Index _ | A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | Q | R | S | T | U | V | W | X _ __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.NMRJob 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 AaronTools.utils.utils module add_basis() (AaronTools.theory.BasisSet method) add_bond_to() (AaronTools.atoms.Atom method) add_dict() (in module AaronTools.utils.utils) 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) angle_between_vectors() (in module AaronTools.utils.utils) AnharmonicVibration (class in AaronTools.spectra) animate() (AaronTools.fileIO.FileReader method) 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) available_memory() (in module AaronTools.utils.utils) B Basis (class in AaronTools.theory) BasisSet (class in AaronTools.theory) biaugmented_trigonal_prismatic_shape() (AaronTools.atoms.Atom class method) boltzmann_average() (in module AaronTools.utils.utils) boltzmann_coefficients() (in module AaronTools.utils.utils) boltzmann_weights() (AaronTools.comp_output.CompOutput static method) bond() (AaronTools.atoms.Atom method) (AaronTools.geometry.Geometry method) bond_change() (AaronTools.comp_output.CompOutput 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) capped_cube_shape() (AaronTools.atoms.Atom class method) capped_octahedral_shape() (AaronTools.atoms.Atom class method) capped_square_antiprismatic_shape() (AaronTools.atoms.Atom class method) capped_trigonal_prismatic_shape() (AaronTools.atoms.Atom class 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) combine_dicts() (in module AaronTools.utils.utils) 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) convert_to_Psi4() (AaronTools.geometry.Geometry method) coord_shift() (AaronTools.geometry.Geometry method) coordinates() (AaronTools.geometry.Geometry method) coords (AaronTools.geometry.Geometry property) copy() (AaronTools.atoms.Atom method) (AaronTools.component.Component method) (AaronTools.geometry.Geometry method) (AaronTools.ring.Ring method) (AaronTools.substituent.Substituent method) cubic_shape() (AaronTools.atoms.Atom class 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) display() (AaronTools.geometry.Geometry method) dist() (AaronTools.atoms.Atom method) dist_is_connected() (AaronTools.atoms.Atom method) draw_atom() (AaronTools.atoms.Atom method) DummyAtoms (class in AaronTools.finders) E ECP (class in AaronTools.theory) element_counts() (AaronTools.geometry.Geometry method) element_is_dummy() (AaronTools.atoms.Atom class method) elements (AaronTools.geometry.Geometry property) elements_in_basis (AaronTools.theory.BasisSet property) elongated_trigonal_bipyramidal_shape() (AaronTools.atoms.Atom class method) EmpiricalDispersion (class in AaronTools.theory) enneagonal_shape() (AaronTools.atoms.Atom class method) equivalent_positions() (AaronTools.symmetry.PointGroup method) ev_to_nm() (AaronTools.spectra.ValenceExcitations static method) examine_constraints() (AaronTools.geometry.Geometry method) F fibonacci_sphere() (in module AaronTools.utils.utils) 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) float_vec() (in module AaronTools.utils.utils) 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_pdb() (AaronTools.geometry.Geometry class method) 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 gauss_legendre_grid() (in module AaronTools.utils.utils) 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_filename() (in module AaronTools.utils.utils) 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.NMRJob 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_graph() (AaronTools.geometry.Geometry method) get_invariant() (AaronTools.atoms.Atom method) get_invariants() (AaronTools.geometry.Geometry method) get_mixed_signals() (AaronTools.spectra.Frequency class method) (AaronTools.spectra.NMR class method) (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.ConformerSearchJob method) (AaronTools.theory.job_types.ForceJob method) (AaronTools.theory.job_types.FrequencyJob method) (AaronTools.theory.job_types.JobType method) (AaronTools.theory.job_types.NMRJob 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_outfile() (in module AaronTools.utils.utils) 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_solvent() (AaronTools.geometry.Geometry class method) get_spectrum_functions() (AaronTools.spectra.NMR method) (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) getuser() (in module AaronTools.utils.utils) glob_files() (in module AaronTools.utils.utils) H HarmonicVibration (class in AaronTools.spectra) HasAttribute (class in AaronTools.finders) heptagonal_bipyramidal_shape() (AaronTools.atoms.Atom class method) hexagonal_bipyramidal_shape() (AaronTools.atoms.Atom class method) hula_hoop_shape() (AaronTools.atoms.Atom