Index

_

_number_of_atoms (arc.species.species.ARCSpecies attribute) _radius (arc.species.species.ARCSpecies attribute)

_sftp (arc.job.ssh.SSHClient attribute) _ssh (arc.job.ssh.SSHClient attribute)

A

adaptive_levels (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) add_dummy_atom() (in module arc.species.zmat) add_hydrogen_for_bde() (arc.main.ARC method) add_label_to_unique_species_labels() (arc.scheduler.Scheduler method) add_lone_pairs_by_atom_valance() (in module arc.species.converter) add_missing_symmetric_torsion_values() (in module arc.species.conformers) add_rads_by_atom_valance() (in module arc.species.converter) address (arc.job.ssh.SSHClient attribute) allow_nonisomorphic_2d (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) almost_equal_coords() (in module arc.common) almost_equal_coords_lists() (in module arc.common) almost_equal_lists() (in module arc.common) almost_equal_tsgs() (arc.species.species.TSGuess method) ARC (class in arc.main) arc.common module arc.job module arc.job.local module arc.job.ssh module arc.job.trsh module arc.level module arc.main module arc.parser module arc.plotter module arc.processor module

arc.reaction module arc.rmgdb module arc.scheduler module arc.species.conformers module arc.species.converter module arc.species.species module arc.species.vectors module arc.species.zmat module arc.utils.scale module arc_reaction (arc.species.species.TSGuess attribute) arc_species_from_rmg_reaction() (arc.reaction.ARCReaction method) ARCReaction (class in arc.reaction) ARCSpecies (class in arc.species.species) are_coords_compliant_with_graph() (in module arc.species.species) arkane_file (arc.species.species.ARCSpecies attribute) arkane_level_of_theory (arc.main.ARC attribute) as_dict() (arc.level.Level method) (arc.main.ARC method) (arc.reaction.ARCReaction method) (arc.species.species.ARCSpecies method) (arc.species.species.TSGuess method) assign_frequency_scale_factor() (in module arc.level) atom_map (arc.reaction.ARCReaction attribute) (arc.reaction.ARCReaction property) augment_arkane_yml_file_with_mol_repr() (in module arc.plotter) auto_label() (in module arc.plotter)

B

bac_type (arc.main.ARC attribute) backup_restart() (arc.main.ARC method) bath_gas (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute)

bdes (arc.species.species.ARCSpecies attribute) bond_corrections (arc.species.species.ARCSpecies attribute) build() (arc.level.Level method)

C

calc_freq_factor (arc.main.ARC attribute) calc_rmsd() (in module arc.common) calculate_angle() (in module arc.species.vectors) calculate_dihedral_angle() (in module arc.species.vectors) calculate_distance() (in module arc.species.vectors) calculate_param() (in module arc.species.vectors) calculate_truhlar_scaling_factors() (in module arc.utils.scale) change_dihedrals_and_force_field_it() (in module arc.species.conformers) change_mode() (arc.job.ssh.SSHClient method) (in module arc.job.local) charge (arc.reaction.ARCReaction attribute) (arc.reaction.ARCReaction property) (arc.species.species.ARCSpecies attribute) cheap_conformer (arc.species.species.ARCSpecies attribute) cheat_sheet() (in module arc.species.conformers) check_all_done() (arc.scheduler.Scheduler method) check_arkane_level_of_theory() (arc.main.ARC method) check_atom_a_constraints() (in module arc.species.zmat) check_atom_balance() (arc.reaction.ARCReaction method) (in module arc.species.species) check_atom_d_constraints() (in module arc.species.zmat) check_atom_r_constraints() (in module arc.species.zmat) check_attributes() (arc.reaction.ARCReaction method) check_connections() (in module arc.job.ssh) check_directed_scan() (arc.scheduler.Scheduler method) check_directed_scan_job() (arc.scheduler.Scheduler method) check_done_opt_r_n_p() (arc.reaction.ARCReaction method) check_ess_settings() (in module arc.common) check_freq_job() (arc.scheduler.Scheduler method) check_freq_scaling_factor() (arc.main.ARC method) check_irc_species() (arc.scheduler.Scheduler method) check_isomorphism() (in module arc.species.converter) check_job_status() (arc.job.ssh.SSHClient method) (in module arc.job.local) check_job_status_in_stdout() (in module arc.job.ssh) check_label() (in module arc.species.species) check_max_simultaneous_jobs_limit() (arc.scheduler.Scheduler method) check_negative_freq() (arc.scheduler.Scheduler method) check_project_name() (arc.main.ARC method) check_running_jobs_ids() (arc.job.ssh.SSHClient method) (in module arc.job.local) check_rxn_e0_by_spc() (arc.scheduler.Scheduler method) check_scan_job() (arc.scheduler.Scheduler method) check_sp_job() (arc.scheduler.Scheduler method) check_special_non_rotor_cases() (in module arc.species.conformers) check_that_all_entries_are_in_list() (in module arc.common) check_torsion_change() (in module arc.common) check_xyz() (in module arc.species.species) check_xyz_dict() (in module arc.species.converter)

