Index

_

_irc_settings (chemsmart.settings.orca.YamlORCAProjectSettings attribute) _modred_settings (chemsmart.settings.orca.YamlORCAProjectSettings attribute) _nci_settings (chemsmart.settings.orca.YamlORCAProjectSettings attribute) _num_hours (chemsmart.settings.server.LSFServer attribute) (chemsmart.settings.server.PBSServer attribute) (chemsmart.settings.server.Server attribute) (chemsmart.settings.server.SGE_Server attribute) (chemsmart.settings.server.SLURMServer attribute) (chemsmart.settings.server.YamlServerSettings attribute) _opt_settings (chemsmart.settings.orca.YamlORCAProjectSettings attribute)

_queue_name (chemsmart.settings.server.LSFServer attribute) (chemsmart.settings.server.PBSServer attribute) (chemsmart.settings.server.Server attribute) (chemsmart.settings.server.SGE_Server attribute) (chemsmart.settings.server.SLURMServer attribute) (chemsmart.settings.server.YamlServerSettings attribute) _scan_settings (chemsmart.settings.orca.YamlORCAProjectSettings attribute) _sp_settings (chemsmart.settings.orca.YamlORCAProjectSettings attribute) _td_settings (chemsmart.settings.orca.YamlORCAProjectSettings attribute) _ts_settings (chemsmart.settings.orca.YamlORCAProjectSettings attribute) _wbi_settings (chemsmart.settings.orca.YamlORCAProjectSettings attribute)

A

acetylene_molecule() (in module tests.conftest) active_atoms (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) add_lines_in_yaml_files() (in module chemsmart.cli.config)

all_available_gaussian_projects (chemsmart.settings.user.ChemsmartUserSettings property) all_available_orca_projects (chemsmart.settings.user.ChemsmartUserSettings property) all_available_servers (chemsmart.settings.user.ChemsmartUserSettings property) available_servers (chemsmart.settings.executable.Executable property)

B

batch (chemsmart.settings.submitters.RunScript attribute) blank_element_pdb_file() (in module tests.conftest)

build() (chemsmart.settings.gaussian.YamlGaussianProjectSettingsBuilder method) (chemsmart.settings.orca.YamlORCAProjectSettingsBuilder method)

C

capture_log() (in module tests.conftest) charge_and_multiplicity_string (chemsmart.jobs.gaussian.settings.GaussianQMMMJobSettings property) charge_high (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) charge_intermediate (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) charge_total (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) check_crystal_qmmm() (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings method) chemdraw_directory() (in module tests.conftest) chemdraw_expected_directory() (in module tests.conftest) chemsmart module chemsmart.cli module chemsmart.cli.config module chemsmart.cli.gaussian module chemsmart.cli.gaussian.com module chemsmart.cli.gaussian.crest module chemsmart.cli.gaussian.custom module chemsmart.cli.gaussian.dias module chemsmart.cli.gaussian.gaussian module chemsmart.cli.gaussian.irc module chemsmart.cli.gaussian.link module chemsmart.cli.gaussian.modred module chemsmart.cli.gaussian.nci module chemsmart.cli.gaussian.opt module chemsmart.cli.gaussian.qmmm module chemsmart.cli.gaussian.resp module chemsmart.cli.gaussian.scan module chemsmart.cli.gaussian.singlepoint module chemsmart.cli.gaussian.tddft module chemsmart.cli.gaussian.traj module chemsmart.cli.gaussian.ts module chemsmart.cli.gaussian.wbi module chemsmart.cli.job module chemsmart.cli.jobrunner module chemsmart.cli.logger module chemsmart.cli.main module chemsmart.cli.mol module chemsmart.cli.mol.irc module chemsmart.cli.mol.mol module chemsmart.cli.mol.movie module chemsmart.cli.mol.visualize module chemsmart.cli.orca module chemsmart.cli.orca.inp module chemsmart.cli.orca.irc module chemsmart.cli.orca.modred module chemsmart.cli.orca.neb module chemsmart.cli.orca.opt module chemsmart.cli.orca.orca module chemsmart.cli.orca.qmmm module chemsmart.cli.orca.scan module chemsmart.cli.orca.singlepoint module chemsmart.cli.orca.ts module

chemsmart.cli.run module chemsmart.cli.sub module chemsmart.cli.subcommands module chemsmart.cli.update module chemsmart.settings module chemsmart.settings.executable module chemsmart.settings.gaussian module chemsmart.settings.orca module chemsmart.settings.server module chemsmart.settings.submitters module chemsmart.settings.user module chemsmart_dest (chemsmart.cli.config.Config property) chemsmart_gaussian (chemsmart.cli.config.Config property) chemsmart_generated_xyz_file() (in module tests.conftest) chemsmart_orca (chemsmart.cli.config.Config property) chemsmart_package_path (chemsmart.cli.config.Config property) chemsmart_server (chemsmart.cli.config.Config property) chemsmart_template (chemsmart.cli.config.Config property) chemsmart_templates_config() (in module tests.conftest) ChemsmartUserSettings (class in chemsmart.settings.user) chiral_molecule() (in module tests.conftest) cli_args (chemsmart.settings.submitters.RunScript attribute) click_file_label_and_index_options() (in module chemsmart.cli.job) click_filename_options() (in module chemsmart.cli.job) click_filenames_options() (in module chemsmart.cli.job) click_folder_options() (in module chemsmart.cli.job) click_gaussian_irc_options() (in module chemsmart.cli.gaussian.gaussian) click_gaussian_jobtype_options() (in module chemsmart.cli.gaussian.gaussian) click_gaussian_options() (in module chemsmart.cli.gaussian.gaussian) click_gaussian_qmmm_options() (in module chemsmart.cli.gaussian.gaussian) click_gaussian_settings_options() (in module chemsmart.cli.gaussian.gaussian) click_gaussian_solvent_group_options() (in module chemsmart.cli.gaussian.gaussian) click_gaussian_solvent_options() (in module chemsmart.cli.gaussian.gaussian) click_gaussian_td_options() (in module chemsmart.cli.gaussian.gaussian) click_grouper_sub_options() (in module chemsmart.cli.gaussian.crest) click_job_options() (in module chemsmart.cli.job) click_jobrunner_options() (in module chemsmart.cli.jobrunner) click_molecule_vibrational_displacement_options() (in module chemsmart.cli.job) click_orca_jobtype_options() (in module chemsmart.cli.orca.orca) click_orca_options() (in module chemsmart.cli.orca.orca) click_orca_settings_options() (in module chemsmart.cli.orca.orca) click_orca_solvent_group_options() (in module chemsmart.cli.orca.orca) click_orca_solvent_options() (in module chemsmart.cli.orca.orca) click_pubchem_options() (in module chemsmart.cli.job) click_pymol_hybrid_visualization_options() (in module chemsmart.cli.mol.mol) click_pymol_mo_options() (in module chemsmart.cli.mol.mol) click_pymol_nci_options() (in module chemsmart.cli.mol.mol) click_pymol_pml_options() (in module chemsmart.cli.mol.mol) click_pymol_save_options() (in module chemsmart.cli.mol.mol) click_pymol_visualization_options() (in module chemsmart.cli.mol.mol) co2_molecule() (in module tests.conftest) complex_molecule_cdxml_file() (in module tests.conftest) conda_folder (chemsmart.cli.config.Config property) conda_path (chemsmart.cli.config.Config property) Config (class in chemsmart.cli.config) config_dir (chemsmart.settings.user.ChemsmartUserSettings attribute) configure_conda_in_server_yaml() (chemsmart.cli.config.Config method) configure_paths_interactively() (chemsmart.cli.config.Config method) conformers_from_rdkit() (in module tests.conftest) constrained_atoms() (in module tests.conftest) constrained_pbc_db_file() (in module tests.conftest) conv_charges (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) conv_charges_conv_thresh (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) conv_charges_max_n_cycles (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) create() (chemsmart.settings.gaussian.GaussianProjectSettingsManager method) (chemsmart.settings.orca.ORCAProjectSettingsManager method) (chemsmart.settings.server.ServerSettingsManager method) create_orca_qmmm_subcommand() (in module chemsmart.cli.orca.qmmm) create_qmmm_subcommand() (in module chemsmart.cli.gaussian.qmmm) cube_test_directory() (in module tests.conftest) current() (chemsmart.settings.server.Server class method) cxsmiles_expected_large_c2_file() (in module tests.conftest) cxsmiles_expected_large_c3_file() (in module tests.conftest) cxsmiles_large_molecule_c2_file() (in module tests.conftest) cxsmiles_large_molecule_c3_file() (in module tests.conftest) cxsmiles_normal_file() (in module tests.conftest) cxsmiles_r_enantiomer_file() (in module tests.conftest) cxsmiles_r_rotamer_file() (in module tests.conftest) cxsmiles_s_enantiomer_file() (in module tests.conftest) cxsmiles_s_rotamer_file() (in module tests.conftest) cxsmiles_test_directory() (in module tests.conftest)

D

data (chemsmart.settings.user.ChemsmartUserSettings attribute) delete_la_bond_double_counting_atoms (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) delete_la_double_counting (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) detect_server_scheduler() (chemsmart.settings.server.Server static method)

dlpno_ccsdt_sp_full_print() (in module tests.conftest) dna_hybrid_visualized_xyz_file() (in module tests.conftest) docs_conf_file_path (chemsmart.cli.update.Updater property) dummy_yaml_file() (in module tests.conftest)

E

ecp_layer (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) ecp_layer_ecp (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) email (chemsmart.settings.user.ChemsmartUserSettings property) embedding_type (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) empty_pdb_file() (in module tests.conftest) env (chemsmart.settings.executable.Executable property) env_vars (chemsmart.cli.config.Config property) esp_cube_file() (in module tests.conftest) ethanol_molecule() (in module tests.conftest) ethylene_molecule() (in module tests.conftest) excel_file() (in module tests.conftest) executable (chemsmart.settings.submitters.Submitter property) Executable (class in chemsmart.settings.executable) expected_benzene_com() (in module tests.conftest) expected_benzene_xyz() (in module tests.conftest) expected_complex_molecule_com() (in module tests.conftest) expected_imidazole_xyz() (in module tests.conftest)

EXPECTED_LARGE_C2 (tests.test_structures.TestInChIKey attribute) EXPECTED_LARGE_C3 (tests.test_structures.TestInChIKey attribute) expected_methane_com() (in module tests.conftest) expected_methane_xyz() (in module tests.conftest) EXPECTED_NORMAL (tests.test_structures.TestCXSMILES attribute) (tests.test_structures.TestInChIKey attribute) EXPECTED_R_ENANTIOMER (tests.test_structures.TestCXSMILES attribute) (tests.test_structures.TestInChIKey attribute) EXPECTED_R_ROTAMER (tests.test_structures.TestCXSMILES attribute) EXPECTED_S_ENANTIOMER (tests.test_structures.TestCXSMILES attribute) (tests.test_structures.TestInChIKey attribute) EXPECTED_S_ROTAMER (tests.test_structures.TestCXSMILES attribute) expected_two_molecules_1_com() (in module tests.conftest) expected_two_molecules_1_xyz() (in module tests.conftest) expected_two_molecules_2_com() (in module tests.conftest) expected_two_molecules_2_xyz() (in module tests.conftest) extended_xyz_file() (in module tests.conftest) extra_commands (chemsmart.settings.server.Server property)

F

fake_iterate_jobrunner() (in module tests.conftest) fe2_quintet_output() (in module tests.conftest) fe2_singlet_output() (in module tests.conftest) fe2_triplet_output() (in module tests.conftest) fe3_doublet_output() (in module tests.conftest) fe3_quartet_output() (in module tests.conftest) fe3_sextet_output() (in module tests.conftest) filename (chemsmart.settings.gaussian.GaussianProjectSettingsManager attribute) (chemsmart.settings.gaussian.YamlGaussianProjectSettingsBuilder attribute) (chemsmart.settings.orca.ORCAProjectSettingsManager attribute) (chemsmart.settings.orca.YamlORCAProjectSettingsBuilder attribute) (chemsmart.settings.server.ServerSettingsManager attribute) (chemsmart.settings.submitters.RunScript attribute) from_dict() (chemsmart.settings.server.Server class method) (chemsmart.settings.submitters.Submitter class method)

from_project() (chemsmart.settings.gaussian.GaussianProjectSettings class method) (chemsmart.settings.orca.ORCAProjectSettings class method) from_scheduler_type() (chemsmart.settings.server.Server class method) (chemsmart.settings.submitters.Submitter class method) from_servername() (chemsmart.settings.executable.Executable class method) (chemsmart.settings.server.Server class method) from_yaml() (chemsmart.settings.gaussian.YamlGaussianProjectSettings class method) (chemsmart.settings.orca.YamlORCAProjectSettings class method) (chemsmart.settings.server.Server class method) (chemsmart.settings.server.YamlServerSettings class method) FUGAKUSubmitter (class in chemsmart.settings.submitters) functional (chemsmart.settings.gaussian.GaussianProjectSettings attribute), [1] (chemsmart.settings.orca.ORCAProjectSettings attribute), [1]

