Index _ | A | B | C | D | E | F | G | I | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y _ __add__() (tqchem.batframe.BATFrame method) __call__() (tqchem.internal_coordinates.MolecularGrid method) (tqchem.ttconf.electronic_structure_interfaces.CrestEnsembleInterface method) (tqchem.ttconf.electronic_structure_interfaces.ElectronicStructureInterface method) (tqchem.ttconf.ttconf.EnergyFilter method) (tqchem.ttconf.ttconf.EnsembleGridObjective method) (tqchem.ttconf.ttconf.MolecularGridObjective method) __pyarmor__ (in module tqchem.pyarmor_runtime_006359) __pyarmor__() (in module tqchem.pyarmor_runtime_006359) __sub__() (tqchem.batframe.BATFrame method) A add_rotatable_bonds() (tqchem.molgraph.MolecularSystem method) adjacency (tqchem.ttconf.electronic_structure_interfaces.CrestEnsembleInterface attribute) (tqchem.ttconf.electronic_structure_interfaces.OpenFFInterface attribute), [1] (tqchem.ttconf.electronic_structure_interfaces.TBliteInterface attribute) adjacency_differs() (in module tqchem.chem) adjacencyMatrix() (in module tqchem.chem) align_molecules() (in module tqchem.chem) align_xyz_strings() (in module tqchem.chem) amberFF_interface() (in module tqchem.ttconf.electronic_structure_interfaces) amide_bonds_grid() (in module tqchem.functional_groups) amino_group_grid() (in module tqchem.functional_groups) Angle (class in tqchem.batframe) angle_mask() (in module tqchem.batframe) angles() (tqchem.batframe.BATFrame method) ase (tqchem.molgraph.MolecularSystem attribute) ase_from_molecule_file_content() (in module tqchem.chem) ase_from_path() (in module tqchem.chem) ase_from_rdkit() (in module tqchem.chem) ase_from_smiles() (in module tqchem.chem) ase_molecule() (in module tqchem.chem) ase_to_graph() (in module tqchem.molgraph) ase_to_rdkit() (in module tqchem.chem) ase_to_xyz_content() (in module tqchem.chem) atoms_collided() (in module tqchem.chem) B bat_component() (in module tqchem.batframe) bat_to_xyz() (in module tqchem.batframe) BATFrame (class in tqchem.batframe) batframe (tqchem.puckering.PuckeringFrame attribute), [1] Bond (class in tqchem.batframe) bond_component() (in module tqchem.molgraph) bond_mask() (in module tqchem.batframe) bondMatrix() (in module tqchem.chem) bonds() (tqchem.batframe.BATFrame method) bonds_from_isomorphism_mappings() (in module tqchem.functional_groups) C cache (tqchem.ttopt.ttopt.TTOpt attribute) calculator (tqchem.ttconf.electronic_structure_interfaces.TBliteInterface attribute), [1] charge (tqchem.ttconf.electronic_structure_interfaces.CrestEnsembleInterface attribute) closest_gridpoint() (tqchem.batframe.BATFrame method) (tqchem.internal_coordinates.MolecularGrid method) (tqchem.puckering.PuckeringFrame method) combine() (tqchem.internal_coordinates.InternalCoordinates method) comp() (tqchem.ttopt.ttopt.TTOpt method) comp_opt() (tqchem.ttopt.ttopt.TTOpt method) component_sweep (tqchem.molgraph.MolecularSystem attribute), [1] component_type() (in module tqchem.molgraph) (tqchem.molgraph.MolecularSystem method) conformer_optimizer() (in module tqchem.