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

A_E (tests.test_GaussianIO.TestGaussian16pKaOutput attribute) A_G (tests.test_GaussianIO.TestGaussian16pKaOutput attribute) A_H (tests.test_GaussianIO.TestGaussian16pKaOutput attribute) A_QH_G (tests.test_GaussianIO.TestGaussian16pKaOutput attribute) A_QH_H (tests.test_GaussianIO.TestGaussian16pKaOutput attribute) A_QH_TS (tests.test_GaussianIO.TestGaussian16pKaOutput attribute) A_TS (tests.test_GaussianIO.TestGaussian16pKaOutput attribute) A_ZPE (tests.test_GaussianIO.TestGaussian16pKaOutput attribute) active_atoms (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute)

add_lines_in_yaml_files() (in module chemsmart.cli.config) added_programs (chemsmart.cli.update.ConfigUpdateReport attribute), [1] all_available_crest_projects (chemsmart.settings.user.CHEMSMARTUserSettings property) 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) all_available_xtb_projects (chemsmart.settings.user.CHEMSMARTUserSettings property) array_submit_script (chemsmart.settings.submitters.Submitter property) available_servers (chemsmart.settings.executable.Executable property)

B

batch (chemsmart.settings.submitters.RunScript attribute)

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

C

changed (chemsmart.cli.update.ConfigUpdateReport attribute), [1] 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) 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.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.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_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) CHEMSMARTUserSettings (class in chemsmart.settings.user) 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) 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) ConfigUpdateError ConfigUpdateReport (class in chemsmart.cli.update) ConfigurationUpdater (class in chemsmart.cli.update) configure_conda_in_server_yaml() (chemsmart.cli.config.Config method) configure_paths_interactively() (chemsmart.cli.config.Config method) 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) crest_project_yaml_files (chemsmart.settings.user.CHEMSMARTUserSettings property) CRESTExecutable (class in chemsmart.settings.executable) current() (chemsmart.settings.server.Server class method)

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)

DependencyUpdater (class in chemsmart.cli.update) detect_server_scheduler() (chemsmart.settings.server.Server static method) docs_conf_file_path (chemsmart.cli.update.VersionUpdater property)

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) env (chemsmart.settings.executable.Executable property) env_vars (chemsmart.cli.config.Config property) executable (chemsmart.settings.submitters.Submitter property) Executable (class in chemsmart.settings.executable) EXPECTED_DG_AU (tests.test_ORCAIO.TestORCApKaOutput attribute) EXPECTED_DG_KCAL (tests.test_ORCAIO.TestORCApKaOutput attribute) EXPECTED_INCHI_NORMAL (tests.test_structures.TestInChI attribute) EXPECTED_INCHI_R_ENANTIOMER (tests.test_structures.TestInChI attribute)

EXPECTED_INCHI_S_ENANTIOMER (tests.test_structures.TestInChI attribute) EXPECTED_LARGE_C2 (tests.test_structures.TestInChI attribute) EXPECTED_LARGE_C3 (tests.test_structures.TestInChI attribute) EXPECTED_NORMAL (tests.test_structures.TestCXSMILES attribute) (tests.test_structures.TestInChI attribute) EXPECTED_R_ENANTIOMER (tests.test_structures.TestCXSMILES attribute) (tests.test_structures.TestInChI attribute) EXPECTED_R_ROTAMER (tests.test_structures.TestCXSMILES attribute) EXPECTED_S_ENANTIOMER (tests.test_structures.TestCXSMILES attribute) (tests.test_structures.TestInChI attribute) EXPECTED_S_ROTAMER (tests.test_structures.TestCXSMILES attribute) extra_commands (chemsmart.settings.server.Server property) extra_scheduler_directives (chemsmart.settings.server.Server property)

F

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) format_mm_atom_label() (chemsmart.jobs.gaussian.settings.GaussianQMMMJobSettings static method) format_mm_link_atom() (chemsmart.jobs.gaussian.settings.GaussianQMMMJobSettings static method) 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_process_pipeline() (in module chemsmart.cli.gaussian.gaussian) gaussian_project_yaml_files (chemsmart.settings.user.CHEMSMARTUserSettings property) 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) get_executable() (chemsmart.settings.executable.CRESTExecutable method) (chemsmart.settings.executable.GaussianExecutable method) (chemsmart.settings.executable.NCIPLOTExecutable method) (chemsmart.settings.executable.ORCAExecutable method) (chemsmart.settings.executable.XTBExecutable method) get_submitter() (chemsmart.settings.server.Server method)