G

gas_route (tests.test_GaussianSettings.TestGaussianRoute attribute) gas_route2 (tests.test_GaussianSettings.TestGaussianRoute attribute) gaussian_acetone_opt_outfile() (in module tests.conftest) gaussian_benzene_opt_outfile() (in module tests.conftest) gaussian_boltzmann_test_directory() (in module tests.conftest) gaussian_co2_opt_outfile() (in module tests.conftest) gaussian_co2_pressure1p5_outfile() (in module tests.conftest) gaussian_co2_pressure3_outfile() (in module tests.conftest) gaussian_conformer1_outfile() (in module tests.conftest) gaussian_conformer2_outfile() (in module tests.conftest) gaussian_dna_link_sp_outputfile() (in module tests.conftest) gaussian_dppeFeCl2_link_opt_failed_outputfile() (in module tests.conftest) gaussian_dppeFeCl2_link_opt_outputfile() (in module tests.conftest) gaussian_failed_link_output() (in module tests.conftest) gaussian_failed_modred_outfile() (in module tests.conftest) gaussian_failed_scan_outfile() (in module tests.conftest) gaussian_frozen_opt_inputfile() (in module tests.conftest) gaussian_frozen_opt_outfile() (in module tests.conftest) gaussian_he_opt_outfile() (in module tests.conftest) gaussian_hirshfeld_outfile() (in module tests.conftest) gaussian_inputs_genecp_directory() (in module tests.conftest) gaussian_inputs_test_directory() (in module tests.conftest) gaussian_jobrunner_no_scratch() (in module tests.conftest) gaussian_jobrunner_scratch() (in module tests.conftest) gaussian_link_failed_outfile() (in module tests.conftest) gaussian_link_inputs_test_directory() (in module tests.conftest) gaussian_link_modred_output() (in module tests.conftest) gaussian_link_opt_input() (in module tests.conftest) gaussian_link_opt_outfile() (in module tests.conftest) gaussian_link_opt_outputfile() (in module tests.conftest) gaussian_link_outputs_test_directory() (in module tests.conftest) gaussian_link_sp_input() (in module tests.conftest) gaussian_link_sp_outfile() (in module tests.conftest) gaussian_link_sp_outputfile() (in module tests.conftest) gaussian_link_ts_input() (in module tests.conftest) gaussian_link_ts_outputfile() (in module tests.conftest) gaussian_modred_inputfile() (in module tests.conftest) gaussian_modred_with_custom_basis_for_all_atoms_from_api() (in module tests.conftest) gaussian_mp2_outputfile() (in module tests.conftest) gaussian_oniom_outputfile() (in module tests.conftest) gaussian_opt_genecp_inputfile() (in module tests.conftest) gaussian_opt_inputfile() (in module tests.conftest) gaussian_outputs_test_directory() (in module tests.conftest) gaussian_ozone_opt_outfile() (in module tests.conftest) gaussian_pbc_1d_inputfile() (in module tests.conftest) gaussian_pbc_2d_outputfile() (in module tests.conftest) gaussian_pbc_3d_outputfile() (in module tests.conftest) gaussian_pbc_inputs_test_directory() (in module tests.conftest) gaussian_pbc_outputs_test_directory() (in module tests.conftest) gaussian_pbc_test_directory() (in module tests.conftest) gaussian_pd_insertion_ts_r_outfile() (in module tests.conftest) gaussian_process_pipeline() (in module chemsmart.cli.gaussian.gaussian)

gaussian_project_yaml_files (chemsmart.settings.user.ChemsmartUserSettings property) gaussian_qmmm_input_test_directory() (in module tests.conftest) gaussian_qmmm_inputfile_2layer() (in module tests.conftest) gaussian_qmmm_inputfile_3layer() (in module tests.conftest) gaussian_quintet_opt_outfile() (in module tests.conftest) gaussian_rc_hirshfeld_outfile() (in module tests.conftest) gaussian_scan_inputfile() (in module tests.conftest) gaussian_semiempirical_pm6_output_file() (in module tests.conftest) gaussian_semiempirical_test_directory() (in module tests.conftest) gaussian_singlet_opt_outfile() (in module tests.conftest) gaussian_test_directory() (in module tests.conftest) gaussian_thermochem_test_directory() (in module tests.conftest) gaussian_triplet_opt_outfile() (in module tests.conftest) gaussian_ts_genecp_outfile() (in module tests.conftest) gaussian_written_files_directory() (in module tests.conftest) gaussian_written_modred_file() (in module tests.conftest) gaussian_written_opt_file() (in module tests.conftest) gaussian_written_opt_file_with_route() (in module tests.conftest) gaussian_written_opt_from_graphite_2d_pbc_log() (in module tests.conftest) gaussian_written_pm6_opt_file() (in module tests.conftest) gaussian_written_qmmm_file() (in module tests.conftest) gaussian_written_qmmm_log_file() (in module tests.conftest) gaussian_written_scan_multiple_degrees_of_freedom_file() (in module tests.conftest) gaussian_written_scan_multiple_degrees_of_freedom_with_constraints_file() (in module tests.conftest) gaussian_written_scan_single_degree_of_freedom_file() (in module tests.conftest) gaussian_written_sp_from_nhc_singlet_log_with_custom_basis_file() (in module tests.conftest) gaussian_written_sp_from_nhc_singlet_log_with_custom_basis_from_api_file() (in module tests.conftest) gaussian_written_sp_from_nhc_singlet_log_with_custom_basis_from_api_file_v2() (in module tests.conftest) gaussian_written_sp_from_nhc_singlet_log_with_custom_solvent_file() (in module tests.conftest) gaussian_written_sp_from_nhc_singlet_log_with_solvent_file() (in module tests.conftest) gaussian_written_ts_file() (in module tests.conftest) gaussian_written_ts_from_nhc_singlet_log_file() (in module tests.conftest) gaussian_yaml_settings_defaults() (in module tests.conftest) gaussian_yaml_settings_directory() (in module tests.conftest) gaussian_yaml_settings_gas_solv() (in module tests.conftest) gaussian_yaml_settings_gas_solv_project_name() (in module tests.conftest) gaussian_yaml_settings_qmmm() (in module tests.conftest) gaussian_yaml_settings_qmmm_project_name() (in module tests.conftest) gaussian_yaml_settings_solv() (in module tests.conftest) GaussianExecutable (class in chemsmart.settings.executable) GaussianProjectSettings (class in chemsmart.settings.gaussian) GaussianProjectSettingsManager (class in chemsmart.settings.gaussian) GaussianQMMMJobSettings (class in chemsmart.jobs.gaussian.settings) gen_text_file_from_web() (in module tests.conftest) gen_txt_file_from_web() (in module tests.conftest) genecp_text_file_from_web() (in module tests.conftest) genecp_txt_file_from_web() (in module tests.conftest) get_executable() (chemsmart.settings.executable.GaussianExecutable method) (chemsmart.settings.executable.NCIPLOTExecutable method) (chemsmart.settings.executable.ORCAExecutable method) get_qmmm_level_of_theory_string() (chemsmart.jobs.gaussian.settings.GaussianQMMMJobSettings method) get_submitter() (chemsmart.settings.server.Server method) gtoint_errfile() (in module tests.conftest)

H

hf_com_filepath() (in module tests.conftest) high_level_atoms (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) high_level_basis (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute)

high_level_functional (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) high_level_h_bond_length (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) hirshfeld_full_print() (in module tests.conftest) hydrogen_molecule() (in module tests.conftest)

I

inchikey_large_molecule_c2_file() (in module tests.conftest) inchikey_large_molecule_c3_file() (in module tests.conftest) inchikey_normal_file() (in module tests.conftest) inchikey_r_enantiomer_file() (in module tests.conftest) inchikey_s_enantiomer_file() (in module tests.conftest) inchikey_test_directory() (in module tests.conftest) inpfile_path() (in module tests.conftest) intermediate_level_atoms (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) intermediate_level_basis (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) INTERMEDIATE_LEVEL_BUILT_IN_METHODS (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) intermediate_level_functional (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) intermediate_level_method (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) intermediate_level_solvation (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) invoke_config_server() (in module tests.conftest) invoke_folder_command() (in module tests.conftest) invoke_mol_cli() (in module tests.conftest)

invoke_mol_with_visualize() (in module tests.conftest) io_test_directory() (in module tests.conftest) irc_settings() (chemsmart.settings.gaussian.GaussianProjectSettings method) (chemsmart.settings.gaussian.YamlGaussianProjectSettings method) (chemsmart.settings.orca.ORCAProjectSettings method) (chemsmart.settings.orca.YamlORCAProjectSettings method) iterate_configs_directory() (in module tests.conftest) iterate_expected_output_directory() (in module tests.conftest) iterate_expected_output_file() (in module tests.conftest) iterate_input_directory() (in module tests.conftest) iterate_integration_config_file() (in module tests.conftest) iterate_invalid_skeleton_link_index_config_file() (in module tests.conftest) iterate_jobrunner() (in module tests.conftest) iterate_template_file() (in module tests.conftest) iterate_test_directory() (in module tests.conftest) iterate_timeout_config_file() (in module tests.conftest)

J

job (chemsmart.settings.submitters.FUGAKUSubmitter attribute) (chemsmart.settings.submitters.PBSSubmitter attribute) (chemsmart.settings.submitters.SLFSubmitter attribute) (chemsmart.settings.submitters.SLURMSubmitter attribute) (chemsmart.settings.submitters.Submitter attribute)

jobtype (chemsmart.jobs.gaussian.settings.GaussianQMMMJobSettings attribute) (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute)

K

kwargs (chemsmart.settings.server.LSFServer attribute) (chemsmart.settings.server.PBSServer attribute) (chemsmart.settings.server.Server attribute) (chemsmart.settings.server.SGE_Server attribute) (chemsmart.settings.server.SLURMServer attribute) (chemsmart.settings.server.YamlServerSettings attribute) (chemsmart.settings.submitters.FUGAKUSubmitter attribute) (chemsmart.settings.submitters.PBSSubmitter attribute) (chemsmart.settings.submitters.SLFSubmitter attribute) (chemsmart.settings.submitters.SLURMSubmitter attribute) (chemsmart.settings.submitters.Submitter attribute)

L

large_basis (chemsmart.settings.gaussian.GaussianProjectSettings attribute), [1] (chemsmart.settings.orca.ORCAProjectSettings attribute), [1]

logger_options() (in module chemsmart.cli.logger) low_level_method (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) LSFServer (class in chemsmart.settings.server)