check_xyz_isomorphism() (arc.species.species.ARCSpecies method) check_xyz_species_for_drawing() (in module arc.plotter) check_zmat_dict() (in module arc.species.converter) checkfile (arc.species.species.ARCSpecies attribute) chirality_dict_to_tuple() (in module arc.species.conformers) chosen_ts (arc.species.species.ARCSpecies attribute) chosen_ts_list (arc.species.species.ARCSpecies attribute) chosen_ts_method (arc.species.species.ARCSpecies attribute) clean_output_directory() (in module arc.processor) clean_rmg_database_object() (in module arc.rmgdb) clean_scan_results() (in module arc.plotter) close() (arc.job.ssh.SSHClient method) cluster (arc.species.species.TSGuess attribute) cluster_confs_by_rmsd() (in module arc.species.converter) cluster_tsgs() (arc.species.species.ARCSpecies method) colliding_atoms() (in module arc.species.species) compare_confs() (in module arc.species.converter) compare_confs_fl() (in module arc.species.converter) compare_rates() (in module arc.processor) compare_thermo() (in module arc.processor) compare_to_rmg (arc.main.ARC attribute) compare_transport() (in module arc.processor) compare_zmats() (in module arc.species.converter) composite_method (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) compute_rates (arc.main.ARC attribute) compute_thermo (arc.main.ARC attribute) (arc.species.species.ARCSpecies attribute) compute_transport (arc.main.ARC attribute) conf_is_isomorphic (arc.species.species.ARCSpecies attribute) conformer_energies (arc.species.species.ARCSpecies attribute) conformer_index (arc.species.species.TSGuess attribute) conformer_opt_level (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) conformer_sp_level (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) conformers (arc.species.species.ARCSpecies attribute) conformers_before_opt (arc.species.species.ARCSpecies attribute) conformers_combinations_by_lowest_conformer() (in module arc.species.conformers) connect() (arc.job.ssh.SSHClient method) consider_all_diastereomers (arc.species.species.ARCSpecies attribute) consolidate_zmat() (in module arc.species.zmat) convert_list_index_0_to_1() (in module arc.common) convert_to_hours() (in module arc.common) copy() (arc.level.Level method) (arc.reaction.ARCReaction method) (arc.species.species.ARCSpecies method) copy_e0_values() (arc.reaction.ARCReaction method) cyclic_index_i_minus_1() (in module arc.species.species) cyclic_index_i_plus_1() (in module arc.species.species)

D

deduce_job_adapter() (arc.scheduler.Scheduler method) deduce_method_type() (arc.level.Level method) deduce_new_conformers() (in module arc.species.conformers) deduce_software() (arc.level.Level method) delete_all_arc_jobs() (in module arc.job.ssh) delete_all_local_arc_jobs() (in module arc.job.local) delete_all_species_jobs() (arc.scheduler.Scheduler method) delete_check_files() (in module arc.common) delete_job() (arc.job.ssh.SSHClient method) (in module arc.job.local) delete_jobs() (arc.job.ssh.SSHClient method) delete_leftovers() (arc.main.ARC method) delete_multi_species_output_file() (in module arc.plotter) determine_a_atoms() (in module arc.species.zmat) determine_adaptive_level() (arc.scheduler.Scheduler method) determine_chirality() (in module arc.species.conformers) determine_compatible_ess() (arc.level.Level method) determine_d_atoms() (in module arc.species.zmat) determine_d_atoms_from_connectivity() (in module arc.species.zmat) determine_d_atoms_without_connectivity() (in module arc.species.zmat) determine_dihedrals() (in module arc.species.conformers) determine_ess() (in module arc.common) determine_ess_settings() (arc.main.ARC method) determine_ess_status() (in module arc.job.trsh) determine_family() (arc.reaction.ARCReaction method) (in module arc.rmgdb) determine_job_log_memory_issues() (in module arc.job.trsh) determine_most_likely_ts_conformer() (arc.scheduler.Scheduler method) determine_most_stable_conformer() (arc.scheduler.Scheduler method) determine_multiplicity() (arc.species.species.ARCSpecies method) determine_multiplicity_from_descriptors() (arc.species.species.ARCSpecies method)