__main__) ConformerResults (class in tqchem.ttconf.conformer_results) constant_coordinates (tqchem.internal_coordinates.MolecularGrid attribute), [1] constant_coordinates() (tqchem.batframe.BATFrame method) (tqchem.internal_coordinates.InternalCoordinates method) (tqchem.puckering.PuckeringFrame method) coordinate_screener() (in module tqchem.viewer) coordinate_screener_from_grid() (in module tqchem.viewer) copy() (tqchem.batframe.BATFrame method) (tqchem.molgraph.MolecularSystem method) CrestEnsembleInterface (class in tqchem.ttconf.electronic_structure_interfaces) cycle (tqchem.puckering.PuckeringFrame attribute), [1] cycle_bridge_tree_decomposition() (in module tqchem.molgraph) D data (tqchem.ttconf.ttconf.EnsembleGridObjective attribute) (tqchem.ttconf.ttconf.MolecularGridObjective attribute) dataframe (tqchem.ttconf.conformer_results.ConformerResults attribute), [1] dataframe_to_csv() (tqchem.ttconf.conformer_results.ConformerResults method) determineBonds() (in module tqchem.chem) dfs_sweep() (in module tqchem.molgraph) DielectricConstant (in module tqchem.ttconf.electronic_structure_interfaces) Dihedral (class in tqchem.batframe) dihedral_mask() (in module tqchem.batframe) dihedrals() (tqchem.batframe.BATFrame method) display_trajectory() (in module tqchem.viewer) draw() (tqchem.molgraph.MolecularSystem method) drawGraph() (in module tqchem.molgraph) E ElectronicStructureInterface (class in tqchem.ttconf.electronic_structure_interfaces) element_color() (in module tqchem.chem) energy_function (tqchem.ttconf.ttconf.EnsembleGridObjective attribute), [1] (tqchem.ttconf.ttconf.MolecularGridObjective attribute), [1] EnergyFilter (class in tqchem.ttconf.ttconf) EnsembleGridObjective (class in tqchem.ttconf.ttconf) escape_new_lines() (in module tqchem.ttconf.conformer_results) evaluate_grid() (tqchem.batframe.BATFrame method) (tqchem.internal_coordinates.InternalCoordinates method) (tqchem.puckering.PuckeringFrame method) extract_energy_from_comment() (in module tqchem.ttconf.crest_wrapper) F filter (tqchem.ttconf.ttconf.EnsembleGridObjective attribute) (tqchem.ttconf.ttconf.MolecularGridObjective attribute) filter_ (tqchem.ttconf.ttconf.EnergyFilter attribute) (tqchem.ttconf.ttconf.EnsembleGridObjective attribute) (tqchem.ttconf.ttconf.MolecularGridObjective attribute) find_alkane_bonds() (in module tqchem.functional_groups) find_amide_groups() (in module tqchem.functional_groups) find_amino_groups() (in module tqchem.functional_groups) find_iso_propyl_groups() (in module tqchem.functional_groups) find_methyl_groups() (in module tqchem.functional_groups) find_single_bonded_chalcogen() (in module tqchem.functional_groups) find_t_butyl_groups() (in module tqchem.functional_groups) function (tqchem.ttopt.ttopt.TTOpt attribute), [1] G generate_conformers() (in module tqchem.__main__) generate_rdkit_conformers() (in module tqchem.chem) generation_parser() (in module tqchem.__main__) get_component_of_atom() (in module tqchem.molgraph) get_component_sweep() (in module tqchem.molgraph) get_dihedral_path() (in module tqchem.batframe) get_path() (in module tqchem.molgraph) (tqchem.molgraph.MolecularSystem method) get_positions() (tqchem.molgraph.MolecularSystem method) get_root() (in module tqchem.molgraph) get_start_frame() (in module tqchem.molgraph) graph (tqchem.molgraph.MolecularSystem attribute), [1] grid (tqchem.batframe.BATFrame attribute) (tqchem.puckering.PuckeringFrame attribute) grid_range() (tqchem.batframe.BATFrame method) (tqchem.internal_coordinates.InternalCoordinates method) (tqchem.puckering.PuckeringFrame method) I i_opt (tqchem.ttopt.ttopt.TTOpt