H

HA_E (tests.test_GaussianIO.TestGaussian16pKaOutput attribute) HA_G (tests.test_GaussianIO.TestGaussian16pKaOutput attribute) HA_H (tests.test_GaussianIO.TestGaussian16pKaOutput attribute) HA_QH_G (tests.test_GaussianIO.TestGaussian16pKaOutput attribute) HA_QH_H (tests.test_GaussianIO.TestGaussian16pKaOutput attribute) HA_QH_TS (tests.test_GaussianIO.TestGaussian16pKaOutput attribute)

HA_TS (tests.test_GaussianIO.TestGaussian16pKaOutput attribute) HA_ZPE (tests.test_GaussianIO.TestGaussian16pKaOutput attribute) 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)

I

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) irc_settings() (chemsmart.settings.gaussian.GaussianProjectSettings method) (chemsmart.settings.gaussian.YamlGaussianProjectSettings method) (chemsmart.settings.orca.ORCAProjectSettings method) (chemsmart.settings.orca.YamlORCAProjectSettings method) is_up_to_date (chemsmart.cli.update.ConfigUpdateReport property)

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

L2_A_E (tests.test_ORCAIO.TestORCApKaOutput attribute) L2_A_QH_G (tests.test_ORCAIO.TestORCApKaOutput attribute) L2_A_SP_E (tests.test_ORCAIO.TestORCApKaOutput attribute) L2_HA_E (tests.test_ORCAIO.TestORCApKaOutput attribute) L2_HA_QH_G (tests.test_ORCAIO.TestORCApKaOutput attribute) L2_HA_SP_E (tests.test_ORCAIO.TestORCApKaOutput attribute)

large_basis (chemsmart.settings.gaussian.GaussianProjectSettings attribute), [1] (chemsmart.settings.orca.ORCAProjectSettings attribute), [1] load_mm_atom_info() (chemsmart.jobs.gaussian.settings.GaussianQMMMJobSettings static method) logger_options() (in module chemsmart.cli.logger) low_level_method (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) LSFServer (class in chemsmart.settings.server)

M

main_settings() (chemsmart.settings.gaussian.GaussianProjectSettings method) (chemsmart.settings.orca.ORCAProjectSettings method) mem_gb (chemsmart.settings.server.Server property) 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.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.update chemsmart.settings chemsmart.settings.executable chemsmart.settings.gaussian chemsmart.settings.orca chemsmart.settings.server chemsmart.settings.submitters chemsmart.settings.user tests tests.test_GaussianGenECP tests.test_GaussianIO tests.test_GaussianSettings tests.test_GaussianWriter tests.test_groupers tests.test_ORCAIO tests.test_organizer tests.test_server tests.test_structures tests.test_utils tests.test_YAMLIO

mult_high (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) mult_intermediate (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute) mult_total (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings attribute)

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)

NCIPLOTExecutable (class in chemsmart.settings.executable) neb_settings() (chemsmart.settings.orca.ORCAProjectSettings method) (chemsmart.settings.orca.YamlORCAProjectSettings method) 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_process_pipeline() (in module chemsmart.cli.orca.orca) orca_project_yaml_files (chemsmart.settings.user.CHEMSMARTUserSettings property) 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)

P

package_path (chemsmart.cli.update.DependencyUpdater property) path (chemsmart.cli.update.ConfigUpdateReport attribute), [1] PBSServer (class in chemsmart.settings.server) PBSSubmitter (class in chemsmart.settings.submitters) PHENOL_B_E (tests.test_ORCAIO.TestORCApKaOutput attribute) PHENOL_B_QH_G (tests.test_ORCAIO.TestORCApKaOutput attribute) PHENOL_B_SP_E (tests.test_ORCAIO.TestORCApKaOutput attribute) PHENOL_HB_E (tests.test_ORCAIO.TestORCApKaOutput attribute) PHENOL_HB_QH_G (tests.test_ORCAIO.TestORCApKaOutput attribute) PHENOL_HB_SP_E (tests.test_ORCAIO.TestORCApKaOutput attribute) PKA_COLLIDINE_REFERENCE (tests.test_GaussianIO.TestGaussian16pKaOutput attribute) powershell_profiles (chemsmart.cli.config.Config property) PROGRAM (chemsmart.settings.executable.CRESTExecutable attribute) (chemsmart.settings.executable.Executable attribute) (chemsmart.settings.executable.GaussianExecutable attribute) (chemsmart.settings.executable.NCIPLOTExecutable attribute) (chemsmart.settings.executable.ORCAExecutable attribute) (chemsmart.settings.executable.XTBExecutable attribute) program_scratch_from_servername() (chemsmart.settings.executable.Executable class method) 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]

