Geometry method) rotate() (AaronTools.geometry.Geometry method) rotate_fragment() (AaronTools.geometry.Geometry method) S sanity_check_basis() (AaronTools.theory.Basis static method) (AaronTools.theory.ECP static method) sanity_check_method() (AaronTools.theory.Method static method) SAPTMethod (class in AaronTools.theory) set_template() (AaronTools.job_control.SubmitProcess method) shortest_path() (AaronTools.geometry.Geometry method) Signal (class in AaronTools.spectra) Signals (class in AaronTools.spectra) SinglePointJob (class in AaronTools.theory.job_types) SOCExcitation (class in AaronTools.spectra) solid_angle() (AaronTools.component.Component method) SpiroCenters (class in AaronTools.finders) steric_map() (AaronTools.geometry.Geometry method) sterimol() (AaronTools.component.Component method) (AaronTools.geometry.Geometry method) (AaronTools.substituent.Substituent method) sub_rotate() (AaronTools.substituent.Substituent method) submit() (AaronTools.job_control.SubmitProcess method) SubmitProcess (class in AaronTools.job_control) Substituent (class in AaronTools.substituent) substitute() (AaronTools.geometry.Geometry method) symmetry_number (AaronTools.symmetry.PointGroup property) T TDDFTJob (class in AaronTools.theory.job_types) tetrahedral_shape() (AaronTools.atoms.Atom class method) Theory (class in AaronTools.theory) therm_corr() (AaronTools.comp_output.CompOutput method) TransientExcitation (class in AaronTools.spectra) trigonal_bipyramidal_shape() (AaronTools.atoms.Atom class method) trigonal_planar_shape() (AaronTools.atoms.Atom class method) U unfinished_jobs_in_dir() (AaronTools.job_control.SubmitProcess static method) update_atom_types() (AaronTools.geometry.Geometry method) update_charges() (AaronTools.geometry.Geometry method) update_geometry() (AaronTools.geometry.Geometry method) V ValenceExcitation (class in AaronTools.spectra) ValenceExcitations (class in AaronTools.spectra) voronoi_integral() (AaronTools.orbitals.Orbitals method) VSEPR (class in AaronTools.finders) W weighted_percent_buried_volume() (AaronTools.geometry.Geometry static method) weighted_sterimol() (AaronTools.substituent.Substituent static method) WithinBondsOf (class in AaronTools.finders) WithinRadiusFromAtom (class in AaronTools.finders) WithinRadiusFromPoint (class in AaronTools.finders) write() (AaronTools.geometry.Geometry method) write_com() (AaronTools.fileIO.FileWriter class method) write_crest() (AaronTools.fileIO.FileWriter class method) write_cube() (AaronTools.fileIO.FileWriter class method) write_dict_files() (AaronTools.fileIO.FileWriter static method) write_file() (AaronTools.fileIO.FileWriter class method) write_in() (AaronTools.fileIO.FileWriter class method) write_inp() (AaronTools.fileIO.FileWriter class method) write_inq() (AaronTools.fileIO.FileWriter class method) write_mol() (AaronTools.fileIO.FileWriter class method) write_multi_xyz() (AaronTools.fileIO.FileWriter class method) write_oniom_xyz() (AaronTools.fileIO.FileWriter class method) write_sqm() (AaronTools.fileIO.FileWriter class method) write_xtb() (AaronTools.fileIO.FileWriter class method) write_xyz() (AaronTools.fileIO.FileWriter class method)