attribute) improper_dihedral_path_ring() (in module tqchem.batframe) in_list_of_lists() (in module tqchem.molgraph) index_list_of_lists() (in module tqchem.molgraph) indices_from_rdkit_conformers() (in module tqchem.ttconf.factory) indices_to_components() (in module tqchem.internal_coordinates) initial_indices (tqchem.ttopt.ttopt.TTOpt attribute), [1] initial_tt_indices() (in module tqchem.ttconf.factory) internal_to_xyz() (in module tqchem.internal_coordinates) InternalCoordinates (class in tqchem.internal_coordinates) InversionDihedral (class in tqchem.batframe) is_edge_in_cycle() (in module tqchem.molgraph) is_existing_file() (in module tqchem.chem) is_improper_dihedral() (in module tqchem.batframe) is_multiline_string() (in module tqchem.chem) is_node_in_cycle() (in module tqchem.molgraph) is_planar_ring() (in module tqchem.puckering) is_proper_dihedral() (in module tqchem.batframe) is_single_bond() (in module tqchem.molgraph) is_single_bond_from_cycle() (in module tqchem.molgraph) is_smiles_string() (in module tqchem.chem) is_terminal_atom_bond() (in module tqchem.molgraph) iso_propyl_groups_grid() (in module tqchem.functional_groups) L launch_crest() (in module tqchem.ttconf.crest_wrapper) linearize() (in module tqchem.internal_coordinates) linearized_component_sweep() (in module tqchem.molgraph) local_optimization (tqchem.ttconf.electronic_structure_interfaces.OpenFFInterface attribute) (tqchem.ttconf.electronic_structure_interfaces.TBliteInterface attribute) longest_path_in_tree() (in module tqchem.molgraph) M main() (in module tqchem.__main__) make_grid() (tqchem.batframe.BATFrame method) (tqchem.internal_coordinates.InternalCoordinates method) (tqchem.puckering.PuckeringFrame method) masked_coordinate() (in module tqchem.batframe) match_atomic_numbers() (in module tqchem.functional_groups) match_bond_order_range() (in module tqchem.functional_groups) maxvol() (in module tqchem.ttopt.maxvol) maxvol_rect() (in module tqchem.ttopt.maxvol) method (tqchem.ttconf.electronic_structure_interfaces.CrestEnsembleInterface attribute) minimum_energy_ensemble() (tqchem.ttconf.conformer_results.ConformerResults method) minimum_energy_unrelaxed_conformer() (tqchem.ttconf.conformer_results.ConformerResults method) minimum_energy_xyz() (tqchem.ttconf.conformer_results.ConformerResults method) minimum_objective_unrelaxed_conformer() (tqchem.ttconf.conformer_results.ConformerResults method) minimum_objective_xyz() (tqchem.ttconf.conformer_results.ConformerResults method) module tqchem tqchem.__main__ tqchem.batframe tqchem.chem tqchem.exceptions tqchem.functional_groups tqchem.internal_coordinates tqchem.molgraph tqchem.puckering tqchem.pyarmor_runtime_006359 tqchem.spectra tqchem.ttconf tqchem.ttconf.conformer_results tqchem.ttconf.crest_wrapper tqchem.ttconf.electronic_structure_interfaces tqchem.ttconf.factory tqchem.ttconf.ttconf tqchem.ttopt tqchem.ttopt.maxvol tqchem.ttopt.ttopt tqchem.viewer tqchem.xtb_api molecular_systems() (in module tqchem.