ARC’s API
- arc.main
- arc.species.species
- arc.species.converter
add_atom_to_xyz_using_internal_coords()add_lone_pairs_by_atom_valance()add_rads_by_atom_valance()angle_constraint()check_isomorphism()check_molecule_list_order()check_xyz_dict()check_zmat_dict()cluster_confs_by_rmsd()compare_confs()compare_confs_fl()compare_zmats()dihedral_constraint()displace_xyz()distance_constraint()elementize()generate_bond_length_initial_guess()generate_initial_guess_r_a()generate_midpoint_initial_guess()generate_perpendicular_initial_guess()get_center_of_mass()get_element_mass_from_xyz()get_most_common_isotope_for_element()get_xyz_radius()get_zmat_param_value()get_zmat_str_var_value()hartree_to_si()ics_to_scan_constraints()modify_coords()molecules_from_xyz()order_atoms()order_atoms_in_mol_list()pybel_to_inchi()rdkit_conf_from_mol()relocate_zmat_dummy_atoms_to_the_end()remove_dummies()rmg_conformer_to_xyz()rmg_mol_from_inchi()s_bonds_mol_from_xyz()set_multiplicity()set_radicals_by_map()set_rdkit_dihedrals()sort_xyz_using_indices()species_to_sdf_file()split_str_zmat()standardize_xyz_string()str_to_xyz()str_to_zmat()to_rdkit_mol()translate_to_center_of_mass()translate_xyz()update_molecule()xyz_file_format_to_xyz()xyz_from_data()xyz_to_ase()xyz_to_coords_and_element_numbers()xyz_to_coords_list()xyz_to_dmat()xyz_to_kinbot_list()xyz_to_np_array()xyz_to_pybel_mol()xyz_to_rmg_conformer()xyz_to_str()xyz_to_turbomol_format()xyz_to_x_y_z()xyz_to_xyz_file_format()zmat_from_xyz()zmat_to_str()zmat_to_xyz()
- arc.species.conformers
add_missing_symmetric_torsion_values()change_dihedrals_and_force_field_it()cheat_sheet()check_special_non_rotor_cases()chirality_dict_to_tuple()conformers_combinations_by_lowest_conformer()deduce_new_conformers()determine_chirality()determine_dihedrals()determine_number_of_conformers_to_generate()determine_rotors()determine_smallest_atom_index_in_scan()determine_torsion_sampling_points()determine_torsion_symmetry()determine_well_width_tolerance()embed_rdkit()find_internal_rotors()generate_all_combinations()generate_conformer_combinations()generate_conformers()generate_diatomic_conformer()generate_force_field_conformers()generate_monoatomic_conformer()get_force_field_energies()get_lowest_confs()get_lowest_diastereomers()get_number_of_chiral_centers()get_top_element_count()get_torsion_angles()get_wells()identify_chiral_nitrogen_centers()initialize_log()inverse_chirality_symbol()mix_rdkit_and_openbabel_force_field()openbabel_force_field()openbabel_force_field_on_rdkit_conformers()prune_enantiomers_dict()rdkit_force_field()read_rdkit_embedded_conformer_i()read_rdkit_embedded_conformers()replace_n_with_c_in_mol()replace_n_with_c_in_xyz()to_group()translate_group()translate_groups()update_mol()
- arc.species.vectors
- arc.species.zmat
add_dummy_atom()check_atom_a_constraints()check_atom_d_constraints()check_atom_r_constraints()consolidate_zmat()determine_a_atoms()determine_d_atoms()determine_d_atoms_from_connectivity()determine_d_atoms_without_connectivity()determine_r_atoms()get_all_neighbors()get_atom_connectivity_from_mol()get_atom_indices_from_zmat_parameter()get_atom_order()get_atom_order_from_mol()get_atom_order_from_xyz()get_connectivity()get_parameter_from_atom_indices()is_atom_in_new_fragment()is_dummy()map_index_to_int()order_fragments_by_constraints()remove_1st_atom()remove_1st_atom_references()up_param()update_zmat_with_new_atom()xyz_to_zmat()zmat_to_coords()
- arc.reaction
- arc.scheduler
- arc.job
- arc.job.ssh
- arc.job.local
- arc.job.trsh
determine_ess_status()determine_job_log_memory_issues()scan_quality_check()trsh_conformer_isomorphism()trsh_ess_job()trsh_job_on_server()trsh_job_queue()trsh_keyword_cartesian()trsh_keyword_checkfile()trsh_keyword_inaccurate_quadrature()trsh_keyword_intaccuracy()trsh_keyword_l123()trsh_keyword_neg_eigen()trsh_keyword_no_qc()trsh_keyword_nosymm()trsh_keyword_opt_maxcycles()trsh_keyword_scf()trsh_keyword_unconverged()trsh_negative_freq()trsh_scan_job()trsh_special_rotor()
- arc.parser
identify_ess()parse_1d_scan_coords()parse_1d_scan_energies()parse_dipole_moment()parse_e_elect()parse_frequencies()parse_geometry()parse_ic_info()parse_ic_values()parse_nd_scan_energies()parse_normal_mode_displacement()parse_polarizability()parse_scan_args()parse_scan_conformers()parse_str_blocks()parse_t1()parse_trajectory()parse_xyz_from_file()parse_zpe()process_conformers_file()
- arc.plotter
augment_arkane_yml_file_with_mol_repr()auto_label()check_xyz_species_for_drawing()clean_scan_results()delete_multi_species_output_file()draw_3d()draw_kinetics_plots()draw_parity_plot()draw_structure()draw_thermo_parity_plots()get_rxn_units_and_conversion_factor()get_text_positions()log_bde_report()log_kinetics()log_thermo()make_multi_species_output_file()plot_1d_rotor_scan()plot_2d_rotor_scan()plot_2d_scan_bond_dihedral()plot_3d_mol_as_scatter()plot_torsion_angles()plot_ts_guesses_by_e_and_method()save_conformers_file()save_geo()save_irc_traj_animation()save_kinetics_lib()save_nd_rotor_yaml()save_rotor_text_file()save_thermo_lib()save_transport_lib()show_sticks()text_plotter()
- arc.processor
- arc.rmgdb
- arc.common
almost_equal_coords()almost_equal_coords_lists()almost_equal_lists()calc_rmsd()calculate_arrhenius_rate_coefficient()check_ess_settings()check_that_all_entries_are_in_list()check_torsion_change()clean_text()convert_list_index_0_to_1()convert_to_hours()delete_check_files()determine_ess()determine_symmetry()determine_top_group_indices()dfs()estimate_orca_mem_cpu_requirement()extremum_list()from_yaml()generate_resonance_structures()get_angle_in_180_range()get_atom_radius()get_bonds_from_dmat()get_close_tuple()get_extremum_index()get_git_branch()get_git_commit()get_logger()get_number_with_ordinal_indicator()get_ordered_intersection_of_two_lists()get_ordinal_indicator()get_single_bond_length()globalize_path()globalize_paths()initialize_job_types()initialize_log()is_angle_linear()is_notebook()is_same_pivot()is_same_sequence_sublist()is_str_float()is_str_int()is_xyz_mol_match()key_by_val()log_footer()log_header()read_yaml_file()rmg_mol_from_dict_repr()rmg_mol_to_dict_repr()safe_copy_file()save_yaml_file()sort_atoms_in_descending_label_order()sort_two_lists_by_the_first()string_representer()sum_list_entries()time_lapse()timedelta_from_str()to_yaml()torsions_to_scans()
- arc.level
- arc.utils.scale