ProjectsUpdater (class in chemsmart.cli.update) ProjectUpdateError ps_env_vars (chemsmart.cli.config.Config property) pyproject_path (chemsmart.cli.update.DependencyUpdater property) (chemsmart.cli.update.VersionUpdater 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)

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)

queue_name (chemsmart.settings.server.Server property)

R

re_init_and_validate() (chemsmart.jobs.orca.settings.ORCAQMMMJobSettings method) register() (chemsmart.settings.server.Server method) (chemsmart.settings.server.YamlServerSettings method)

requires_mm_atom_info() (chemsmart.jobs.gaussian.settings.GaussianQMMMJobSettings method) resolve_config_dir() (chemsmart.settings.user.CHEMSMARTUserSettings class method) run_script (chemsmart.settings.submitters.Submitter property) 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) 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_files (chemsmart.settings.user.CHEMSMARTUserSettings property)

ServerSettingsManager (class in chemsmart.settings.server) 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) 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] 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) submit() (chemsmart.settings.server.Server method) submit_array_job() (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_settings() (chemsmart.settings.gaussian.YamlGaussianProjectSettings method) (chemsmart.settings.orca.YamlORCAProjectSettings method) 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) 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_append_mm_parameters_skips_plain_molecule() (tests.test_GaussianWriter.TestGaussianInputWriter 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_permutation_preserves_both_ids() (tests.test_structures.TestMoleculeAndStructureIdentifiers method) test_atomic_radii_lists() (tests.test_structures.TestStructureCoverageBoost 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_auto_assigns_link_atoms_for_cut_covalent_bonds() (tests.test_structures.TestQMMMMolecule 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_bond_lengths_helper() (tests.test_structures.TestStructureCoverageBoost method) test_bond_orders_and_graphs() (tests.test_structures.TestStructureCoverageBoost method) test_boundary_checking_enabled() (tests.test_utils.TestParseIndexSpecification method) test_builtin_mm_helpers() (tests.test_GaussianSettings.TestGaussianQMMMJobSettings 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_charge_and_multiplicity_handling() (tests.test_structures.TestMoleculeAdvanced method) test_charge_and_multiplicity_population() (tests.test_ORCAIO.TestORCAQMMMJobSettings method) test_chiral_aromatic_ring() (tests.test_structures.TestStructureCoverageBoost 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_compute_pka() (tests.test_GaussianIO.TestGaussian16pKaOutput method) test_compute_pka_direct_scheme() (tests.test_GaussianIO.TestGaussian16pKaOutput method) test_compute_pka_energy_values() (tests.test_GaussianIO.TestGaussian16pKaOutput method) test_compute_pka_thermochemistry_ha_and_a() (tests.test_GaussianIO.TestGaussian16pKaOutput method) (tests.test_ORCAIO.TestORCApKaOutput method) test_compute_pka_uses_requested_files() (tests.test_ORCAIO.TestORCApKaOutput method) test_compute_thermochemistry_ha() (tests.test_GaussianIO.TestGaussian16pKaOutput 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_conjugate_base_job_property() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_conjugate_base_molecule_method() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_conjugate_base_molecule_property() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_conjugate_pair_job_settings_method() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_conjugate_pair_molecules_method() (tests.test_GaussianSettings.TestGaussianpKaJobSettings 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_converts_sdf_string_to_molecule_object() (tests.test_structures.TestSDFFile method) test_coordinate_block_basic() (tests.test_structures.TestStructureCoverageBoost method) test_coordinate_block_symbol_token_fallback() (tests.test_structures.TestStructureCoverageBoost method) test_coordinate_block_variants() (tests.test_structures.TestStructureCoverageBoost 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_conjugate_base_molecule() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_create_conjugate_base_molecule_custom_charge() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_create_conjugate_base_molecule_invalid_index() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_create_conjugate_base_molecule_no_proton_index() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_create_conjugate_base_molecule_not_hydrogen() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_create_job_settings() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_create_molecule_list() (tests.test_utils.TestIOUtilities