M

main() (in module chemsmart.cli.main) main_settings() (chemsmart.settings.gaussian.GaussianProjectSettings method) (chemsmart.settings.orca.ORCAProjectSettings method) make_cli_ctx_obj() (in module tests.conftest) make_thermochemistry_mock() (in module tests.conftest) mem_gb (chemsmart.settings.server.Server property) metal_ligand_molecules_cdxml_file() (in module tests.conftest) methane_molecule() (in module tests.conftest) methanol_and_ethanol() (in module tests.conftest) methanol_molecule() (in module tests.conftest) methanol_molecules() (in module tests.conftest) methyl3hexane_molecule() (in module tests.conftest) mock_popen() (in module tests.conftest) modred_gen_inputfile() (in module tests.conftest) modred_genecp_custom_solvent_inputfile() (in module tests.conftest) modred_genecp_inputfile() (in module tests.conftest) modred_settings() (chemsmart.settings.gaussian.GaussianProjectSettings method) (chemsmart.settings.gaussian.YamlGaussianProjectSettings method) (chemsmart.settings.orca.ORCAProjectSettings method) (chemsmart.settings.orca.YamlORCAProjectSettings method) module chemsmart chemsmart.cli chemsmart.cli.config chemsmart.cli.gaussian chemsmart.cli.gaussian.com chemsmart.cli.gaussian.crest chemsmart.cli.gaussian.custom chemsmart.cli.gaussian.dias chemsmart.cli.gaussian.gaussian chemsmart.cli.gaussian.irc chemsmart.cli.gaussian.link chemsmart.cli.gaussian.modred chemsmart.cli.gaussian.nci chemsmart.cli.gaussian.opt chemsmart.cli.gaussian.qmmm chemsmart.cli.gaussian.resp chemsmart.cli.gaussian.scan chemsmart.cli.gaussian.singlepoint chemsmart.cli.gaussian.tddft chemsmart.cli.gaussian.traj chemsmart.cli.gaussian.ts chemsmart.cli.gaussian.wbi chemsmart.cli.job chemsmart.cli.jobrunner chemsmart.cli.logger chemsmart.cli.main chemsmart.cli.mol chemsmart.cli.mol.irc chemsmart.cli.mol.mol chemsmart.cli.mol.movie chemsmart.cli.mol.visualize chemsmart.cli.orca chemsmart.cli.orca.inp chemsmart.cli.orca.irc chemsmart.cli.orca.modred chemsmart.cli.orca.neb chemsmart.cli.orca.opt chemsmart.cli.orca.orca chemsmart.cli.orca.qmmm chemsmart.cli.orca.scan chemsmart.cli.orca.singlepoint chemsmart.cli.orca.ts chemsmart.cli.run chemsmart.cli.sub chemsmart.cli.subcommands chemsmart.cli.update chemsmart.settings chemsmart.settings.executable chemsmart.settings.gaussian chemsmart.settings.orca chemsmart.settings.server chemsmart.settings.submitters chemsmart.settings.user tests tests.conftest tests.test_converter tests.test_GaussianGenECP tests.test_GaussianIO tests.test_GaussianSettings tests.test_GaussianWriter tests.test_groupers tests.test_ORCAIO tests.test_organizer tests.test_PyMOLJobs tests.test_server tests.test_structures tests.test_utils tests.test_YAMLIO

mol_process_pipeline() (in module chemsmart.cli.mol.mol) mol_qmmm_process_pipeline() (in module chemsmart.cli.mol.mol) mult_high (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) mult_intermediate (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) mult_total (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) multi_model_pdb_file() (in module tests.conftest) multi_molecule_cdxml_file() (in module tests.conftest) multiple_molecules_xyz_file() (in module tests.conftest)

N

n_unit_cell_atoms (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) NAME (chemsmart.settings.server.LSFServer attribute), [1] name (chemsmart.settings.server.LSFServer attribute) NAME (chemsmart.settings.server.PBSServer attribute), [1] name (chemsmart.settings.server.PBSServer attribute) (chemsmart.settings.server.Server attribute) NAME (chemsmart.settings.server.SGE_Server attribute), [1] name (chemsmart.settings.server.SGE_Server attribute) NAME (chemsmart.settings.server.SLURMServer attribute), [1] name (chemsmart.settings.server.SLURMServer attribute) NAME (chemsmart.settings.server.YamlServerSettings attribute), [1] name (chemsmart.settings.server.YamlServerSettings attribute) NAME (chemsmart.settings.submitters.FUGAKUSubmitter attribute), [1] name (chemsmart.settings.submitters.FUGAKUSubmitter attribute) NAME (chemsmart.settings.submitters.PBSSubmitter attribute), [1] name (chemsmart.settings.submitters.PBSSubmitter attribute) NAME (chemsmart.settings.submitters.SLFSubmitter attribute), [1] name (chemsmart.settings.submitters.SLFSubmitter attribute) NAME (chemsmart.settings.submitters.SLURMSubmitter attribute), [1] name (chemsmart.settings.submitters.SLURMSubmitter attribute) NAME (chemsmart.settings.submitters.Submitter attribute), [1] name (chemsmart.settings.submitters.Submitter attribute) nci_settings() (chemsmart.settings.gaussian.GaussianProjectSettings method) (chemsmart.settings.gaussian.YamlGaussianProjectSettings method) (chemsmart.settings.orca.ORCAProjectSettings method) (chemsmart.settings.orca.YamlORCAProjectSettings method)

nciplot_jobrunner_no_scratch() (in module tests.conftest) nciplot_jobrunner_scratch() (in module tests.conftest) NCIPLOTExecutable (class in chemsmart.settings.executable) neb_settings() (chemsmart.settings.orca.ORCAProjectSettings method) (chemsmart.settings.orca.YamlORCAProjectSettings method) Ni_def2tzvp_PCHOSi_svp_text_file() (in module tests.conftest) Ni_def2tzvp_PCHOSi_svp_txt_file() (in module tests.conftest) num_cores (chemsmart.settings.server.Server property) num_gpus (chemsmart.settings.server.Server property) num_hours (chemsmart.settings.server.Server property) NUM_PROCS (tests.test_groupers.Test_BasicRMSD_grouper_and_basic_functionality attribute) (tests.test_groupers.Test_conformer_ids_functionality attribute) (tests.test_groupers.Test_EnergyGrouper attribute) (tests.test_groupers.Test_grouper_complete_linkage attribute) (tests.test_groupers.Test_grouper_utility_functions attribute) (tests.test_groupers.Test_HungarianRMSD_grouper attribute) (tests.test_groupers.Test_IRMSD_grouper attribute) (tests.test_groupers.Test_label_and_append_label attribute) (tests.test_groupers.Test_other_groupers attribute) (tests.test_groupers.Test_output_file_generation attribute) (tests.test_groupers.Test_PymolRMSD_grouper attribute) (tests.test_groupers.Test_SpyRMSD_grouper attribute) (tests.test_groupers.Test_Tanimoto_similarity_grouper attribute) (tests.test_groupers.Test_TorsionFingerprint_grouper attribute) num_threads (chemsmart.settings.server.Server property)

O

opt_settings() (chemsmart.settings.gaussian.GaussianProjectSettings method) (chemsmart.settings.gaussian.YamlGaussianProjectSettings method) (chemsmart.settings.orca.ORCAProjectSettings method) (chemsmart.settings.orca.YamlORCAProjectSettings method) optregion_fixed_atoms (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) orca_co2_output() (in module tests.conftest) orca_dias_directory() (in module tests.conftest) orca_epr_solv() (in module tests.conftest) orca_errors_directory() (in module tests.conftest) orca_faulty_solv() (in module tests.conftest) orca_fixed_atoms() (in module tests.conftest) orca_fixed_bonds_and_angles() (in module tests.conftest) orca_fixed_dihedral() (in module tests.conftest) orca_he_output_freq() (in module tests.conftest) orca_input_nebts_file() (in module tests.conftest) orca_input_nebts_product_xyz_file() (in module tests.conftest) orca_input_nebts_reactant_xyz_file() (in module tests.conftest) orca_input_nebts_ts_xyz_file() (in module tests.conftest) orca_inputs_directory() (in module tests.conftest) orca_inputs_xyz_directory() (in module tests.conftest) orca_jobrunner_no_scratch() (in module tests.conftest) orca_jobrunner_scratch() (in module tests.conftest) orca_neb_output_file() (in module tests.conftest) orca_outputs_directory() (in module tests.conftest) orca_process_pipeline() (in module chemsmart.cli.orca.orca) orca_project_yaml_files (chemsmart.settings.user.ChemsmartUserSettings property) orca_qmmm_input_file() (in module tests.conftest) orca_sn2_ts_output() (in module tests.conftest)

orca_test_directory() (in module tests.conftest) orca_two_layer_qmmmm_output_file() (in module tests.conftest) orca_written_files_directory() (in module tests.conftest) orca_written_he_monoatomic_opt_file() (in module tests.conftest) orca_written_modred_file() (in module tests.conftest) orca_written_neb_file() (in module tests.conftest) orca_written_opt_file() (in module tests.conftest) orca_written_opt_file_with_route() (in module tests.conftest) orca_written_scan_multiple_degrees_of_freedom_file() (in module tests.conftest) orca_written_scan_multiple_degrees_of_freedom_with_constraints_file() (in module tests.conftest) orca_written_scan_single_degree_of_freedom_file() (in module tests.conftest) orca_written_sp_from_nhc_singlet_log_with_solvent_file() (in module tests.conftest) orca_written_ts_file() (in module tests.conftest) orca_written_ts_from_nhc_singlet_log_file() (in module tests.conftest) orca_yaml_settings_custom_solv_cosmors_project_name() (in module tests.conftest) orca_yaml_settings_custom_solv_project_name() (in module tests.conftest) orca_yaml_settings_defaults() (in module tests.conftest) orca_yaml_settings_directory() (in module tests.conftest) orca_yaml_settings_gas_solv() (in module tests.conftest) orca_yaml_settings_gas_solv_project_name() (in module tests.conftest) orca_yaml_settings_neb_project_name() (in module tests.conftest) orca_yaml_settings_orca_project_name() (in module tests.conftest) orca_yaml_settings_solv() (in module tests.conftest) orca_yaml_settings_solv_project_name() (in module tests.conftest) ORCAExecutable (class in chemsmart.settings.executable) ORCAProjectSettings (class in chemsmart.settings.orca) ORCAProjectSettingsManager (class in chemsmart.settings.orca) ORCAQMMMJobSettings (class in chemsmart.jobs.orca.settings) outputs_test_directory() (in module tests.conftest)

P

package_path (chemsmart.cli.update.Updater property) pbs_server() (in module tests.conftest) PBSServer (class in chemsmart.settings.server) PBSSubmitter (class in chemsmart.settings.submitters) powershell_profiles (chemsmart.cli.config.Config property) process_pipeline() (in module chemsmart.cli.run) (in module chemsmart.cli.sub) PROGRAM (chemsmart.settings.executable.Executable attribute) (chemsmart.settings.executable.GaussianExecutable attribute) (chemsmart.settings.executable.NCIPLOTExecutable attribute) (chemsmart.settings.executable.ORCAExecutable attribute) project (chemsmart.settings.user.ChemsmartUserSettings property) PROJECT_NAME (chemsmart.settings.gaussian.GaussianProjectSettings attribute), [1] (chemsmart.settings.gaussian.YamlGaussianProjectSettings attribute), [1] (chemsmart.settings.orca.ORCAProjectSettings attribute), [1] (chemsmart.settings.orca.YamlORCAProjectSettings attribute), [1] ps_env_vars (chemsmart.cli.config.Config property) pymol_align_jobrunner() (in module tests.conftest) pymol_hybrid_visualization_jobrunner() (in module tests.conftest) pymol_ircmovie_jobrunner() (in module tests.conftest) pymol_mo_jobrunner() (in module tests.conftest)

pymol_movie_jobrunner() (in module tests.conftest) pymol_visualization_jobrunner() (in module tests.conftest) pyproject_path (chemsmart.cli.update.Updater property) pytestmark (tests.test_groupers.Test_BasicRMSD_grouper_and_basic_functionality attribute) (tests.test_groupers.Test_conformer_ids_functionality attribute) (tests.test_groupers.Test_edge_cases attribute) (tests.test_groupers.Test_energy_extraction_function attribute) (tests.test_groupers.Test_EnergyGrouper attribute) (tests.test_groupers.Test_grouper_complete_linkage attribute) (tests.test_groupers.Test_grouper_utility_functions attribute) (tests.test_groupers.Test_HungarianRMSD_grouper attribute) (tests.test_groupers.Test_IRMSD_grouper attribute) (tests.test_groupers.Test_label_and_append_label attribute) (tests.test_groupers.Test_other_groupers attribute) (tests.test_groupers.Test_output_file_generation attribute) (tests.test_groupers.Test_PymolRMSD_grouper attribute) (tests.test_groupers.Test_SpyRMSD_grouper attribute) (tests.test_groupers.Test_Tanimoto_similarity_grouper attribute) (tests.test_groupers.Test_TorsionFingerprint_grouper attribute) (tests.test_groupers.Testfactory attribute) (tests.test_PyMOLJobs.TestPyMOLJobs attribute)