determine_multiplicity_from_xyz() (arc.species.species.ARCSpecies method) determine_number_of_conformers_to_generate() (in module arc.species.conformers) determine_occ() (in module arc.species.species) determine_r_atoms() (in module arc.species.zmat) determine_reaction_family() (in module arc.rmgdb) determine_rmg_kinetics() (in module arc.rmgdb) determine_rotor_symmetry() (in module arc.species.species) determine_rotor_type() (in module arc.species.species) determine_rotors() (arc.species.species.ARCSpecies method) (in module arc.species.conformers) determine_scaling_factors() (in module arc.utils.scale) determine_smallest_atom_index_in_scan() (in module arc.species.conformers) determine_symmetry() (arc.species.species.ARCSpecies method) (in module arc.common) determine_top_group_indices() (in module arc.common) determine_torsion_sampling_points() (in module arc.species.conformers) determine_torsion_symmetry() (in module arc.species.conformers) determine_unique_species_labels() (arc.main.ARC method) determine_well_width_tolerance() (in module arc.species.conformers) dfs() (in module arc.common) dh_rxn298 (arc.reaction.ARCReaction attribute) directed_rotors (arc.species.species.ARCSpecies attribute) displace_xyz() (in module arc.species.converter) done_opt_r_n_p (arc.reaction.ARCReaction attribute) dont_gen_confs (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) download_file() (arc.job.ssh.SSHClient method) draw_3d() (in module arc.plotter) draw_kinetics_plots() (in module arc.plotter) draw_parity_plot() (in module arc.plotter) draw_structure() (in module arc.plotter) draw_thermo_parity_plots() (in module arc.plotter)

E

e0 (arc.species.species.ARCSpecies attribute) e0_only (arc.species.species.ARCSpecies attribute) e_confs (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) e_elect (arc.species.species.ARCSpecies attribute) elementize() (in module arc.species.converter) embed_rdkit() (in module arc.species.conformers) end_job() (arc.scheduler.Scheduler method) energy (arc.species.species.TSGuess attribute) enumerate_bonds() (in module arc.species.species)

errors (arc.species.species.TSGuess attribute) ess_settings (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) estimate_orca_mem_cpu_requirement() (in module arc.common) execute() (arc.main.ARC method) execute_command() (in module arc.job.local) execution_time (arc.main.ARC attribute) (arc.species.species.TSGuess attribute) external_symmetry (arc.species.species.ARCSpecies attribute) extremum_list() (in module arc.common)

F

family (arc.reaction.ARCReaction attribute) (arc.species.species.TSGuess attribute) family_own_reverse (arc.reaction.ARCReaction attribute) final_xyz (arc.species.species.ARCSpecies attribute) find_internal_rotors() (in module arc.species.conformers) find_package() (arc.job.ssh.SSHClient method) fine_only (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) flip_reaction() (arc.reaction.ARCReaction method) force_field (arc.species.species.ARCSpecies attribute)

fragments (arc.species.species.ARCSpecies attribute) freq_level (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) freq_scale_factor (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) from_dict() (arc.reaction.ARCReaction method) (arc.species.species.ARCSpecies method) (arc.species.species.TSGuess method) from_yaml() (in module arc.common) from_yml_file() (arc.species.species.ARCSpecies method)

G

generate_all_combinations() (in module arc.species.conformers) generate_conformer_combinations() (in module arc.species.conformers) generate_conformers() (arc.species.species.ARCSpecies method) (in module arc.species.conformers) generate_diatomic_conformer() (in module arc.species.conformers) generate_final_ts_guess_report() (arc.scheduler.Scheduler method) generate_force_field_conformers() (in module arc.species.conformers) generate_monoatomic_conformer() (in module arc.species.conformers) generate_resonance_structures() (in module arc.common) get_all_neighbors() (in module arc.species.zmat) get_angle() (in module arc.species.vectors) get_angle_in_180_range() (in module arc.common) get_atom_connectivity_from_mol() (in module arc.species.zmat) get_atom_indices_from_zmat_parameter() (in module arc.species.zmat) get_atom_order() (in module arc.species.zmat) get_atom_order_from_mol() (in module arc.species.zmat) get_atom_order_from_xyz() (in module arc.species.zmat) get_atom_radius() (in module arc.common) get_bonds() (arc.reaction.ARCReaction method) get_bonds_from_dmat() (in module arc.common) get_center_of_mass() (in module arc.species.converter) get_cheap_conformer() (arc.species.species.ARCSpecies method) get_close_tuple() (in module arc.common) get_completed_incore_jobs() (arc.scheduler.Scheduler method) get_connectivity() (in module arc.species.zmat) get_delta_angle() (in module arc.species.vectors) get_dihedral() (in module arc.species.vectors) get_element_mass() (arc.reaction.ARCReaction method) get_element_mass_from_xyz() (in module arc.species.converter) get_expected_changing_bonds() (arc.reaction.ARCReaction method) get_extremum_index() (in module arc.common) get_family() (in module arc.rmgdb) get_force_field_energies() (in module arc.species.conformers) get_git_branch() (in module arc.common) get_git_commit() (in module arc.common) get_last_modified_time() (in module arc.job.local)