method) test_create_molecules() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_crest_executable() (tests.test_server.TestServer method) test_crest_missing_section_raises() (tests.test_server.TestMissingProgramSectionFallback method) test_cube_file_format() (tests.test_structures.TestCoordinateBlockAdvanced method) test_custom_solvent_smd_generic() (tests.test_GaussianIO.TestGaussian16Output method) test_db_neither_chemsmart_nor_ase() (tests.test_structures.TestStructureCoverageBoost method) test_default_scheme() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_delete_atoms_paths() (tests.test_structures.TestStructureCoverageBoost method) test_deprotonation_energy_difference() (tests.test_GaussianIO.TestGaussian16pKaOutput method) test_detect_proton_in_fragment_explicit_h() (tests.test_structures.TestpKaCDXFile method) test_detect_proton_in_fragment_uniform_color_raises() (tests.test_structures.TestpKaCDXFile method) 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_determine_level_from_atom_index() (tests.test_structures.TestStructureCoverageBoost method) test_determine_level_on_molecule() (tests.test_structures.TestStructureCoverageBoost method) test_different_electronic_state_changes_structure_id_not_molecule_id() (tests.test_structures.TestMoleculeAndStructureIdentifiers 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_different_species_differ_in_both_ids() (tests.test_structures.TestMoleculeAndStructureIdentifiers method) test_direct_cycle_custom_delta_g() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_direct_cycle_no_reference() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_discover_pka_reference_companion_outputs() (tests.test_utils.TestPKaTableParsing method) test_discover_pka_target_companion_outputs_matches_batch_suffixes() (tests.test_utils.TestPKaTableParsing 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_echo_pka_output_table_results_writes_same_table_to_file() (tests.test_utils.TestPKaTableParsing method) Test_edge_cases (class in tests.test_groupers) test_electronic_energy_a() (tests.test_GaussianIO.TestGaussian16pKaOutput method) test_electronic_energy_and_qh_gibbs_match_combined_dat() (tests.test_ORCAIO.TestORCApKaOutput method) test_electronic_energy_ha() (tests.test_GaussianIO.TestGaussian16pKaOutput method) test_embedding_type_helpers() (tests.test_ORCAIO.TestORCAQMMMJobSettings method) test_empty_filepath_returns_none() (tests.test_structures.TestStructureCoverageBoost 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_differ_in_both_ids() (tests.test_structures.TestMoleculeAndStructureIdentifiers method) test_enantiomers_share_connectivity_layer() (tests.test_structures.TestInChI method) test_energy_and_positions_setters() (tests.test_structures.TestStructureCoverageBoost 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_energy_units_conversion_kcal_mol() (tests.test_GaussianIO.TestGaussian16pKaOutput method) test_energy_units_conversion_kj_mol() (tests.test_GaussianIO.TestGaussian16pKaOutput method) Test_EnergyGrouper (class in tests.test_groupers) test_enthalpy_ha() (tests.test_GaussianIO.TestGaussian16pKaOutput method) 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_export_pka_results_table_direct_scheme() (tests.test_utils.TestPKaTableParsing method) test_export_pka_results_table_matches_stdout_format() (tests.test_utils.TestPKaTableParsing 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_formula_grouper() (tests.test_groupers.Test_other_groupers method) test_fragment_colors_match_flat_colors() (tests.test_structures.TestpKaCDXFile 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_ase_and_copy() (tests.test_structures.TestStructureCoverageBoost method) test_from_filepath_missing() (tests.test_structures.TestStructureCoverageBoost method) test_from_molecule_copy_dict() (tests.test_structures.TestStructureCoverageBoost 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_from_pubchem_mocked() (tests.test_structures.TestStructureCoverageBoost method) test_from_rdkit() (tests.test_structures.TestStructureCoverageBoost method) test_frozen_atoms_manipulation() (tests.test_structures.TestMoleculeAdvanced method) test_functional_group_proton_user_color_phenol() (tests.test_structures.TestpKaCDXFile