Q

qmmm_block (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings property) qmmm_route_string (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings property) qmmm_settings() (chemsmart.settings.gaussian.GaussianProjectSettings method) (chemsmart.settings.gaussian.YamlGaussianProjectSettings method) (chemsmart.settings.orca.ORCAProjectSettings method) (chemsmart.settings.orca.YamlORCAProjectSettings method)

qmmm_written_xyz_file() (in module tests.conftest) qmmm_written_xyz_only_file() (in module tests.conftest) queue_name (chemsmart.settings.server.Server property)

R

re_init_and_validate() (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings method) reference_genecp_txt_file_from_api() (in module tests.conftest) register() (chemsmart.settings.server.Server method) (chemsmart.settings.server.YamlServerSettings method) run_gaussian_and_capture_settings() (in module tests.conftest)

run_orca_and_capture_settings() (in module tests.conftest) run_script (chemsmart.settings.submitters.Submitter property) run_thermochemistry_and_capture_settings() (in module tests.conftest) run_thermochemistry_with_directory() (in module tests.conftest) RunScript (class in chemsmart.settings.submitters)

S

scale_formal_charge_ecp_atom (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) scale_formal_charge_mm_atom (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) scan_settings() (chemsmart.settings.gaussian.GaussianProjectSettings method) (chemsmart.settings.gaussian.YamlGaussianProjectSettings method) (chemsmart.settings.orca.ORCAProjectSettings method) (chemsmart.settings.orca.YamlORCAProjectSettings method) scheduler (chemsmart.settings.server.Server property) SCHEDULER_TYPE (chemsmart.settings.server.LSFServer attribute), [1] (chemsmart.settings.server.PBSServer attribute), [1] (chemsmart.settings.server.SGE_Server attribute), [1] (chemsmart.settings.server.SLURMServer attribute), [1] scratch (chemsmart.settings.server.Server property) (chemsmart.settings.user.ChemsmartUserSettings property) scratch_dir (chemsmart.settings.executable.Executable property) (chemsmart.settings.server.Server property) sdf_file() (in module tests.conftest) server (chemsmart.settings.submitters.FUGAKUSubmitter attribute) (chemsmart.settings.submitters.PBSSubmitter attribute) (chemsmart.settings.submitters.SLFSubmitter attribute) (chemsmart.settings.submitters.SLURMSubmitter attribute) (chemsmart.settings.submitters.Submitter attribute) Server (class in chemsmart.settings.server) server_yaml_file() (in module tests.conftest) server_yaml_files (chemsmart.settings.user.ChemsmartUserSettings property) ServerSettingsManager (class in chemsmart.settings.server) session_mocker() (in module tests.conftest) setup_class() (tests.test_groupers.Test_PymolRMSD_grouper class method) setup_environment() (chemsmart.cli.config.Config method)

SGE_Server (class in chemsmart.settings.server) shell_config (chemsmart.cli.config.Config property) single_atom_molecule() (in module tests.conftest) single_model_pdb_file() (in module tests.conftest) single_molecule_cdx_file_imidazole() (in module tests.conftest) single_molecule_cdxml_file_benzene() (in module tests.conftest) single_molecule_cdxml_file_methane() (in module tests.conftest) single_molecule_xyz_file() (in module tests.conftest) skip_if_no_pymol() (in module tests.test_PyMOLJobs) SLFSubmitter (class in chemsmart.settings.submitters) SLURMServer (class in chemsmart.settings.server) SLURMSubmitter (class in chemsmart.settings.submitters) small_basis (chemsmart.settings.gaussian.GaussianProjectSettings attribute), [1] (chemsmart.settings.orca.ORCAProjectSettings attribute), [1] smd_TBME_solvent_parameters_text_file() (in module tests.conftest) smd_TBME_solvent_parameters_txt_file() (in module tests.conftest) solv_route (tests.test_GaussianSettings.TestGaussianRoute attribute) solv_route2 (tests.test_GaussianSettings.TestGaussianRoute attribute) sp_settings() (chemsmart.settings.gaussian.GaussianProjectSettings method) (chemsmart.settings.gaussian.YamlGaussianProjectSettings method) (chemsmart.settings.orca.ORCAProjectSettings method) (chemsmart.settings.orca.YamlORCAProjectSettings method) spin_cube_file() (in module tests.conftest) structure_test_directory() (in module tests.conftest) submit() (chemsmart.settings.server.Server method) submit_command (chemsmart.settings.server.Server property) submit_folder (chemsmart.settings.submitters.Submitter property) submit_script (chemsmart.settings.submitters.Submitter property) Submitter (class in chemsmart.settings.submitters)