get_logger() (in module arc.common) get_lowest_confs() (in module arc.species.conformers) get_lowest_diastereomers() (in module arc.species.conformers) get_lp_vector() (in module arc.species.vectors) get_most_common_isotope_for_element() (in module arc.species.converter) get_normal() (in module arc.species.vectors) get_number_of_atoms_in_reaction_zone() (arc.reaction.ARCReaction method) get_number_of_chiral_centers() (in module arc.species.conformers) get_number_with_ordinal_indicator() (in module arc.common) get_ordered_intersection_of_two_lists() (in module arc.common) get_ordinal_indicator() (in module arc.common) get_parameter_from_atom_indices() (in module arc.species.zmat) get_params_from_arkane_level_of_theory_as_str() (in module arc.level) get_products_xyz() (arc.reaction.ARCReaction method) get_reactants_and_products() (arc.reaction.ARCReaction method) get_reactants_xyz() (arc.reaction.ARCReaction method) get_rxn_charge() (arc.reaction.ARCReaction method) get_rxn_multiplicity() (arc.reaction.ARCReaction method) get_rxn_smiles() (arc.reaction.ARCReaction method) get_server_job_ids() (arc.scheduler.Scheduler method) get_single_bond_length() (in module arc.common) get_single_mapped_product_xyz() (arc.reaction.ARCReaction method) get_species_count() (arc.reaction.ARCReaction method) get_species_list() (in module arc.utils.scale) get_text_positions() (in module arc.plotter) get_top_element_count() (in module arc.species.conformers) get_torsion_angles() (in module arc.species.conformers) get_vector() (in module arc.species.vectors) get_vector_length() (in module arc.species.vectors) get_wells() (in module arc.species.conformers) get_xyz() (arc.species.species.ARCSpecies method) (arc.species.species.TSGuess method) get_xyz_radius() (in module arc.species.converter) get_zmat_param_value() (in module arc.species.converter) get_zmat_str_var_value() (in module arc.species.converter) globalize_path() (in module arc.common) globalize_paths() (in module arc.common)

H

hartree_to_si() (in module arc.species.converter)

I

ics_to_scan_constraints() (in module arc.species.converter) identify_chiral_nitrogen_centers() (in module arc.species.conformers) identify_ess() (in module arc.parser) imaginary_freqs (arc.species.species.TSGuess attribute) include_in_thermo_lib (arc.species.species.ARCSpecies attribute) index (arc.reaction.ARCReaction attribute) (arc.species.species.TSGuess attribute) initial_xyz (arc.species.species.ARCSpecies attribute) (arc.species.species.TSGuess attribute) (arc.species.species.TSGuess property) initialize_directed_rotors() (arc.species.species.ARCSpecies method) initialize_job_types() (in module arc.common) initialize_log() (in module arc.common) (in module arc.species.conformers) initialize_output_dict() (arc.scheduler.Scheduler method) inverse_chirality_symbol() (in module arc.species.conformers)

irc_label (arc.species.species.ARCSpecies attribute) irc_level (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) is_angle_linear() (in module arc.common) is_atom_in_new_fragment() (in module arc.species.zmat) is_diatomic() (arc.species.species.ARCSpecies method) is_dummy() (in module arc.species.zmat) is_isomerization() (arc.reaction.ARCReaction method) is_isomorphic() (arc.species.species.ARCSpecies method) is_monoatomic() (arc.species.species.ARCSpecies method) is_notebook() (in module arc.common) is_same_pivot() (in module arc.common) is_same_sequence_sublist() (in module arc.common) is_str_float() (in module arc.common) is_str_int() (in module arc.common) is_ts (arc.species.species.ARCSpecies attribute) is_xyz_mol_match() (in module arc.common)

J

job_dict (arc.scheduler.Scheduler attribute)

job_types (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute)