method) test_gas_phase_optimization_settings() (tests.test_GaussianSettings.TestGaussianpKaJobSettings 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_geometry_distortion_changes_structure_id_not_molecule_id() (tests.test_structures.TestMoleculeAndStructureIdentifiers method) test_geometry_helpers() (tests.test_structures.TestStructureCoverageBoost method) test_get_colored_proton_index_auto_detect() (tests.test_structures.TestpKaCDXFile method) test_get_colored_proton_index_invalid_color_code_raises() (tests.test_structures.TestpKaCDXFile method) test_get_colored_proton_index_multiple_atoms_same_color_raises() (tests.test_structures.TestpKaCDXFile method) test_get_colored_proton_index_no_hydrogen_raises() (tests.test_structures.TestpKaCDXFile method) test_get_colored_proton_index_no_unique_color_raises() (tests.test_structures.TestpKaCDXFile method) test_get_colored_proton_index_user_specified() (tests.test_structures.TestpKaCDXFile 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_pka_molecule_explicit_proton_index() (tests.test_structures.TestpKaCDXFile method) test_get_pka_molecules_auto_implicit_h() (tests.test_structures.TestpKaCDXFile method) test_get_pka_molecules_auto_nested_fragment_groups() (tests.test_structures.TestpKaCDXFile method) test_get_pka_molecules_auto_single_fragment() (tests.test_structures.TestpKaCDXFile method) test_get_pka_molecules_auto_two_fragments() (tests.test_structures.TestpKaCDXFile method) test_get_pka_molecules_delegates_to_auto() (tests.test_structures.TestpKaCDXFile method) test_get_pka_molecules_with_explicit_proton_index() (tests.test_structures.TestpKaCDXFile method) test_get_range_from_list() (tests.test_utils.TestUtils method) test_get_reference_conjugate_base_molecule() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_get_reference_molecule() (tests.test_GaussianSettings.TestGaussianpKaJobSettings 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_getitem_and_len() (tests.test_structures.TestStructureCoverageBoost method) test_gibbs_energy_extraction_function() (tests.test_groupers.Test_EnergyGrouper method) test_gibbs_free_energy_ha() (tests.test_GaussianIO.TestGaussian16pKaOutput method) test_graph_properties() (tests.test_structures.TestGraphFeatures method) test_graphs_and_bond_orders_water() (tests.test_structures.TestStructureCoverageBoost 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_has_vibrations_props() (tests.test_structures.TestStructureCoverageBoost 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_ids_are_deterministic() (tests.test_structures.TestMoleculeAndStructureIdentifiers method) 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_implicit_proton_removal_phenol() (tests.test_structures.TestpKaCDXFile method) test_inchi_import_error() (tests.test_structures.TestStructureCoverageBoost method) test_inchikey_inchi_smiles() (tests.test_structures.TestStructureCoverageBoost method) test_include_solvent() (tests.test_GaussianSettings.TestGaussianJobFromComFile method) test_index_zero_raises_value_error() (tests.test_utils.TestReturnObjectsAndIndicesFromStringIndex method) test_infer_pdb_element_from_uppercase_atom_names() (tests.test_structures.TestMoleculeAdvanced method) test_inheritance() (tests.test_ORCAIO.TestORCANEBJobSettings method) test_init_custom_values() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_init_default() (tests.test_ORCAIO.TestORCANEBJobSettings method) test_init_invalid_settings_type() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_init_no_proton_index() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_init_rejects_empty_symbols() (tests.test_structures.TestStructureCoverageBoost method) test_init_validation_branches() (tests.test_structures.TestStructureCoverageBoost method) test_init_with_custom_settings() (tests.test_GaussianIO.TestGaussian16pKaOutput method) test_init_with_default_settings() (tests.test_GaussianIO.TestGaussian16pKaOutput method) (tests.test_ORCAIO.TestORCApKaOutput 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_is_linear_three_atom_collinear() (tests.test_structures.TestStructureCoverageBoost 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_job_init_valid_settings() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_job_labels() (tests.test_GaussianSettings.TestGaussianpKaJobSettings 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.TestInChI method) test_large_molecule_c3_cxsmiles() (tests.test_structures.TestCXSMILES method) test_large_molecule_c3_inchikey() (tests.test_structures.TestInChI method) test_large_molecules_differ() (tests.test_structures.TestCXSMILES method) (tests.test_structures.TestInChI 