T

td_outputfile() (in module tests.conftest) td_settings() (chemsmart.settings.gaussian.YamlGaussianProjectSettings method) (chemsmart.settings.orca.YamlORCAProjectSettings method) tddft_test_directory() (in module tests.conftest) teardown_class() (tests.test_groupers.Test_PymolRMSD_grouper class method) (tests.test_groupers.Testfactory class method) teardown_method() (tests.test_groupers.Test_PymolRMSD_grouper method) temp_folder_with_files() (in module tests.conftest) temp_text_file() (in module tests.conftest) temp_working_dir() (in module tests.test_groupers) test_accumulates_settings() (tests.test_GaussianSettings.TestGaussianJobFromLogFile method) test_all_files_without_cxx_pattern() (tests.test_groupers.TestConformerIdExtraction method) test_alphanumeric() (tests.test_utils.TestNaturallySorted method) test_args_and_bare_keyword_keeps_args_form() (tests.test_utils.TestDeduplicateStringKeywords method) test_ase_style_single_indices() (tests.test_utils.TestParseIndexSpecification method) test_ase_style_slices() (tests.test_utils.TestParseIndexSpecification method) test_atom_names() (tests.test_converter.TestPDBFile method) test_atoms_in_levels_default_low_level() (tests.test_structures.TestQMMMinMolecule method) test_atoms_in_levels_wrong_low_level() (tests.test_structures.TestQMMMinMolecule method) test_bare_and_args_keyword_keeps_args_form() (tests.test_utils.TestDeduplicateStringKeywords method) test_bare_keyword_duplicate_keeps_first() (tests.test_utils.TestDeduplicateStringKeywords method) test_base_record_template_method() (tests.test_groupers.Test_other_groupers method) test_basic_conversion() (tests.test_utils.TestIOUtilities method) Test_BasicRMSD_grouper_and_basic_functionality (class in tests.test_groupers) test_blank_element_columns_infer_two_letter_elements() (tests.test_converter.TestPDBFile method) test_boundary_checking_enabled() (tests.test_utils.TestParseIndexSpecification method) test_case_insensitive_matching() (tests.test_utils.TestDeduplicateStringKeywords method) test_cdx_molecule_to_graph() (tests.test_structures.TestCDXFile method) test_cdx_molecule_to_rdkit_conversion() (tests.test_structures.TestCDXFile method) test_cdxfile_get_molecules_index() (tests.test_structures.TestCDXFile method) test_chain_ids() (tests.test_converter.TestPDBFile method) test_charge_and_multiplicity_handling() (tests.test_structures.TestMoleculeAdvanced method) test_charge_and_multiplicity_population() (tests.test_ORCAIO.TestORCAQMMMJobSettings method) test_clean_duplicate_structure() (tests.test_utils.TestIOUtilities method) test_clean_label() (tests.test_utils.TestIOUtilities method) test_cli_group_remove_solvent_overrides_project_settings() (tests.test_GaussianSettings.TestGaussianJobFromComFile method) test_cli_group_solvent_options_propagate_to_opt() (tests.test_GaussianSettings.TestGaussianJobFromComFile method) test_cli_group_solvent_options_propagate_to_td() (tests.test_GaussianSettings.TestGaussianJobFromComFile method) test_cmp_with_ignore_list() (tests.test_utils.TestUtils method) test_cmp_with_ignore_string() (tests.test_utils.TestUtils method) test_command_exception() (tests.test_utils.TestRunCommand method) test_command_failure() (tests.test_utils.TestRunCommand method) test_complete_linkage_prevents_chaining() (tests.test_groupers.Test_grouper_complete_linkage method) test_conformer_id_fallback_to_filename() (tests.test_groupers.TestConformerIdExtraction method) test_conformer_ids_from_log_directory() (tests.test_groupers.Test_conformer_ids_functionality method) Test_conformer_ids_functionality (class in tests.test_groupers) test_conformer_ids_molecules_correspondence() (tests.test_groupers.TestConformerIdExtraction method) test_connectivity_grouper() (tests.test_groupers.Test_other_groupers method) test_connectivity_grouper_for_crest_conformers() (tests.test_groupers.Test_other_groupers method) test_content_blocking() (tests.test_utils.TestUtils method) test_contribution_percentage_spin_scaling() (tests.test_GaussianIO.TestGaussian16Output method) test_conversion_strips_whitespace() (tests.test_utils.TestIOUtilities method) test_convert_ase_atoms_with_constraints_to_molecule() (tests.test_structures.TestMoleculeAdvanced method) test_convert_cdxml_folder_to_com() (tests.test_converter.TestPDBFile method) test_convert_cdxml_folder_to_xyz() (tests.test_converter.TestPDBFile method) test_convert_com_folder_to_xyz() (tests.test_converter.TestConverter method) test_convert_log_folder_to_com() (tests.test_converter.TestConverter method) test_convert_log_folder_to_xyz() (tests.test_converter.TestConverter method) test_convert_multi_molecule_cdxml_to_xyz_splits_files() (tests.test_converter.TestPDBFile method) test_convert_single_cdx_to_xyz() (tests.test_converter.TestPDBFile method) test_convert_single_cdxml_to_com() (tests.test_converter.TestPDBFile method) test_convert_single_cdxml_to_xyz() (tests.test_converter.TestPDBFile method) test_convert_single_comfile_to_xyz() (tests.test_converter.TestConverter method) test_convert_single_failed_modred_log_file_to_xyz() (tests.test_converter.TestConverter method) test_convert_single_failed_oniom_log_file_to_xyz() (tests.test_converter.TestConverter method) test_convert_single_link_logfile_to_xyz() (tests.test_converter.TestConverter method) test_convert_single_link_opt_logfile_to_com() (tests.test_converter.TestConverter method) test_convert_single_link_opt_logfile_to_xyz() (tests.test_converter.TestConverter method) test_convert_single_link_sp_logfile_to_xyz() (tests.test_converter.TestConverter method) test_convert_single_link_ts_logfile_to_xyz() (tests.test_converter.TestConverter method) test_convert_single_logfile_to_com() (tests.test_converter.TestConverter method) test_convert_single_opt_log_file_to_xyz() (tests.test_converter.TestConverter method) test_convert_single_sp_log_file_to_xyz() (tests.test_converter.TestConverter method) test_convert_single_wbi_log_file_to_xyz() (tests.test_converter.TestConverter method) test_convert_xyz_folder_to_com() (tests.test_converter.TestConverter method) test_converts_sdf_string_to_molecule_object() (tests.test_structures.TestSDFFile method) test_coordinate_block_with_partitions_returns_qmmm_molecule() (tests.test_structures.TestCoordinateBlock method) test_coordinate_block_without_partitions_returns_molecule() (tests.test_structures.TestCoordinateBlock method) test_corrupted_file_handling() (tests.test_structures.TestFileHandlingAdvanced method) test_count_groups_matches_complete_linkage_iteration_order() (tests.test_groupers.Test_TorsionFingerprint_grouper method) test_create_molecule_list() (tests.test_utils.TestIOUtilities method) test_cube_file_format() (tests.test_structures.TestCoordinateBlockAdvanced method) test_data_directory() (in module tests.conftest) test_determine_basis_keyword_mixed_elements() (tests.test_GaussianGenECP.TestGenGenECPBasisDetermination method) test_determine_basis_keyword_no_heavy_elements() (tests.test_GaussianGenECP.TestGenGenECPBasisDetermination method) test_determine_basis_keyword_non_gen_basis() (tests.test_GaussianGenECP.TestGenGenECPBasisDetermination method) test_determine_basis_keyword_with_br() (tests.test_GaussianGenECP.TestGenGenECPBasisDetermination method) test_determine_basis_keyword_with_i() (tests.test_GaussianGenECP.TestGenGenECPBasisDetermination method) test_determine_basis_keyword_with_pd() (tests.test_GaussianGenECP.TestGenGenECPBasisDetermination method) test_different_formulas_always_separate() (tests.test_groupers.Test_edge_cases method) test_different_labels_create_different_outputs() (tests.test_groupers.Test_label_and_append_label method) test_directory_filetype_label_auto_generated() (tests.test_PyMOLJobs.TestPyMOLCLIFolderOptions method) test_directory_filetype_options_accepted() (tests.test_PyMOLJobs.TestPyMOLCLIFolderOptions method) test_directory_program_label_auto_generated() (tests.test_PyMOLJobs.TestPyMOLCLIFolderOptions method) test_directory_program_options_accepted() (tests.test_PyMOLJobs.TestPyMOLCLIFolderOptions method) test_distance_calculation() (tests.test_structures.TestMoleculeAdvanced method) test_docstring_example() (tests.test_utils.TestDeduplicateStringKeywords method) test_duplicate_detection_enabled() (tests.test_utils.TestParseIndexSpecification method) Test_edge_cases (class in tests.test_groupers) test_empty_file_raises_value_error() (tests.test_converter.TestPDBFile method) test_empty_keywords_list_returns_unchanged() (tests.test_utils.TestDeduplicateStringKeywords method) test_empty_keywords_returns_unchanged() (tests.test_utils.TestDeduplicateStringKeywords method) test_empty_list() (tests.test_utils.TestNaturallySorted method) test_empty_list_raises_index_error() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_empty_molecule_handling() (tests.test_structures.TestMoleculeAdvanced method) test_empty_route_string_returns_unchanged() (tests.test_utils.TestDeduplicateStringKeywords method) test_enantiomers_differ() (tests.test_structures.TestCXSMILES method) test_enantiomers_share_connectivity_layer() (tests.test_structures.TestInChIKey method) test_energy_extraction_from_gaussian_output_file() (tests.test_GaussianIO.TestGaussian16Output method) test_energy_extraction_from_ts_log_files() (tests.test_groupers.Test_EnergyGrouper method) test_energy_extraction_from_xyz_file() (tests.test_groupers.Test_EnergyGrouper method) Test_energy_extraction_function (class in tests.test_groupers) test_energy_extraction_gaussian() (tests.test_groupers.Test_energy_extraction_function method) test_energy_extraction_orca() (tests.test_groupers.Test_energy_extraction_function method) test_energy_grouper_for_crest_conformers() (tests.test_groupers.Test_EnergyGrouper method) test_energy_grouper_for_log_conformers() (tests.test_groupers.Test_EnergyGrouper method) test_energy_grouper_raises_error_for_missing_energy() (tests.test_groupers.Test_EnergyGrouper method) Test_EnergyGrouper (class in tests.test_groupers) test_equality_different_intermediate_xyzfile() (tests.test_ORCAIO.TestORCANEBJobSettings method) test_equality_different_joboption() (tests.test_ORCAIO.TestORCANEBJobSettings method) test_equality_different_nimages() (tests.test_ORCAIO.TestORCANEBJobSettings method) test_equality_different_parent_attributes() (tests.test_ORCAIO.TestORCANEBJobSettings method) test_equality_different_preopt_ends() (tests.test_ORCAIO.TestORCANEBJobSettings method) test_equality_different_restarting_xyzfile() (tests.test_ORCAIO.TestORCANEBJobSettings method) test_equality_different_semiempirical() (tests.test_ORCAIO.TestORCANEBJobSettings method) test_equality_identical_settings() (tests.test_ORCAIO.TestORCANEBJobSettings method) test_equality_includes_all_neb_attributes() (tests.test_ORCAIO.TestORCANEBJobSettings method) test_extract_conformer_id_with_pattern() (tests.test_groupers.TestConformerIdExtraction method) test_extract_conformer_id_without_pattern() (tests.test_groupers.TestConformerIdExtraction method) test_fe2_quintet_orbital_properties() (tests.test_ORCAIO.TestORCAOutput method) test_fe2_singlet_orbital_properties() (tests.test_ORCAIO.TestORCAOutput method) test_fe2_triplet_orbital_properties() (tests.test_ORCAIO.TestORCAOutput method) test_fe3_doublet_orbital_properties() (tests.test_ORCAIO.TestORCAOutput method) test_fe3_quartet_orbital_properties() (tests.test_ORCAIO.TestORCAOutput method) test_fe3_sextet_orbital_properties() (tests.test_ORCAIO.TestORCAOutput method) test_file_names() (tests.test_utils.TestNaturallySorted method) test_file_organizer() (tests.test_organizer.TestOrganizer method) test_filepath_resolves_absolute() (tests.test_converter.TestPDBFile method) test_formula_grouper() (tests.test_groupers.Test_other_groupers method) test_free_format_comma_separated() (tests.test_utils.TestParseIndexSpecification method) test_free_format_hyphen_ranges() (tests.test_utils.TestParseIndexSpecification method) test_free_format_mixed() (tests.test_utils.TestParseIndexSpecification method) test_free_format_with_negative_indices() (tests.test_utils.TestParseIndexSpecification method) test_from_pdb_file_infers_uppercase_two_letter_elements_when_blank() (tests.test_structures.TestMoleculeAdvanced method) test_from_pdb_file_preserves_atom_and_residue_metadata() (tests.test_structures.TestMoleculeAdvanced method) test_from_pdb_file_supports_model_index_selection() (tests.test_structures.TestMoleculeAdvanced method) test_frozen_atoms_manipulation() (tests.test_structures.TestMoleculeAdvanced method) test_gaussian_executable() (tests.test_server.TestServer method) test_gen_fallback_when_heavy_element_does_not_require_ecp() (tests.test_GaussianGenECP.TestGaussianGenGenECP method) test_gen_replacement_does_not_affect_noeigentest() (tests.test_GaussianGenECP.TestGenECPReplacementInRoute method) test_gen_to_genecp_replacement() (tests.test_GaussianGenECP.TestGenECPReplacementInRoute method) test_genecp_fallback_when_basis_missing_from_bse() (tests.test_GaussianGenECP.TestGaussianGenGenECP method) test_genecp_from_base_api() (tests.test_GaussianGenECP.TestGaussianGenGenECP method) test_genecp_from_base_api_accepts_hyphenless_def2_heavy_basis() (tests.test_GaussianGenECP.TestGaussianGenGenECP method) test_genecp_from_comfile() (tests.test_GaussianGenECP.TestGaussianGenGenECP method) test_genecp_from_modred_gen_comfile() (tests.test_GaussianGenECP.TestGaussianGenGenECP method) test_genecp_from_modred_genecp_comfile() (tests.test_GaussianGenECP.TestGaussianGenGenECP method) test_genecp_from_modred_genecp_solvent_comfile() (tests.test_GaussianGenECP.TestGaussianGenGenECP method) test_genecp_replacement_does_not_affect_other_keywords() (tests.test_GaussianGenECP.TestGenECPReplacementInRoute method) test_generate_fchk_uses_source_basename_not_label() (tests.test_PyMOLJobs.TestPyMOLFileProcessingUsesSourceFilename