K

keep_checks (arc.main.ARC attribute) keep_mol (arc.species.species.ARCSpecies attribute) key (arc.job.ssh.SSHClient attribute)

key_by_val() (in module arc.common) kinetics (arc.reaction.ARCReaction attribute) kinetics_adapter (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute)

L

label (arc.reaction.ARCReaction attribute) (arc.species.species.ARCSpecies attribute) label_atoms() (arc.species.species.ARCSpecies method) Level (class in arc.level) level_of_theory (arc.main.ARC attribute) lib_long_desc (arc.main.ARC attribute) list_available_nodes() (arc.job.ssh.SSHClient method) list_dir() (arc.job.ssh.SSHClient method) load_families_only() (in module arc.rmgdb) load_rmg_database() (in module arc.processor) (in module arc.rmgdb)

log_bde_report() (in module arc.plotter) log_footer() (in module arc.common) log_header() (in module arc.common) log_kinetics() (in module arc.plotter) log_thermo() (in module arc.plotter) long_kinetic_description (arc.reaction.ARCReaction attribute) long_thermo_description (arc.species.species.ARCSpecies attribute) loop_families() (in module arc.rmgdb) lower() (arc.level.Level method)

M

make_multi_species_output_file() (in module arc.plotter) make_reaction_labels_info_file() (arc.scheduler.Scheduler method) make_rmg_database_object() (in module arc.rmgdb) make_ts_report() (arc.species.species.ARCSpecies method) map_index_to_int() (in module arc.species.zmat) max_job_time (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) memory (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) method (arc.species.species.TSGuess attribute) method_direction (arc.species.species.TSGuess attribute) method_index (arc.species.species.TSGuess attribute) mix_rdkit_and_openbabel_force_field() (in module arc.species.conformers) modify_coords() (in module arc.species.converter) module arc.common arc.job arc.job.local arc.job.ssh arc.job.trsh arc.level arc.main arc.parser arc.plotter arc.processor arc.reaction arc.rmgdb arc.scheduler arc.species.conformers arc.species.converter arc.species.species arc.species.vectors arc.species.zmat arc.utils.scale

mol (arc.species.species.ARCSpecies attribute) mol_from_xyz() (arc.species.species.ARCSpecies method) mol_list (arc.species.species.ARCSpecies attribute) molecules_from_xyz() (in module arc.species.converter) most_stable_conformer (arc.species.species.ARCSpecies attribute) multi_species (arc.species.species.ARCSpecies attribute) multiplicity (arc.reaction.ARCReaction attribute) (arc.reaction.ARCReaction property) (arc.species.species.ARCSpecies attribute)

N

n_confs (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) neg_freqs_trshed (arc.species.species.ARCSpecies attribute)

number_of_atoms (arc.species.species.ARCSpecies property) number_of_heavy_atoms (arc.species.species.ARCSpecies property) number_of_radicals (arc.species.species.ARCSpecies attribute) number_of_rotors (arc.species.species.ARCSpecies attribute)

O

occ (arc.species.species.ARCSpecies attribute) openbabel_force_field() (in module arc.species.conformers) openbabel_force_field_on_rdkit_conformers() (in module arc.species.conformers) opt_level (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) (arc.species.species.ARCSpecies attribute) opt_xyz (arc.species.species.TSGuess attribute) (arc.species.species.TSGuess property) optical_isomers (arc.species.species.ARCSpecies attribute)

orbitals_level (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) order_atoms() (in module arc.species.converter) order_atoms_in_mol_list() (in module arc.species.converter) order_fragments_by_constraints() (in module arc.species.zmat) original_label (arc.species.species.ARCSpecies attribute) output (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) output_multi_spc (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute)

P

p_species (arc.reaction.ARCReaction attribute) parse_1d_scan_coords() (in module arc.parser) parse_1d_scan_energies() (in module arc.parser) parse_composite_geo() (arc.scheduler.Scheduler method) parse_conformer() (arc.scheduler.Scheduler method) parse_dipole_moment() (in module arc.parser) parse_e_elect() (in module arc.parser) parse_frequencies() (in module arc.parser) parse_geometry() (in module arc.parser) parse_ic_info() (in module arc.parser) parse_ic_values() (in module arc.parser) parse_nd_scan_energies() (in module arc.parser) parse_normal_mode_displacement() (in module arc.parser) parse_opt_e_elect() (arc.scheduler.Scheduler method) parse_opt_geo() (arc.scheduler.Scheduler method) parse_polarizability() (in module arc.parser) parse_running_jobs_ids() (in module arc.job.local) parse_scan_args() (in module arc.parser) parse_scan_conformers() (in module arc.parser) parse_str_blocks() (in module arc.parser) parse_t1() (in module arc.parser) parse_trajectory() (in module arc.parser) parse_xyz_from_file() (in module arc.parser) parse_zpe() (in module arc.parser) plot_1d_rotor_scan() (in module arc.plotter) plot_2d_rotor_scan() (in module arc.plotter)