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_mass_properties() (tests.test_structures.TestStructureCoverageBoost 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_mm_atom_info_from_coordinate_lines() (tests.test_structures.TestQMMMMolecule 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_cdx() (tests.test_structures.TestCDXFile 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_graph_generation() (tests.test_structures.TestMoleculeAdvanced method) test_molecule_label_format() (tests.test_structures.TestMoleculeAndStructureIdentifiers method) test_molecule_to_rdkit_conversion() (tests.test_structures.TestMoleculeAdvanced method) test_molecules() (tests.test_GaussianIO.TestGaussianWBIOutput method) test_moments_and_rot_temps() (tests.test_structures.TestStructureCoverageBoost method) test_monoatomic_diatomic_linear() (tests.test_structures.TestStructureCoverageBoost method) test_monoatomic_moi_and_rot_temps() (tests.test_structures.TestStructureCoverageBoost 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_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_setter() (tests.test_structures.TestStructureCoverageBoost 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_oniom_charge_multiplicity_2layer() (tests.test_GaussianIO.TestGaussian16Input method) test_oniom_connectivity_only_has_no_mm_parameters() (tests.test_GaussianIO.TestGaussian16Input method) test_oniom_freeze_flags_are_preserved() (tests.test_GaussianIO.TestGaussian16Input method) test_oniom_mm_parameters_empty_parts_and_groups() (tests.test_GaussianIO.TestGaussian16Input method) test_oniom_mm_parameters_extracted_after_connectivity() (tests.test_GaussianIO.TestGaussian16Input method) test_oniom_mm_parameters_skips_empty_and_non_mm_groups() (tests.test_GaussianIO.TestGaussian16Input method) test_oniom_model_charge_defaults_when_absent() (tests.test_GaussianIO.TestGaussian16Input method) test_oniom_negative_charge_line() (tests.test_GaussianIO.TestGaussian16Input method) test_oniom_partition_recursion_error_is_tolerated() (tests.test_GaussianIO.TestGaussian16Input method) test_oniom_route_without_layer_labels_returns_plain_molecule() (tests.test_GaussianIO.TestGaussian16Input method) test_oniom_single_pair_charge_defaults_model() (tests.test_GaussianIO.TestGaussian16Input method) test_oniom_three_layer_full_charge_line_maps_model() (tests.test_GaussianIO.TestGaussian16Input method) test_oniom_three_layer_short_charge_line() (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_and_resolve_multi_row_table() (tests.test_utils.TestPKaTableParsing method) test_parse_cdxml_atom_colors() (tests.test_structures.TestpKaCDXFile method) test_parse_cdxml_atom_colors_benzene_no_color() (tests.test_structures.TestpKaCDXFile method) test_parse_cdxml_fragment_colors_single_fragment() (tests.test_structures.TestpKaCDXFile method) test_parse_cdxml_fragment_colors_two_fragments() (tests.test_structures.TestpKaCDXFile method) 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_parse_pka_output_table_alias_columns() (tests.test_utils.TestPKaTableParsing method) test_parse_pka_output_table_csv() (tests.test_utils.TestPKaTableParsing method) test_parse_pka_output_table_empty() (tests.test_utils.TestPKaTableParsing method) test_parse_pka_output_table_empty_cells_become_none() (tests.test_utils.TestPKaTableParsing method) test_parse_pka_output_table_file_not_found() (tests.test_utils.TestPKaTableParsing method) test_parse_pka_table_blank_proton_index_for_cdxml() (tests.test_utils.TestPKaTableParsing method) test_parse_pka_table_blank_proton_index_for_xyz_raises() (tests.test_utils.TestPKaTableParsing method) test_parse_pka_table_csv() (tests.test_utils.TestPKaTableParsing method) test_parse_pka_table_empty_raises() (tests.test_utils.TestPKaTableParsing method) test_parse_pka_table_file_not_found() (tests.test_utils.TestPKaTableParsing method) test_parse_pka_table_invalid_column_count() (tests.test_utils.TestPKaTableParsing method) test_parse_pka_table_invalid_integer() (tests.test_utils.TestPKaTableParsing method) test_parse_pka_table_skip_comments_and_empty_lines() (tests.test_utils.TestPKaTableParsing method) test_parse_pka_table_txt() (tests.test_utils.TestPKaTableParsing 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_pbc_property() (tests.test_structures.TestStructureCoverageBoost method) test_pbc_write_gaussian_coords() (tests.test_structures.TestStructureCoverageBoost method) test_pbs_submitter_writes_extra_scheduler_directives() (tests.test_server.TestServer method) test_pd_insertion_ts_r_logfile() (tests.test_GaussianIO.TestGaussian16Output 