class method) I idealize_geometry() (AaronTools.symmetry.PointGroup method) ImplicitSolvent (class in AaronTools.theory) integrate() (in module AaronTools.utils.utils) IntegrationGrid (class in AaronTools.theory) invert() (AaronTools.geometry.Geometry method) is_connected() (AaronTools.atoms.Atom method) is_dummy (AaronTools.atoms.Atom property) 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 lebedev_sphere() (in module AaronTools.utils.utils) linear_shape() (AaronTools.atoms.Atom class method) list() (AaronTools.component.Component class method) (AaronTools.ring.Ring class method) (AaronTools.substituent.Substituent class method) list_solvents() (AaronTools.geometry.Geometry static 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) mirror_matrix() (in module AaronTools.utils.utils) mo_value() (AaronTools.orbitals.Orbitals method) module AaronTools.finders AaronTools.json_extension AaronTools.spectra AaronTools.theory AaronTools.theory.job_types AaronTools.utils.utils muffin_shape() (AaronTools.atoms.Atom class method) N new_shape() (AaronTools.atoms.Atom static method) next_conformer() (AaronTools.geometry.Geometry method) nm_to_ev() (AaronTools.spectra.ValenceExcitations static method) NMR (class in AaronTools.spectra) NMRJob (class in AaronTools.theory.job_types) NotAny (class in AaronTools.finders) num_atoms (AaronTools.geometry.Geometry property) NumberOfBonds (class in AaronTools.finders) O octagonal_pyramidal_shape() (AaronTools.atoms.Atom class method) 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.NMR method) (AaronTools.spectra.Signals method) (AaronTools.spectra.ValenceExcitations method) parse_orca_lines() (AaronTools.spectra.Frequency method) (AaronTools.spectra.NMR 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) pascals_triangle() (in module AaronTools.utils.utils) pentagonal_bipyramidal_shape() (AaronTools.atoms.Atom class method) percent_buried_volume() (AaronTools.geometry.Geometry method) perp_vector() (in module AaronTools.utils.utils) plot() (AaronTools.geometry.Geometry method) plot_ir() (AaronTools.spectra.Frequency method) plot_nmr() (AaronTools.spectra.NMR 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) proj() (in module AaronTools.utils.utils) prune_branches() (in module AaronTools.utils.utils) Q quat_matrix() (in module AaronTools.utils.utils) R range_list() (in module AaronTools.utils.utils) 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) Residue (class in AaronTools.finders) resolve_concatenation() (in module AaronTools.utils.utils) 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_conformers() (AaronTools.geometry.Geometry class method) ring_substitute() (AaronTools.geometry.Geometry method) RMSD() (AaronTools.geometry.Geometry method) RMSD_permute() (AaronTools.geometry.Geometry method) rotate() (AaronTools.geometry.Geometry method) rotate_fragment() (AaronTools.geometry.Geometry method) rotation_matrix() (in module AaronTools.utils.utils) S same_cycle() (in module AaronTools.utils.utils) 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) Shift (class in AaronTools.spectra) shortest_path() (AaronTools.geometry.Geometry method) (in module AaronTools.utils.utils) 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) square_antiprismatic_shape() (AaronTools.atoms.Atom class method) steric_map() (AaronTools.geometry.Geometry method) sterimol() (AaronTools.component.Component method) (AaronTools.geometry.Geometry method) (AaronTools.substituent.Substituent method) sub_link_hosts() (AaronTools.geometry.Geometry method) sub_links() (AaronTools.geometry.Geometry 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) subtract_dicts() (in module AaronTools.utils.utils) symmetry_number (AaronTools.symmetry.PointGroup property) T tag() (AaronTools.geometry.Geometry method) 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) to_closing() (in module AaronTools.utils.utils) TransientExcitation (class in AaronTools.spectra) triangular_cupola_shape() (AaronTools.atoms.Atom class method) tricapped_trigonal_prismatic_shape() (AaronTools.atoms.Atom class method) tridiminished_icosahedral_shape() (AaronTools.atoms.Atom class method) trigonal_bipyramidal_shape() (AaronTools.atoms.Atom class method) trigonal_dodecahedral_shape() (AaronTools.atoms.Atom class method) trigonal_planar_shape() (AaronTools.atoms.Atom class method) trigonal_prismatic_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) uptri2sym() (in module AaronTools.utils.utils) 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_mode() (AaronTools.fileIO.FileReader 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_pdb() (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) X xyzzy_cross() (in module AaronTools.utils.utils)