plot_2d_scan_bond_dihedral() (in module arc.plotter) plot_3d_mol_as_scatter() (in module arc.plotter) plot_torsion_angles() (in module arc.plotter) plot_ts_guesses_by_e_and_method() (in module arc.plotter) populate_ts_checks() (arc.species.species.ARCSpecies method) post_opt_geo_work() (arc.scheduler.Scheduler method) post_sp_actions() (arc.scheduler.Scheduler method) preserve_param_in_scan (arc.reaction.ARCReaction attribute) (arc.species.species.ARCSpecies attribute) process_adaptive_levels() (in module arc.main) process_arc_project() (in module arc.processor) process_bdes() (in module arc.processor) process_completed_tsg_queue_jobs() (arc.species.species.ARCSpecies method) process_conformers() (arc.scheduler.Scheduler method) process_conformers_file() (in module arc.parser) process_directed_scans() (arc.scheduler.Scheduler method) process_level_of_theory() (arc.main.ARC method) process_xyz() (arc.species.species.ARCSpecies method) (arc.species.species.TSGuess method) products (arc.reaction.ARCReaction attribute) project (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) project_directory (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) (arc.species.species.ARCSpecies attribute) prune_enantiomers_dict() (in module arc.species.conformers) pybel_to_inchi() (in module arc.species.converter)

R

r_species (arc.reaction.ARCReaction attribute) radius (arc.species.species.ARCSpecies property) rdkit_conf_from_mol() (in module arc.species.converter) rdkit_force_field() (in module arc.species.conformers) reactants (arc.reaction.ARCReaction attribute) reactions (arc.main.ARC attribute) read_rdkit_embedded_conformer_i() (in module arc.species.conformers) read_rdkit_embedded_conformers() (in module arc.species.conformers) read_yaml_file() (in module arc.common) recent_md_conformer (arc.species.species.ARCSpecies attribute) relocate_zmat_dummy_atoms_to_the_end() (in module arc.species.converter) remove_1st_atom() (in module arc.species.zmat) remove_1st_atom_references() (in module arc.species.zmat) remove_dummies() (in module arc.species.converter) remove_dup_species() (arc.reaction.ARCReaction method) (in module arc.reaction) rename_level() (in module arc.utils.scale) rename_output() (in module arc.job.local) replace_n_with_c_in_mol() (in module arc.species.conformers) replace_n_with_c_in_xyz() (in module arc.species.conformers) report_e_elect (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) restart_dict (arc.scheduler.Scheduler attribute) restart_path (arc.scheduler.Scheduler attribute) restore_running_jobs() (arc.scheduler.Scheduler method) rmg_conformer_to_xyz() (in module arc.species.converter) rmg_database (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute), [1] rmg_kinetics (arc.reaction.ARCReaction attribute) rmg_mol_from_dict_repr() (in module arc.common)

rmg_mol_from_inchi() (in module arc.species.converter) rmg_mol_to_dict_repr() (in module arc.common) rmg_reaction (arc.reaction.ARCReaction attribute) (arc.species.species.TSGuess attribute) rmg_reaction_from_arc_species() (arc.reaction.ARCReaction method) rmg_reaction_from_str() (arc.reaction.ARCReaction method) rmg_reaction_to_str() (arc.reaction.ARCReaction method) rmg_reactions (arc.reaction.ARCReaction attribute) rmg_species (arc.species.species.ARCSpecies attribute) rmg_thermo (arc.species.species.ARCSpecies attribute) rotate_vector() (in module arc.species.vectors) rotors_dict (arc.species.species.ARCSpecies attribute) run_composite_job() (arc.scheduler.Scheduler method) run_conformer_jobs() (arc.scheduler.Scheduler method) run_freq_job() (arc.scheduler.Scheduler method) run_irc_job() (arc.scheduler.Scheduler method) run_job() (arc.scheduler.Scheduler method) run_onedmin_job() (arc.scheduler.Scheduler method) run_opt_job() (arc.scheduler.Scheduler method) run_orbitals_job() (arc.scheduler.Scheduler method) run_scan_jobs() (arc.scheduler.Scheduler method) run_sp_job() (arc.scheduler.Scheduler method) run_time (arc.species.species.ARCSpecies attribute) run_ts_conformer_jobs() (arc.scheduler.Scheduler method) running_jobs (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) rxn_index (arc.species.species.ARCSpecies attribute) rxn_label (arc.species.species.ARCSpecies attribute) rxn_list (arc.scheduler.Scheduler attribute) rxn_zone_atom_indices (arc.species.species.ARCSpecies attribute)