method) test_get_constrained_atoms() (tests.test_ORCAIO.TestORCAOutput method) test_get_constrained_bond_lengths_and_angles() (tests.test_ORCAIO.TestORCAOutput method) test_get_constrained_dihedral_angles() (tests.test_ORCAIO.TestORCAOutput method) test_get_indices_from_string() (tests.test_utils.TestUtils method) test_get_label_function() (tests.test_groupers.Test_label_and_append_label method) test_get_list_from_string() (tests.test_utils.TestGetListFromStringRange method) test_get_list_from_string_range() (tests.test_utils.TestGetListFromStringRange method) (tests.test_utils.TestUtils method) test_get_molecules_all() (tests.test_converter.TestPDBFile method) test_get_molecules_first() (tests.test_converter.TestPDBFile method) test_get_molecules_last() (tests.test_converter.TestPDBFile method) test_get_range_from_list() (tests.test_utils.TestUtils method) test_get_settings_from_yaml_gas_solv() (tests.test_GaussianSettings.TestGaussianJobSettings method) test_get_settings_from_yaml_solv() (tests.test_GaussianSettings.TestGaussianJobSettings method) test_gibbs_energy_extraction_function() (tests.test_groupers.Test_EnergyGrouper method) test_graph_properties() (tests.test_structures.TestGraphFeatures method) test_group_xyz_files_contain_energy_and_index_info() (tests.test_groupers.Test_output_file_generation method) test_group_xyz_files_energy_from_log_files() (tests.test_groupers.Test_output_file_generation method) test_group_xyz_files_sorted_by_energy() (tests.test_groupers.Test_output_file_generation method) Test_grouper_complete_linkage (class in tests.test_groupers) Test_grouper_utility_functions (class in tests.test_groupers) test_grouping_result_caching() (tests.test_groupers.Test_grouper_utility_functions method) test_gtoint_errfile() (tests.test_ORCAIO.TestORCAOutput method) test_he_freq_output() (tests.test_ORCAIO.TestORCAOutput method) test_header_like_then_data_like() (tests.test_utils.TestIOUtilities method) test_hrmsd_grouper_for_crest_molecules() (tests.test_groupers.Test_HungarianRMSD_grouper method) test_hrmsd_grouper_for_rotated_molecules() (tests.test_groupers.Test_HungarianRMSD_grouper method) Test_HungarianRMSD_grouper (class in tests.test_groupers) test_ignore_hydrogen() (tests.test_groupers.Test_HungarianRMSD_grouper method) (tests.test_groupers.Test_IRMSD_grouper method) (tests.test_groupers.Test_PymolRMSD_grouper method) (tests.test_groupers.Test_SpyRMSD_grouper method) test_include_solvent() (tests.test_GaussianSettings.TestGaussianJobFromComFile method) test_index_zero_raises_value_error() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_infer_element_ca_is_carbon() (tests.test_converter.TestPDBFile method) test_infer_element_cl() (tests.test_converter.TestPDBFile method) test_infer_element_digits_only_raises() (tests.test_converter.TestPDBFile method) test_infer_element_empty_raises() (tests.test_converter.TestPDBFile method) test_infer_element_fe() (tests.test_converter.TestPDBFile method) test_infer_element_leading_digit() (tests.test_converter.TestPDBFile method) test_infer_element_zn() (tests.test_converter.TestPDBFile method) test_infer_pdb_element_from_uppercase_atom_names() (tests.test_structures.TestMoleculeAdvanced method) test_info_dict_populated() (tests.test_converter.TestPDBFile method) test_inheritance() (tests.test_ORCAIO.TestORCANEBJobSettings method) test_init_default() (tests.test_ORCAIO.TestORCANEBJobSettings method) test_init_stores_filename() (tests.test_converter.TestPDBFile method) test_init_with_parameters() (tests.test_ORCAIO.TestORCANEBJobSettings method) test_invalid_input_type() (tests.test_utils.TestRunCommand method) test_invalid_inputs() (tests.test_utils.TestParseIndexSpecification method) (tests.test_utils.TestString2Index1Based method) test_invalid_molecule_creation() (tests.test_structures.TestMoleculeAdvanced method) Test_IRMSD_grouper (class in tests.test_groupers) test_irmsd_grouper_for_crest_molecules() (tests.test_groupers.Test_IRMSD_grouper method) test_irmsd_grouper_for_rotated_molecules() (tests.test_groupers.Test_IRMSD_grouper method) test_is_aromatic_non_aromatic_molecules() (tests.test_structures.TestMoleculeAdvanced method) test_is_float() (tests.test_utils.TestUtils method) test_iterative_compare_list_of_dicts() (tests.test_utils.TestUtils method) test_iterative_compare_list_of_elements() (tests.test_utils.TestUtils method) test_iterative_compare_list_of_lists() (tests.test_utils.TestUtils method) test_iterative_compare_list_of_string() (tests.test_utils.TestUtils method) test_iterative_compare_list_of_tuples() (tests.test_utils.TestUtils method) test_keyword_as_list() (tests.test_utils.TestDeduplicateStringKeywords method) test_keyword_as_string() (tests.test_utils.TestDeduplicateStringKeywords method) test_keyword_as_tuple() (tests.test_utils.TestDeduplicateStringKeywords method) test_keyword_not_present_returns_unchanged() (tests.test_utils.TestDeduplicateStringKeywords method) test_keyword_with_longer_args_preferred_over_shorter() (tests.test_utils.TestDeduplicateStringKeywords method) Test_label_and_append_label (class in tests.test_groupers) test_label_in_group_xyz_files() (tests.test_groupers.Test_label_and_append_label method) test_label_in_output_directory() (tests.test_groupers.Test_label_and_append_label method) test_label_with_num_groups() (tests.test_groupers.Test_label_and_append_label method) test_large_file_handling() (tests.test_structures.TestFileHandlingAdvanced method) test_large_molecule_c2_cxsmiles() (tests.test_structures.TestCXSMILES method) test_large_molecule_c2_inchikey() (tests.test_structures.TestInChIKey method) test_large_molecule_c3_cxsmiles() (tests.test_structures.TestCXSMILES method) test_large_molecule_c3_inchikey() (tests.test_structures.TestInChIKey method) test_large_molecules_differ() (tests.test_structures.TestCXSMILES method) (tests.test_structures.TestInChIKey method) test_large_numbers() (tests.test_utils.TestNaturallySorted method) test_line_of_all_integers() (tests.test_utils.TestIOUtilities method) test_line_of_integer_followed_by_floats() (tests.test_utils.TestIOUtilities method) test_list_command_success() (tests.test_utils.TestRunCommand method) test_merge_dict() (tests.test_GaussianSettings.TestGaussianJobSettings method) test_merge_other_settings() (tests.test_GaussianSettings.TestGaussianJobSettings method) test_mixed_case() (tests.test_utils.TestNaturallySorted method) test_mixed_case_keyword_argument() (tests.test_utils.TestDeduplicateStringKeywords method) test_mixed_coordinate_formats() (tests.test_structures.TestCoordinateBlockAdvanced method) test_mixed_pattern_files_correspondence() (tests.test_groupers.TestConformerIdExtraction method) test_mixed_types() (tests.test_utils.TestNaturallySorted method) test_molecular_geometry() (tests.test_structures.TestStructures method) test_molecule_from_db_with_pbc_and_constraints() (tests.test_structures.TestMoleculeAdvanced method) test_molecule_from_filepath_cdxml() (tests.test_structures.TestCDXFile method) test_molecule_from_filepath_cdxml_multi_molecules() (tests.test_structures.TestCDXFile method) test_molecule_from_filepath_cdxml_pathlib() (tests.test_structures.TestCDXFile method) test_molecule_from_filepath_cdxml_return_list() (tests.test_structures.TestCDXFile method) test_molecule_from_filepath_uses_pdbfile() (tests.test_converter.TestPDBFile method) test_molecule_graph_generation() (tests.test_structures.TestMoleculeAdvanced method) test_molecule_property_raises_on_empty() (tests.test_converter.TestPDBFile method) test_molecule_property_returns_last_model() (tests.test_converter.TestPDBFile method) test_molecule_returns_molecule_object() (tests.test_converter.TestPDBFile method) test_molecule_to_rdkit_conversion() (tests.test_structures.TestMoleculeAdvanced method) test_molecules() (tests.test_GaussianIO.TestGaussianWBIOutput method) test_more_stereochemistry_handling() (tests.test_structures.TestChemicalFeatures method) test_multiple_guess_options_with_parentheses() (tests.test_GaussianSettings.TestGaussianLinkJobSettingsGuess method) test_multiple_keywords_deduplicated() (tests.test_utils.TestDeduplicateStringKeywords method) test_nci_uses_source_basename_for_cube_loading_and_command() (tests.test_PyMOLJobs.TestPyMOLFileProcessingUsesSourceFilename method) test_neb_block_basic() (tests.test_ORCAIO.TestORCANEBJobSettings method) test_neb_input_all_properties() (tests.test_ORCAIO.TestORCANEBInput method) test_neb_input_case_insensitive() (tests.test_ORCAIO.TestORCANEBInput method) test_neb_input_charge_and_multiplicity() (tests.test_ORCAIO.TestORCANEBInput method) test_neb_input_ending_xyzfile() (tests.test_ORCAIO.TestORCANEBInput method) test_neb_input_inherits_from_orca_input() (tests.test_ORCAIO.TestORCANEBInput method) test_neb_input_nimages() (tests.test_ORCAIO.TestORCANEBInput method) test_neb_input_pre_optimization_false() (tests.test_ORCAIO.TestORCANEBInput method) test_neb_input_restarting_allxyzfile_none() (tests.test_ORCAIO.TestORCANEBInput method) test_neb_input_starting_xyzfile() (tests.test_ORCAIO.TestORCANEBInput method) test_neb_input_ts_xyzfile() (tests.test_ORCAIO.TestORCANEBInput method) test_neb_input_with_preopt_true() (tests.test_ORCAIO.TestORCANEBInput method) test_neb_input_with_restart_file() (tests.test_ORCAIO.TestORCANEBInput method) test_neb_input_without_ts_file() (tests.test_ORCAIO.TestORCANEBInput method) test_no_duplicates_returns_unchanged() (tests.test_utils.TestDeduplicateStringKeywords method) test_no_numbers() (tests.test_utils.TestNaturallySorted method) test_none_route_string_returns_unchanged() (tests.test_utils.TestDeduplicateStringKeywords method) test_normal_termination_semiempirical_pm6_output_file() (tests.test_GaussianIO.TestGaussian16Output method) test_normal_termination_with_forces_and_frequencies() (tests.test_GaussianIO.TestGaussian16Output method) (tests.test_GaussianIO.TestGaussianWBIOutput method) test_normal_termination_with_trailing_blank_lines() (tests.test_GaussianIO.TestGaussian16Output method) test_num_atoms() (tests.test_converter.TestPDBFile method) test_num_groups_equals_num_molecules() (tests.test_groupers.Test_edge_cases method) test_num_groups_exceeds_num_molecules() (tests.test_groupers.Test_edge_cases method) test_num_groups_parameter() (tests.test_groupers.Test_BasicRMSD_grouper_and_basic_functionality method) test_numeric_order() (tests.test_utils.TestNaturallySorted method) test_oldform_redundant_coordinates_atomic_numbers() (tests.test_GaussianIO.TestGaussian16Output method) test_oniom_charge_multiplicity() (tests.test_GaussianIO.TestGaussian16Input method) test_open_ended_slice() (tests.test_utils.TestString2Index1Based method) test_orca_all_auxiliary_basis_sets() (tests.test_ORCAIO.TestORCABasis method) test_orca_executable() (tests.test_server.TestServer method) test_orca_faulty_solvent() (tests.test_ORCAIO.TestORCAInput method) test_orca_neb_input_with_xyz_files_specified() (tests.test_ORCAIO.TestORCAInput method) test_orca_qmmm_input() (tests.test_ORCAIO.TestORCAInput method) Test_other_groupers (class in tests.test_groupers) test_out_of_range_raises_index_error() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) Test_output_file_generation (class in tests.test_groupers) test_parse_index_boundary_detection_disabled() (tests.test_utils.TestParseIndexSpecification method) test_parse_index_boundary_detection_enabled() (tests.test_utils.TestParseIndexSpecification method) test_parse_index_duplicate_detection_disabled() (tests.test_utils.TestParseIndexSpecification method) test_parse_index_duplicate_detection_enabled() (tests.test_utils.TestParseIndexSpecification method) test_partition() (tests.test_GaussianIO.TestGaussian16Input method) test_partition_string_empty_and_none() (tests.test_ORCAIO.TestORCAQMMMJobSettings method) test_partition_string_qm_and_qm2() (tests.test_ORCAIO.TestORCAQMMMJobSettings method) test_partition_string_single_and_list_input() (tests.test_ORCAIO.TestORCAQMMMJobSettings method) test_pbc_1d_input() (tests.test_GaussianIO.TestGaussian16Input method) test_pbc_handling() (tests.test_structures.TestMoleculeAdvanced method) test_pd_insertion_ts_r_logfile() (tests.test_GaussianIO.TestGaussian16Output method) test_pdb_infer_pdb_element() (tests.test_converter.TestPDBFile method) test_pdb_molecule_from_pdb_atom_lines() (tests.test_converter.TestPDBFile method) test_pdb_parse_pdb_models() (tests.test_converter.TestPDBFile method) test_pdb_with_different_flavors() (tests.test_structures.TestMoleculeAdvanced method) test_pdb_with_no_bonds() (tests.test_structures.TestMoleculeAdvanced method) test_periodic_table_requires_ecp() (tests.test_GaussianGenECP.TestGenGenECPBasisDetermination method) test_pick_the_lowestenergy_conformers() (tests.test_groupers.Test_BasicRMSD_grouper_and_basic_functionality method) test_positions() (tests.test_converter.TestPDBFile method) test_pre_parenthesized_input_no_double_wrapping() (tests.test_GaussianSettings.TestGaussianLinkJobSettingsGuess method) test_pre_parenthesized_input_with_whitespace() (tests.test_GaussianSettings.TestGaussianLinkJobSettingsGuess method) test_pymol_align_job_on_three_files() (tests.test_PyMOLJobs.TestPyMOLJobs method) test_pymol_grouper_rejects_multiproc() (tests.test_groupers.Test_PymolRMSD_grouper method) test_pymol_hybrid_visualization_job_custom_light_colors_on_xyz_file() (tests.test_PyMOLJobs.TestPyMOLJobs method) test_pymol_hybrid_visualization_job_on_xyz_file() (tests.test_PyMOLJobs.TestPyMOLJobs method) test_pymol_hybrid_visualization_job_with_redundant_colors_on_xyz_file() (tests.test_PyMOLJobs.TestPyMOLJobs method) test_pymol_irc_movie_job_on_gaussian_log_multiple_structures() (tests.test_PyMOLJobs.TestPyMOLJobs method) test_pymol_MO_job_parameters() (tests.test_PyMOLJobs.TestPyMOLJobs method)