__main__) MolecularGrid (class in tqchem.internal_coordinates) MolecularGridObjective (class in tqchem.ttconf.ttconf) molecularGridObjective() (in module tqchem.ttconf.factory) MolecularSystem (class in tqchem.molgraph) molecularSystem() (in module tqchem.molgraph) molecule (tqchem.internal_coordinates.MolecularGrid attribute), [1] molecule_from_ase() (in module tqchem.molgraph) molecule_from_file() (in module tqchem.molgraph) molecule_from_rdkit() (in module tqchem.molgraph) molecule_from_smiles() (in module tqchem.molgraph) molgrid (tqchem.ttconf.conformer_results.ConformerResults attribute), [1] (tqchem.ttconf.ttconf.EnsembleGridObjective attribute), [1] (tqchem.ttconf.ttconf.MolecularGridObjective attribute), [1] multiple_indices_function (tqchem.ttopt.ttopt.TTOpt attribute), [1] N n_points_per_torsion (tqchem.ttopt.ttopt.TTOpt attribute) n_points_per_variable (tqchem.ttopt.ttopt.TTOpt attribute) n_sweeps (tqchem.ttopt.ttopt.TTOpt attribute), [1] n_torsions (tqchem.ttopt.ttopt.TTOpt attribute) n_variables() (tqchem.internal_coordinates.MolecularGrid method) nitrogen_inversion() (in module tqchem.batframe) O objective (tqchem.ttconf.ttconf.TTopt_Optimizer attribute), [1] open_graph (tqchem.molgraph.MolecularSystem attribute), [1] open_multiring_graph() (in module tqchem.molgraph) OpenFFInterface (class in tqchem.ttconf.electronic_structure_interfaces) opt_opt (tqchem.ttopt.ttopt.TTOpt property) opt_opt_list (tqchem.ttopt.ttopt.TTOpt attribute) optimize() (tqchem.ttconf.ttconf.TTopt_Optimizer method) (tqchem.ttopt.ttopt.TTOpt method) optlevel (tqchem.ttconf.electronic_structure_interfaces.CrestEnsembleInterface attribute) overwrite_rotatable_bonds() (tqchem.molgraph.MolecularSystem method) P parse_commandline() (in module tqchem.__main__) phi (tqchem.puckering.PuckeringFrame attribute), [1] planar_conformer() (in module tqchem.puckering) planar_only (tqchem.puckering.PuckeringFrame attribute), [1] plot_3D_molecule() (in module tqchem.viewer) plot_spectrum() (in module tqchem.spectra) pucker_coordinate_5ring() (in module tqchem.puckering) pucker_coordinate_6ring() (in module tqchem.puckering) pucker_coordinate_6ring_smart() (in module tqchem.puckering) puckering_to_xyz() (in module tqchem.puckering) PuckeringFrame (class in tqchem.puckering) Q q (tqchem.puckering.PuckeringFrame attribute), [1] R raise_internal_tqchem_error() (in module tqchem.exceptions) rank (tqchem.ttopt.ttopt.TTOpt attribute), [1] rdkit_from_smiles() (in module tqchem.chem) rdkit_molecules_to_xyz() (in module tqchem.chem) read_crest_ensemble_xyz() (in module tqchem.ttconf.crest_wrapper) read_xtb_vibspectrum() (in module tqchem.xtb_api) reference_coordinate_system() (in module tqchem.puckering) reference_energy (tqchem.ttconf.ttconf.EnergyFilter attribute) remove_cycle_overlap() (in module tqchem.molgraph) residual_trees() (in module tqchem.molgraph) root() (tqchem.molgraph.MolecularSystem method) rotatable_bonds() (in module tqchem.batframe) run_conformer_search() (in module tqchem.__main__) S sageFF_interface() (in module tqchem.ttconf.electronic_structure_interfaces) sampled_unrelaxed_conformers() (tqchem.ttconf.conformer_results.ConformerResults method) seed (tqchem.ttopt.ttopt.TTOpt attribute) set_bond_orders() (tqchem.molgraph.MolecularSystem method) set_rotatable_bond_grids() (in module tqchem.molgraph) (tqchem.molgraph.MolecularSystem method) shape() (tqchem.internal_coordinates.MolecularGrid method) simple_alkanes_grid() (in module tqchem.functional_groups) simulation (tqchem.ttconf.electronic_structure_interfaces.OpenFFInterface attribute), [1] single_bonded_chalcogens_grid() (in module tqchem.functional_groups) smiles_to_filename() (in module tqchem.