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_pka_jobs_property() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_pka_molecule() (tests.test_structures.TestStructureCoverageBoost method) test_pka_non_hydrogen_proton_index() (tests.test_structures.TestStructureCoverageBoost method) test_pka_output_table_entry_repr() (tests.test_utils.TestPKaTableParsing method) test_pka_output_table_entry_resolve_filenames_gaussian_log() (tests.test_utils.TestPKaTableParsing method) test_pka_output_table_entry_resolve_filenames_orca_default_extension() (tests.test_utils.TestPKaTableParsing method) test_pka_output_table_entry_resolve_filenames_orca_out() (tests.test_utils.TestPKaTableParsing method) test_pka_output_table_entry_to_dict() (tests.test_utils.TestPKaTableParsing method) test_pka_output_table_entry_validate_missing_basename() (tests.test_utils.TestPKaTableParsing method) test_pka_output_table_entry_validate_missing_file() (tests.test_utils.TestPKaTableParsing method) test_pka_output_table_entry_validate_valid() (tests.test_utils.TestPKaTableParsing method) test_pka_output_table_prepare_autodetects_files_and_inherits_references() (tests.test_utils.TestPKaTableParsing method) test_pka_output_table_run_pka() (tests.test_utils.TestPKaTableParsing method) test_pka_output_table_run_pka_direct() (tests.test_utils.TestPKaTableParsing method) test_pka_table_entry_alias_resolution() (tests.test_utils.TestPKaTableParsing method) test_pka_table_entry_dict_and_kwargs_helpers() (tests.test_utils.TestPKaTableParsing method) test_pka_table_entry_from_headers_and_row_dynamic() (tests.test_utils.TestPKaTableParsing method) test_pka_table_entry_repr() (tests.test_utils.TestPKaTableParsing method) test_pka_table_entry_validate_invalid_multiplicity() (tests.test_utils.TestPKaTableParsing method) test_pka_table_entry_validate_invalid_proton_index() (tests.test_utils.TestPKaTableParsing method) test_pka_table_entry_validate_missing_file() (tests.test_utils.TestPKaTableParsing 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_present_section_still_parsed_correctly() (tests.test_server.TestMissingProgramSectionFallback method) test_print_pka_summary() (tests.test_GaussianIO.TestGaussian16pKaOutput method) test_print_pka_thermochemistry_summary() (tests.test_GaussianIO.TestGaussian16pKaOutput method) test_proton_exchange_with_reference_file() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_proton_exchange_without_reference_file() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_proton_removal_phenol() (tests.test_structures.TestpKaCDXFile method) test_protonated_charge_multiplicity_properties() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_protonated_job_property() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_protonated_molecule_property() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_pymol_grouper_rejects_multiproc() (tests.test_groupers.Test_PymolRMSD_grouper 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_qh_enthalpy_ha() (tests.test_GaussianIO.TestGaussian16pKaOutput method) test_qh_gibbs_free_energy_a() (tests.test_GaussianIO.TestGaussian16pKaOutput method) test_qh_gibbs_free_energy_ha() (tests.test_GaussianIO.TestGaussian16pKaOutput 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_block_uses_orca_keywords() (tests.test_ORCAIO.TestORCAQMMMJobSettings method) test_qmmm_helpers_for_uncovered_branches() (tests.test_structures.TestQMMMMolecule method) test_qmmm_high_none_raises() (tests.test_structures.TestStructureCoverageBoost method) test_qmmm_link_atoms_and_scale() (tests.test_structures.TestStructureCoverageBoost method) test_qmmm_overlap_raises() (tests.test_structures.TestStructureCoverageBoost method) test_qmmm_partition_levels() (tests.test_structures.TestStructureCoverageBoost method) test_qmmm_partition_out_of_range_raises() (tests.test_structures.TestQMMMinMolecule method) (tests.test_structures.TestQMMMMolecule method) test_qmmm_partition_overlap_raises() (tests.test_structures.TestQMMMinMolecule method) (tests.test_structures.TestQMMMMolecule method) test_qmmm_partition_validation() (tests.test_structures.TestStructureCoverageBoost method) test_qmmm_real_charge_sets_state() (tests.test_structures.TestStructureCoverageBoost 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_qmmm_string_layer_specs_with_link_atoms() (tests.test_structures.TestQMMMMolecule method) test_qmmm_xyz_line_does_not_fall_back_to_total_charge() (tests.test_ORCAIO.TestORCAQMMMJobSettings method) test_qmmm_xyz_line_uses_charge_high_not_total() (tests.test_ORCAIO.TestORCAQMMMJobSettings 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.TestInChI 