test_pymol_movie_job_on_gaussian_com_file() (tests.test_PyMOLJobs.TestPyMOLJobs method) test_pymol_nci_job_on_gaussian_com_file() (tests.test_PyMOLJobs.TestPyMOLJobs method) test_pymol_nci_job_parameters() (tests.test_PyMOLJobs.TestPyMOLJobs method) test_pymol_spin_job_on_gaussian_com_file() (tests.test_PyMOLJobs.TestPyMOLJobs method) test_pymol_spin_job_parameters() (tests.test_PyMOLJobs.TestPyMOLJobs method) test_pymol_visualization_job_on_gaussian_com_file() (tests.test_PyMOLJobs.TestPyMOLJobs method) test_pymol_visualization_job_on_gaussian_log_file() (tests.test_PyMOLJobs.TestPyMOLJobs method) test_pymol_visualization_job_on_gaussian_log_multiple_structures() (tests.test_PyMOLJobs.TestPyMOLJobs method) test_pymol_visualization_job_on_orca_inp_file() (tests.test_PyMOLJobs.TestPyMOLJobs method) test_pymol_visualization_job_on_orca_out_file() (tests.test_PyMOLJobs.TestPyMOLJobs method) test_pymol_visualization_job_on_pubchem_id() (tests.test_PyMOLJobs.TestPyMOLJobs method) test_pymol_visualization_job_on_smiles() (tests.test_PyMOLJobs.TestPyMOLJobs method) Test_PymolRMSD_grouper (class in tests.test_groupers) test_pymolrmsd_grouper_for_crest_molecules() (tests.test_groupers.Test_PymolRMSD_grouper method) test_pymolrmsd_grouper_for_rotated_molecules() (tests.test_groupers.Test_PymolRMSD_grouper method) test_qmmm_additional_opt_options_in_route() (tests.test_GaussianSettings.TestGaussianQMMMJobSettings method) test_qmmm_additional_route_parameters() (tests.test_GaussianSettings.TestGaussianQMMMJobSettings method) test_qmmm_atoms_handling() (tests.test_structures.TestQMMMinMolecule method) test_qmmm_partition_out_of_range_raises() (tests.test_structures.TestQMMMinMolecule method) test_qmmm_partition_overlap_raises() (tests.test_structures.TestQMMMinMolecule method) test_qmmm_settings() (tests.test_GaussianSettings.TestGaussianQMMMJobSettings method) test_qmmm_settings_for_atoms() (tests.test_GaussianSettings.TestGaussianQMMMJobSettings method) test_qmmm_settings_for_charge_and_multiplicity() (tests.test_GaussianSettings.TestGaussianQMMMJobSettings method) test_quintet_opt_output() (tests.test_GaussianIO.TestGaussian16Output method) test_r_enantiomer_cxsmiles() (tests.test_structures.TestCXSMILES method) test_r_enantiomer_inchikey() (tests.test_structures.TestInChIKey method) test_r_rotamer_cxsmiles() (tests.test_structures.TestCXSMILES method) test_raises_value_error_on_empty_or_invalid_input() (tests.test_utils.TestIOUtilities method) test_range_with_brackets() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_raw_lines_preserves_column_whitespace() (tests.test_converter.TestPDBFile method) test_raw_lines_strips_trailing_newlines() (tests.test_converter.TestPDBFile method) test_rdkit_isomorphism_grouper() (tests.test_groupers.Test_other_groupers method) test_read_2d_pbc_output() (tests.test_GaussianIO.TestGaussianPBCOutputFile method) test_read_additional_route_parameters() (tests.test_GaussianIO.TestRouteString method) test_read_complex_molecule_cdxml_file_() (tests.test_structures.TestCDXFile method) test_read_coordinate_block() (tests.test_structures.TestCoordinateBlock method) test_read_failed_link_job() (tests.test_GaussianIO.TestGaussian16Output method) test_read_file_content() (tests.test_GaussianIO.TestGaussianCubeFile method) test_read_frozen_coords() (tests.test_GaussianIO.TestGaussian16Input method) test_read_frozen_opt_outputfile() (tests.test_GaussianIO.TestGaussian16Output method) test_read_gaussian_cb_frozen_atoms() (tests.test_structures.TestCoordinateBlock method) test_read_gaussian_cb_with_tv() (tests.test_structures.TestCoordinateBlock method) test_read_gaussian_hf_comfile() (tests.test_GaussianSettings.TestGaussianJobSettings method) test_read_gaussian_input() (tests.test_GaussianIO.TestGaussian16Input method) test_read_gaussian_link_modred_output_file() (tests.test_GaussianIO.TestGaussian16Output method) test_read_gaussian_link_opt_input() (tests.test_GaussianIO.TestGaussian16Input method) test_read_gaussian_link_opt_output_file() (tests.test_GaussianIO.TestGaussian16Output method) test_read_gaussian_link_sp_output_file() (tests.test_GaussianIO.TestGaussian16Output method) test_read_gaussian_link_ts_input() (tests.test_GaussianIO.TestGaussian16Input method) test_read_gaussian_link_ts_output_file() (tests.test_GaussianIO.TestGaussian16Output method) test_read_gaussian_settings_from_orca_inp() (tests.test_GaussianSettings.TestGaussianJobSettings method) test_read_gausssian_link_sp_input() (tests.test_GaussianIO.TestGaussian16Input method) test_read_genecp_inputfile() (tests.test_GaussianIO.TestGaussian16Input method) test_read_genecp_outputfile() (tests.test_GaussianIO.TestGaussian16Output method) test_read_hirshfeld_charges_outputfile() (tests.test_GaussianIO.TestGaussian16Output method) test_read_hirshfeld_full_print_output() (tests.test_ORCAIO.TestORCAOutput method) test_read_hirshfeld_rc_charges_outputfile() (tests.test_GaussianIO.TestGaussian16Output method) test_read_metal_ligand_molecules_cdxml_file_() (tests.test_structures.TestCDXFile method) test_read_modred_inputfile() (tests.test_GaussianIO.TestGaussian16Input method) test_read_modred_outputfile() (tests.test_GaussianIO.TestGaussian16Output method) test_read_molecule_energy_from_xyz_file() (tests.test_structures.TestStructures method) test_read_molecule_from_gaussian_frozen_opt() (tests.test_structures.TestStructuresFromGaussianInput method) test_read_molecule_from_gaussian_modred() (tests.test_structures.TestStructuresFromGaussianInput method) test_read_molecule_from_gaussian_opt_input() (tests.test_structures.TestStructuresFromGaussianInput method) test_read_molecule_from_gaussian_pbc() (tests.test_structures.TestStructuresFromGaussianInput method) test_read_molecule_from_gaussian_scan() (tests.test_structures.TestStructuresFromGaussianInput method) test_read_molecule_from_modred_gen() (tests.test_structures.TestStructuresFromGaussianInput method) test_read_molecule_from_modred_genecp() (tests.test_structures.TestStructuresFromGaussianInput method) test_read_molecule_from_modred_genecp_custom_solvent() (tests.test_structures.TestStructuresFromGaussianInput method) test_read_molecule_from_multiple_molecules_xyz_file() (tests.test_structures.TestStructures method) test_read_molecule_from_opt_genecp() (tests.test_structures.TestStructuresFromGaussianInput method) test_read_molecule_from_single_molecule_xyz_file() (tests.test_structures.TestStructures method) test_read_mp2_outputfile() (tests.test_GaussianIO.TestGaussian16Output method) test_read_multi_molecule_cdxml_file() (tests.test_structures.TestCDXFile method) test_read_neb_input_basic() (tests.test_ORCAIO.TestORCANEBInput method) test_read_neb_output() (tests.test_ORCAIO.TestORCANEB method) test_read_oniom_outputfile() (tests.test_GaussianIO.TestGaussian16Output method) test_read_qmmm_output() (tests.test_ORCAIO.TestORCAQMMM method) test_read_route() (tests.test_ORCAIO.TestORCARoute method) test_read_route_semiempirical() (tests.test_GaussianIO.TestRouteString method) test_read_route_string_nonstandard() (tests.test_GaussianIO.TestRouteString method) test_read_route_string_opt_options() (tests.test_GaussianIO.TestRouteString method) test_read_route_string_standard() (tests.test_GaussianIO.TestRouteString method) test_read_route_string_standard2() (tests.test_GaussianIO.TestRouteString method) test_read_route_string_standard3a() (tests.test_GaussianIO.TestRouteString method) test_read_route_string_standard3b() (tests.test_GaussianIO.TestRouteString method) test_read_route_string_standard4() (tests.test_GaussianIO.TestRouteString method) test_read_route_string_standard5() (tests.test_GaussianIO.TestRouteString method) test_read_route_string_standard6() (tests.test_GaussianIO.TestRouteString method) test_read_route_string_standard7() (tests.test_GaussianIO.TestRouteString method) test_read_scan_inputfile() (tests.test_GaussianIO.TestGaussian16Input method) test_read_scan_outputfile() (tests.test_GaussianIO.TestGaussian16Output method) test_read_single_molecule_cdx_file_imidazole() (tests.test_structures.TestCDXFile method) test_read_single_molecule_cdxml_file_benzene() (tests.test_structures.TestCDXFile method) test_read_single_molecule_cdxml_file_methane() (tests.test_structures.TestCDXFile method) test_read_solvent() (tests.test_ORCAIO.TestORCAInput method) test_read_sp_full_print_output() (tests.test_ORCAIO.TestORCAOutput method) test_read_sp_output() (tests.test_ORCAIO.TestORCAOutput method) test_read_water_opt_input() (tests.test_ORCAIO.TestORCAInput method) test_read_water_output() (tests.test_ORCAIO.TestORCAEngrad method) (tests.test_ORCAIO.TestORCAOutput method) test_read_water_sp_input() (tests.test_ORCAIO.TestORCAInput method) test_reads_com_file() (tests.test_GaussianSettings.TestGaussianJobFromComFile method) test_reads_gaussian_pm6_outfile() (tests.test_GaussianSettings.TestGaussianJobFromLogFile method) test_reads_gaussian_ts_genecp_outfile() (tests.test_GaussianSettings.TestGaussianJobFromLogFile method) test_reads_oldform_redundant_coordinates_with_atomic_numbers() (tests.test_GaussianSettings.TestGaussianJobFromLogFile method) test_reads_pd_insertion_ts_r_logfile() (tests.test_GaussianSettings.TestGaussianJobFromLogFile method) test_record_types() (tests.test_converter.TestPDBFile method) test_record_writes_formula_outputs_with_headers() (tests.test_groupers.Test_other_groupers method) test_record_writes_rmsd_matrix_with_headers() (tests.test_groupers.Test_other_groupers method) test_regression_cxsmiles() (tests.test_structures.TestCXSMILES method) test_regression_inchikey() (tests.test_structures.TestInChIKey method) test_reject_plain_ints_as_floats() (tests.test_utils.TestIOUtilities method) test_replacement_with_various_delimiters() (tests.test_GaussianGenECP.TestGenECPReplacementInRoute method) test_repr() (tests.test_converter.TestPDBFile method) test_residue_names() (tests.test_converter.TestPDBFile method) test_residue_numbers() (tests.test_converter.TestPDBFile method) test_resonance_handling() (tests.test_structures.TestChemicalFeatures method) test_return_list_wraps_single() (tests.test_converter.TestPDBFile method) test_rmsd_grouper() (tests.test_groupers.Test_BasicRMSD_grouper_and_basic_functionality method) test_rmsd_grouper_for_crest_conformers() (tests.test_groupers.Test_BasicRMSD_grouper_and_basic_functionality method) test_rmsd_grouper_for_crest_conformers_ignore_Hs() (tests.test_groupers.Test_BasicRMSD_grouper_and_basic_functionality method) test_rmsd_grouper_for_rotated_molecules() (tests.test_groupers.Test_BasicRMSD_grouper_and_basic_functionality method) test_rmsd_infinity_for_different_molecules() (tests.test_groupers.Test_edge_cases method) test_rmsd_matrix_with_num_groups() (tests.test_groupers.Test_grouper_utility_functions method) test_rotamers_differ() (tests.test_structures.TestCXSMILES method) test_route_string_generation() (tests.test_ORCAIO.TestORCANEBJobSettings method) test_s_enantiomer_cxsmiles() (tests.test_structures.TestCXSMILES method) test_s_enantiomer_inchikey() (tests.test_structures.TestInChIKey method) test_s_rotamer_cxsmiles() (tests.test_structures.TestCXSMILES method) test_server_yaml() (tests.test_server.TestServer method) (tests.test_YAMLIO.TestYAMLFile method) test_settings_from_route() (tests.test_GaussianSettings.TestGaussianRoute method) test_settings_from_route2() (tests.test_GaussianSettings.TestGaussianRoute method) test_settings_from_route3() (tests.test_GaussianSettings.TestGaussianRoute method) test_settings_from_route4() (tests.test_GaussianSettings.TestGaussianRoute method) test_single_guess_option_no_parentheses() (tests.test_GaussianSettings.TestGaussianLinkJobSettingsGuess method) test_single_index_last() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_single_index_middle() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_single_index_string() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_single_integer() (tests.test_utils.TestString2Index1Based method) test_single_item() (tests.test_utils.TestNaturallySorted method) test_single_negative_index() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_singlet_opt_output() (tests.test_GaussianIO.TestGaussian16Output method) test_slice() (tests.test_utils.TestString2Index1Based method) test_slice_all() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_slice_from_beginning() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_slice_from_start() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_slice_range() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_slice_to_end() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_slice_with_step() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) (tests.test_utils.TestString2Index1Based method) test_sn2_ts_orca_output() (tests.test_ORCAIO.TestORCAOutput method) test_solvent_in_route() (tests.test_GaussianIO.TestRouteString method) test_special_characters() (tests.test_utils.TestNaturallySorted method) test_specified_indices_5_to_8() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_spin_cli_custom_label_uses_source_basename_and_exact_output_name() (tests.test_PyMOLJobs.TestPyMOLFileProcessingUsesSourceFilename method) test_spin_cubegen_uses_source_basename_fchk() (tests.test_PyMOLJobs.TestPyMOLFileProcessingUsesSourceFilename method) Test_SpyRMSD_grouper (class in tests.test_groupers) test_spyrmsd_grouper_for_crest_molecules() (tests.test_groupers.Test_SpyRMSD_grouper method) test_spyrmsd_grouper_for_rotated_molecules() (tests.test_groupers.Test_SpyRMSD_grouper method) test_stereochemistry_handling() (tests.test_structures.TestChemicalFeatures method) test_str() (tests.test_converter.TestPDBFile method) test_string_command_success() (tests.test_utils.TestRunCommand method) test_string_command_with_quotes() (tests.test_utils.TestRunCommand method) test_structure_grouper_factory() (tests.test_groupers.Testfactory method) test_structure_grouper_factory_energy() (tests.test_groupers.Testfactory method) test_symbols() (tests.test_converter.TestPDBFile method) test_tanimoto_grouper_for_crest_conformers() (tests.test_groupers.Test_Tanimoto_similarity_grouper method) Test_Tanimoto_similarity_grouper (class in tests.test_groupers) test_tanimoto_similarity_grouper() (tests.test_groupers.Test_Tanimoto_similarity_grouper method) test_three_bare_duplicates_keeps_first() (tests.test_utils.TestDeduplicateStringKeywords method) test_to_ase_energy_unit_conversion() (tests.test_structures.TestMoleculeAdvanced method) test_to_ase_energy_with_none_forces() (tests.test_structures.TestMoleculeAdvanced method) test_to_ase_forces_unit_conversion() (tests.test_structures.TestMoleculeAdvanced method) test_to_ase_none_energy_and_forces() (tests.test_structures.TestMoleculeAdvanced method) test_to_ase_none_energy_with_forces() (tests.test_structures.TestMoleculeAdvanced method) test_to_pdb_conversion() (tests.test_structures.TestMoleculeAdvanced method) test_to_pdb_strict_columns_and_final_end_record() (tests.test_structures.TestMoleculeAdvanced method) test_to_pdb_uses_molecule_attributes_for_chain_and_residue_metadata() (tests.test_structures.TestMoleculeAdvanced method) Test_TorsionFingerprint_grouper (class in tests.test_groupers) test_torsionfingerprint_grouper_for_crest_molecules() (tests.test_groupers.Test_TorsionFingerprint_grouper method) test_torsionfingerprint_grouper_for_rotated_molecules() (tests.test_groupers.Test_TorsionFingerprint_grouper method) test_trailing_and_leading_spaces() (tests.test_utils.TestIOUtilities method) test_trailing_comma_is_ignored() (tests.test_utils.TestIOUtilities method) test_traj_conformer_ids_original_indices() (tests.test_groupers.Test_conformer_ids_functionality method) test_triplet_opt_output() (tests.test_GaussianIO.TestGaussian16Output method) test_two_molecules_grouping() (tests.test_groupers.Test_edge_cases method) test_unique_returns_lowest_energy_representative() (tests.test_groupers.Test_grouper_utility_functions method) test_unrelated_tokens_preserved() (tests.test_utils.TestDeduplicateStringKeywords method) test_update_solvent() (tests.test_GaussianSettings.TestGaussianJobFromComFile method) test_use_maxdev_parameter() (tests.test_groupers.Test_TorsionFingerprint_grouper method) test_use_weights_parameter() (tests.test_groupers.Test_TorsionFingerprint_grouper method) test_user_defined_range() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_user_defined_range_complex() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_user_defined_range_with_hyphen() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_validation_errors() (tests.test_ORCAIO.TestORCANEBJobSettings method) test_variable_bond_cutoffs() (tests.test_structures.TestGraphFeatures method) test_very_high_threshold() (tests.test_groupers.Test_edge_cases method) test_very_low_threshold() (tests.test_groupers.Test_edge_cases method) test_volume() (tests.test_structures.TestChemicalFeatures method) test_water_optimized_output() (tests.test_ORCAIO.TestORCAOutput method) test_with_actual_lists() (tests.test_utils.TestParseIndexSpecification method) test_with_integer_objects() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_with_mixed_objects() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_write_creates_file() (tests.test_converter.TestPDBFile method) test_write_gaussian_input_from_pbc_logfile() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_generic_method_with_pdb_format() (tests.test_structures.TestMoleculeAdvanced method) test_write_modred_job() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_modred_with_custom_basis_for_all_elements_in_structure_using_api() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_opt_input_from_logfile() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_opt_job() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_opt_job_with_route() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_output_contains_atom_records() (tests.test_converter.TestPDBFile method) test_write_pdb_file() (tests.test_structures.TestMoleculeAdvanced method) test_write_pdb_rejects_unexpected_keyword_argument() (tests.test_structures.TestMoleculeAdvanced method) test_write_qmmm_input_from_logfile() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_qmmm_job() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_round_trip_preserves_atom_count() (tests.test_converter.TestPDBFile method) test_write_round_trip_preserves_positions() (tests.test_converter.TestPDBFile method) test_write_round_trip_preserves_symbols() (tests.test_converter.TestPDBFile method) test_write_scan_job_multiple_degrees_of_freedom() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_scan_job_multiple_degrees_of_freedom_with_constraints() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_scan_job_single_degree_of_freedom() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_semiempirical_opt_job() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_sp_input_with_solvation_from_logfile() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_sp_with_custom_solvation_from_logfile() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_ts_job() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_ts_with_custom_basis_from_logfile() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_ts_with_custom_basis_using_api() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_writes_gaussian_input_from_pbc_comfile() (tests.test_GaussianSettings.TestGaussianPBCJob method) TestCDXFile (class in tests.test_structures) TestChemicalFeatures (class in tests.test_structures) TestConformerIdExtraction (class in tests.test_groupers) TestConverter (class in tests.test_converter) TestCoordinateBlock (class in tests.test_structures) TestCoordinateBlockAdvanced (class in tests.test_structures) TestCXSMILES (class in tests.test_structures) TestDeduplicateStringKeywords (class in tests.test_utils) Testfactory (class in tests.test_groupers) TestFileHandlingAdvanced (class in tests.test_structures) TestGaussian16Input (class in tests.test_GaussianIO) TestGaussian16Output (class in tests.test_GaussianIO) TestGaussianCubeFile (class in tests.test_GaussianIO) TestGaussianGenGenECP (class in tests.test_GaussianGenECP) TestGaussianInputWriter (class in tests.test_GaussianWriter) TestGaussianJobFromComFile (class in tests.test_GaussianSettings) TestGaussianJobFromLogFile (class in tests.test_GaussianSettings) TestGaussianJobSettings (class in tests.test_GaussianSettings) TestGaussianLinkJobSettingsGuess (class in tests.test_GaussianSettings) TestGaussianPBCJob (class in tests.test_GaussianSettings) TestGaussianPBCOutputFile (class in tests.test_GaussianIO) TestGaussianQMMMJobSettings (class in tests.test_GaussianSettings) TestGaussianRoute (class in tests.test_GaussianSettings) TestGaussianWBIOutput (class in tests.test_GaussianIO) TestGenECPReplacementInRoute (class in tests.test_GaussianGenECP) TestGenGenECPBasisDetermination (class in tests.test_GaussianGenECP) TestGetListFromStringRange (class in tests.test_utils) TestGraphFeatures (class in tests.test_structures) TestInChIKey (class in tests.test_structures) TestIOUtilities (class in tests.test_utils) TestMoleculeAdvanced (class in tests.test_structures) TestNaturallySorted (class in tests.test_utils) TestORCABasis (class in tests.test_ORCAIO) TestORCAEngrad (class in tests.test_ORCAIO) TestORCAInput (class in tests.test_ORCAIO) TestORCANEB (class in tests.test_ORCAIO) TestORCANEBInput (class in tests.test_ORCAIO) TestORCANEBJobSettings (class in tests.test_ORCAIO) TestORCAOutput (class in tests.test_ORCAIO) TestORCAQMMM (class in tests.test_ORCAIO) TestORCAQMMMJobSettings (class in tests.test_ORCAIO) TestORCARoute (class in tests.test_ORCAIO) TestOrganizer (class in tests.test_organizer) TestParseIndexSpecification (class in tests.test_utils) TestPDBFile (class in tests.test_converter) TestPyMOLCLIFolderOptions (class in tests.test_PyMOLJobs) TestPyMOLFileProcessingUsesSourceFilename (class in tests.test_PyMOLJobs) TestPyMOLJobs (class in tests.test_PyMOLJobs) TestQMMMinMolecule (class in tests.test_structures) TestReturnObjectsAndIndicesFromStringIndex (class in tests.test_utils) TestRouteString (class in tests.test_GaussianIO) TestRunCommand (class in tests.test_utils) tests module tests.conftest module tests.test_converter module tests.test_GaussianGenECP module tests.test_GaussianIO module tests.test_GaussianSettings module tests.test_GaussianWriter module tests.test_groupers module tests.test_ORCAIO module tests.test_organizer module tests.test_PyMOLJobs module tests.test_server module tests.test_structures module tests.test_utils module tests.test_YAMLIO module tests_logger() (in module tests.conftest) TestSDFFile (class in tests.test_structures) TestServer (class in tests.test_server) TestString2Index1Based (class in tests.test_utils) TestStructures (class in tests.test_structures) TestStructuresFromGaussianInput (class in tests.test_structures) TestUtils (class in tests.test_utils) TestYAMLFile (class in tests.test_YAMLIO) tetrahydrofuran_molecule() (in module tests.conftest) text_directory() (in module tests.conftest) ts_conformers_log_directory() (in module tests.conftest) ts_settings() (chemsmart.settings.gaussian.GaussianProjectSettings method) (chemsmart.settings.gaussian.YamlGaussianProjectSettings method) (chemsmart.settings.orca.ORCAProjectSettings method) (chemsmart.settings.orca.YamlORCAProjectSettings method) two_rotated_molecules_xyz_file() (in module tests.conftest) txt_path() (in module tests.conftest)