__main__) solve_atom_collisions() (in module tqchem.ttconf.factory) solvent (tqchem.ttconf.electronic_structure_interfaces.CrestEnsembleInterface attribute) sort_tree_component() (in module tqchem.molgraph) sorted_atoms_within_components() (in module tqchem.molgraph) sorted_components() (in module tqchem.molgraph) sorted_ring() (in module tqchem.molgraph) split_bond_to_components() (in module tqchem.molgraph) split_bond_to_subgraphs() (in module tqchem.molgraph) T t_butyl_groups_grid() (in module tqchem.functional_groups) TBliteInterface (class in tqchem.ttconf.electronic_structure_interfaces) threads (tqchem.ttconf.electronic_structure_interfaces.CrestEnsembleInterface attribute) torsion_from_bond() (in module tqchem.batframe) torsions_from_bonds() (tqchem.batframe.BATFrame method) tqchem module tqchem.__main__ module tqchem.batframe module tqchem.chem module tqchem.exceptions module tqchem.functional_groups module tqchem.internal_coordinates module tqchem.molgraph module tqchem.puckering module tqchem.pyarmor_runtime_006359 module tqchem.spectra module tqchem.ttconf module tqchem.ttconf.conformer_results module tqchem.ttconf.crest_wrapper module tqchem.ttconf.electronic_structure_interfaces module tqchem.ttconf.factory module tqchem.ttconf.ttconf module tqchem.ttopt module tqchem.ttopt.maxvol module tqchem.ttopt.ttopt module tqchem.viewer module tqchem.xtb_api module TQchemImportError tree_from_graph() (in module tqchem.molgraph) ttconf_optimizer() (in module tqchem.ttconf.factory) ttconf_parser() (in module tqchem.__main__) TTConfObjective (class in tqchem.ttconf.ttconf) TTOpt (class in tqchem.ttopt.ttopt) ttopt_find() (in module tqchem.ttopt.ttopt) ttopt_init() (in module tqchem.ttopt.ttopt) TTopt_Optimizer (class in tqchem.ttconf.ttconf) ttopt_parameters (tqchem.ttconf.ttconf.TTopt_Optimizer attribute), [1] tuple (tqchem.batframe.Angle attribute) (tqchem.batframe.Bond attribute) (tqchem.batframe.Dihedral attribute) U update() (tqchem.internal_coordinates.InternalCoordinates method) (tqchem.puckering.PuckeringFrame method) V variable_atom_indices() (tqchem.internal_coordinates.MolecularGrid method) variable_coordinates() (tqchem.batframe.BATFrame method) (tqchem.internal_coordinates.InternalCoordinates method) (tqchem.puckering.PuckeringFrame method) variables (tqchem.internal_coordinates.MolecularGrid attribute), [1] W wiberg_bond_orders() (in module tqchem.chem) write() (tqchem.molgraph.MolecularSystem method) write_minimum_energy_ensemble() (tqchem.ttconf.conformer_results.ConformerResults method) write_results() (in module tqchem.__main__) write_sampled_unrelaxed_conformers() (tqchem.ttconf.conformer_results.ConformerResults method) write_xyz_list() (in module tqchem.ttconf.conformer_results) X x (tqchem.puckering.PuckeringFrame attribute), [1] xtb_ir_spectrum() (in module tqchem.xtb_api) XTB_METHODS (in module tqchem.xtb_api) xtb_optimize() (in module tqchem.xtb_api) xtb_singlepoint() (in module tqchem.xtb_api) xyz_contents() (in module tqchem.chem) xyz_to_bat() (in module tqchem.batframe) xyz_to_internal() (in module tqchem.internal_coordinates) xyz_to_puckering() (in module tqchem.puckering) Y y (tqchem.puckering.PuckeringFrame attribute), [1] y_opt (tqchem.ttopt.ttopt.TTOpt property) y_opt_list (tqchem.ttopt.ttopt.TTOpt attribute)