S

s_bonds_mol_from_xyz() (in module arc.species.converter) safe_copy_file() (in module arc.common) save_conformers_file() (in module arc.plotter) save_e_elect() (arc.scheduler.Scheduler method) save_geo() (in module arc.plotter) save_irc_traj_animation() (in module arc.plotter) save_kinetics_lib() (in module arc.plotter) save_nd_rotor_yaml() (in module arc.plotter) save_project_info_file() (arc.main.ARC method) save_restart (arc.scheduler.Scheduler attribute) save_restart_dict() (arc.scheduler.Scheduler method) save_rotor_text_file() (in module arc.plotter) save_thermo_lib() (in module arc.plotter) save_transport_lib() (in module arc.plotter) save_yaml_file() (in module arc.common) scan_level (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) scan_quality_check() (in module arc.job.trsh) schedule_jobs() (arc.scheduler.Scheduler method) Scheduler (class in arc.scheduler) scissors() (arc.species.species.ARCSpecies method) server (arc.job.ssh.SSHClient attribute) server_job_ids (arc.scheduler.Scheduler attribute) servers (arc.scheduler.Scheduler attribute) set_dihedral() (arc.species.species.ARCSpecies method) set_label_reactants_products() (arc.reaction.ARCReaction method) set_levels_of_theory() (arc.main.ARC method) set_mol_list() (arc.species.species.ARCSpecies method) set_multiplicity() (in module arc.species.converter) set_radicals_by_map() (in module arc.species.converter) set_rdkit_dihedrals() (in module arc.species.converter) set_transport_data() (arc.species.species.ARCSpecies method) set_vector_length() (in module arc.species.vectors) show_sticks() (in module arc.plotter) simple() (arc.level.Level method) skip_nmd (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute)

sort_atoms_in_descending_label_order() (in module arc.common) sort_two_lists_by_the_first() (in module arc.common) sort_xyz_using_indices() (in module arc.species.converter) sp_level (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) spawn_directed_scan_jobs() (arc.scheduler.Scheduler method) spawn_post_irc_jobs() (arc.scheduler.Scheduler method) spawn_post_opt_jobs() (arc.scheduler.Scheduler method) spawn_ts_jobs() (arc.scheduler.Scheduler method) species (arc.main.ARC attribute) species_dict (arc.scheduler.Scheduler attribute) species_has_freq() (in module arc.scheduler) species_has_geo() (in module arc.scheduler) species_has_sp() (in module arc.scheduler) species_has_sp_and_freq() (in module arc.scheduler) species_list (arc.scheduler.Scheduler attribute) species_to_sdf_file() (in module arc.species.converter) specific_job_type (arc.main.ARC attribute) split_mol() (in module arc.species.species) split_str_zmat() (in module arc.species.converter) SSHClient (class in arc.job.ssh) standardize_output_paths() (arc.main.ARC method) standardize_xyz_string() (in module arc.species.converter) StatmechEnum (class in arc.main) str_to_xyz() (in module arc.species.converter) str_to_zmat() (in module arc.species.converter) string_representer() (in module arc.common) submit_job() (arc.job.ssh.SSHClient method) (in module arc.job.local) success (arc.species.species.TSGuess attribute) successful_irc (arc.species.species.TSGuess attribute) successful_methods (arc.species.species.ARCSpecies attribute) successful_normal_mode (arc.species.species.TSGuess attribute) sum_list_entries() (in module arc.common) summarize_results() (in module arc.utils.scale) summary() (arc.main.ARC method) switch_ts() (arc.scheduler.Scheduler method)