U

update_pyproject_toml() (chemsmart.cli.update.Updater method) update_version_number() (chemsmart.cli.update.Updater method) update_yaml_files() (in module chemsmart.cli.config) Updater (class in chemsmart.cli.update) use_active_info_from_pbc (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) use_hosts (chemsmart.settings.server.Server property) USER_CONFIG_DIR (chemsmart.settings.user.ChemsmartUserSettings attribute), [1] user_gaussian_envars (chemsmart.settings.user.ChemsmartUserSettings property) user_gaussian_modules (chemsmart.settings.user.ChemsmartUserSettings property)

user_gaussian_script (chemsmart.settings.user.ChemsmartUserSettings property) user_gaussian_settings_dir (chemsmart.settings.user.ChemsmartUserSettings property) user_orca_envars (chemsmart.settings.user.ChemsmartUserSettings property) user_orca_modules (chemsmart.settings.user.ChemsmartUserSettings property) user_orca_script (chemsmart.settings.user.ChemsmartUserSettings property) user_orca_settings_dir (chemsmart.settings.user.ChemsmartUserSettings property) user_server_dir (chemsmart.settings.user.ChemsmartUserSettings property) USER_YAML_FILE (chemsmart.settings.user.ChemsmartUserSettings attribute), [1] utils_test_directory() (in module tests.conftest)

V

validate_and_assign_level() (chemsmart.jobs.gaussian.settings.GaussianQMMMJobSettings method) (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings method)

version_file_path (chemsmart.cli.update.Updater property)

W

water_engrad_path() (in module tests.conftest) water_molecule() (in module tests.conftest) water_opt_input_path() (in module tests.conftest) water_output_gas_path() (in module tests.conftest) water_sp_gas_input_path() (in module tests.conftest) water_sp_gas_path() (in module tests.conftest) water_sp_input_path() (in module tests.conftest) water_sp_solv_input_path() (in module tests.conftest)

water_sp_solv_path() (in module tests.conftest) water_with_metadata_molecule() (in module tests.conftest) wbi_outputfile() (in module tests.conftest) wbi_settings() (chemsmart.settings.gaussian.GaussianProjectSettings method) (chemsmart.settings.gaussian.YamlGaussianProjectSettings method) (chemsmart.settings.orca.ORCAProjectSettings method) (chemsmart.settings.orca.YamlORCAProjectSettings method) write() (chemsmart.settings.submitters.RunScript method) (chemsmart.settings.submitters.Submitter method)

X

xtb_optimized_xyz_file() (in module tests.conftest)

xyz_directory() (in module tests.conftest)

Y

yaml (chemsmart.settings.user.ChemsmartUserSettings attribute) YamlGaussianProjectSettings (class in chemsmart.settings.gaussian) YamlGaussianProjectSettingsBuilder (class in chemsmart.settings.gaussian)

YamlORCAProjectSettings (class in chemsmart.settings.orca) YamlORCAProjectSettingsBuilder (class in chemsmart.settings.orca) YamlServerSettings (class in chemsmart.settings.server)