T

t0 (arc.main.ARC attribute) (arc.species.species.TSGuess attribute) t1 (arc.species.species.ARCSpecies attribute) T_count (arc.main.ARC attribute) T_max (arc.main.ARC attribute) T_min (arc.main.ARC attribute) testing (arc.scheduler.Scheduler attribute) text_plotter() (in module arc.plotter) thermo (arc.species.species.ARCSpecies attribute) thermo_adapter (arc.main.ARC attribute) three_params (arc.main.ARC attribute) tic() (arc.species.species.TSGuess method) time_lapse() (in module arc.common) timedelta_from_str() (in module arc.common) to_arkane_level_of_theory() (arc.level.Level method) to_group() (in module arc.species.conformers) to_rdkit_mol() (in module arc.species.converter) to_yaml() (in module arc.common) tok() (arc.species.species.TSGuess method) torsions_to_scans() (in module arc.common) translate_group() (in module arc.species.conformers) translate_groups() (in module arc.species.conformers) translate_to_center_of_mass() (in module arc.species.converter) translate_xyz() (in module arc.species.converter) transport_data (arc.species.species.ARCSpecies attribute) troubleshoot_conformer_isomorphism() (arc.scheduler.Scheduler method) troubleshoot_ess() (arc.scheduler.Scheduler method) troubleshoot_negative_freq() (arc.scheduler.Scheduler method) troubleshoot_opt_jobs() (arc.scheduler.Scheduler method) troubleshoot_scan_job() (arc.scheduler.Scheduler method) trsh_conformer_isomorphism() (in module arc.job.trsh) trsh_ess_job() (in module arc.job.trsh)

trsh_ess_jobs (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) trsh_job_on_server() (in module arc.job.trsh) trsh_job_queue() (in module arc.job.trsh) trsh_keyword_cartesian() (in module arc.job.trsh) trsh_keyword_checkfile() (in module arc.job.trsh) trsh_keyword_inaccurate_quadrature() (in module arc.job.trsh) trsh_keyword_intaccuracy() (in module arc.job.trsh) trsh_keyword_l123() (in module arc.job.trsh) trsh_keyword_neg_eigen() (in module arc.job.trsh) trsh_keyword_no_qc() (in module arc.job.trsh) trsh_keyword_nosymm() (in module arc.job.trsh) trsh_keyword_opt_maxcycles() (in module arc.job.trsh) trsh_keyword_scf() (in module arc.job.trsh) trsh_keyword_unconverged() (in module arc.job.trsh) trsh_negative_freq() (in module arc.job.trsh) trsh_scan_job() (in module arc.job.trsh) trsh_special_rotor() (in module arc.job.trsh) ts_adapters (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) ts_checks (arc.species.species.ARCSpecies attribute) ts_conf_spawned (arc.species.species.ARCSpecies attribute) ts_guess_level (arc.main.ARC attribute) (arc.scheduler.Scheduler attribute) ts_guesses (arc.species.species.ARCSpecies attribute) ts_guesses_exhausted (arc.species.species.ARCSpecies attribute) ts_label (arc.reaction.ARCReaction attribute) ts_number (arc.species.species.ARCSpecies attribute) ts_report (arc.species.species.ARCSpecies attribute) ts_species (arc.reaction.ARCReaction attribute) ts_xyz_guess (arc.reaction.ARCReaction attribute) tsg_spawned (arc.species.species.ARCSpecies attribute) TSGuess (class in arc.species.species)

U

un (arc.job.ssh.SSHClient attribute) unique_species_labels (arc.scheduler.Scheduler attribute) unit_vector() (in module arc.species.vectors) unsuccessful_methods (arc.species.species.ARCSpecies attribute)

up_param() (in module arc.species.zmat) update_mol() (in module arc.species.conformers) update_molecule() (in module arc.species.converter) update_zmat_with_new_atom() (in module arc.species.zmat) upload_file() (arc.job.ssh.SSHClient method)

W

write_file() (in module arc.job.local)

write_input_file() (arc.main.ARC method) write_unconverged_log() (in module arc.processor)

X

xyz_file_format_to_xyz() (in module arc.species.converter) xyz_from_data() (in module arc.species.converter) xyz_to_ase() (in module arc.species.converter) xyz_to_coords_and_element_numbers() (in module arc.species.converter) xyz_to_coords_list() (in module arc.species.converter) xyz_to_dmat() (in module arc.species.converter) xyz_to_kinbot_list() (in module arc.species.converter)

xyz_to_np_array() (in module arc.species.converter) xyz_to_pybel_mol() (in module arc.species.converter) xyz_to_rmg_conformer() (in module arc.species.converter) xyz_to_str() (in module arc.species.converter) xyz_to_turbomol_format() (in module arc.species.converter) xyz_to_x_y_z() (in module arc.species.converter) xyz_to_xyz_file_format() (in module arc.species.converter) xyz_to_zmat() (in module arc.species.zmat)

Y

yml_path (arc.species.species.ARCSpecies attribute)

Z

zmat (arc.species.species.ARCSpecies attribute) zmat_from_xyz() (in module arc.species.converter)

zmat_to_coords() (in module arc.species.zmat) zmat_to_str() (in module arc.species.converter) zmat_to_xyz() (in module arc.species.converter)