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_rdkit_fingerprints() (tests.test_structures.TestStructureCoverageBoost method) test_rdkit_isomorphism_grouper() (tests.test_groupers.Test_other_groupers method) test_rdkit_vectorized_bond_types() (tests.test_structures.TestStructureCoverageBoost method) test_read_2d_pbc_output() (tests.test_GaussianIO.TestGaussianPBCOutputFile method) test_read_additional_route_parameters() (tests.test_GaussianIO.TestRouteString method) test_read_chemsmart_db() (tests.test_structures.TestStructureCoverageBoost method) test_read_complex_molecule_cdxml_file_() (tests.test_structures.TestCDXFile method) test_read_coordinate_block() (tests.test_structures.TestCoordinateBlock method) test_read_crest_dynamics_trj_as_xyz() (tests.test_structures.TestStructures method) test_read_crestopt_log_as_xyz() (tests.test_structures.TestStructures 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_full_gen_outputfile() (tests.test_GaussianIO.TestGaussian16Output method) test_read_full_genecp_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_pdb_return_list() (tests.test_structures.TestStructureCoverageBoost 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_oniom_layer_methods_and_bases() (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_sdf_and_other_list() (tests.test_structures.TestStructureCoverageBoost 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_unsupported_out_and_gaussian_inp_error() (tests.test_structures.TestStructureCoverageBoost 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_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_reference_gas_phase_job_settings() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_reference_solution_phase_sp_settings() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_reference_validation() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_reference_validation_missing_proton_index() (tests.test_GaussianSettings.TestGaussianpKaJobSettings method) test_regression_cxsmiles() (tests.test_structures.TestCXSMILES method) test_regression_inchikey() (tests.test_structures.TestInChI method) test_reject_plain_ints_as_floats() (tests.test_utils.TestIOUtilities method) test_replacement_with_various_delimiters() (tests.test_GaussianGenECP.TestGenECPReplacementInRoute method) test_repr_str_and_chemical_symbols_none() (tests.test_structures.TestStructureCoverageBoost method) test_resolve_pka_output_references_carry_forward() (tests.test_utils.TestPKaTableParsing method) test_resolve_pka_output_references_first_row_blank_raises() (tests.test_utils.TestPKaTableParsing method) test_resolve_pka_output_references_partial_carry_forward() (tests.test_utils.TestPKaTableParsing method) test_resonance_handling() (tests.test_structures.TestChemicalFeatures method) test_return_list_from_filepath() (tests.test_structures.TestStructureCoverageBoost method) test_rigid_transform_preserves_both_ids_3b() (tests.test_structures.TestMoleculeAndStructureIdentifiers method) test_rigid_transform_preserves_both_ids_formaldehyde() (tests.test_structures.TestMoleculeAndStructureIdentifiers method) test_rigid_transform_preserves_both_ids_methane() (tests.test_structures.TestMoleculeAndStructureIdentifiers 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_route_string_without_parent_jobtype() (tests.test_ORCAIO.TestORCAQMMMJobSettings method) test_s_enantiomer_cxsmiles() (tests.test_structures.TestCXSMILES method) test_s_enantiomer_inchikey() (tests.test_structures.TestInChI 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_slurm_submitter_writes_extra_scheduler_directives() (tests.test_server.TestServer method) test_sn2_ts_orca_output() (tests.test_ORCAIO.TestORCAOutput method) test_solution_phase_sp_settings() (tests.test_GaussianSettings.TestGaussianpKaJobSettings 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_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_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_structure_label_format() (tests.test_structures.TestMoleculeAndStructureIdentifiers method) test_sub_threshold_perturbation_preserves_both_ids() (tests.test_structures.TestMoleculeAndStructureIdentifiers 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_thermochemistry_property_caching() (tests.test_GaussianIO.TestGaussian16pKaOutput 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_to_pymatgen_and_x_data() (tests.test_structures.TestStructureCoverageBoost method) test_to_x_data_no_positions_raises() (tests.test_structures.TestStructureCoverageBoost 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_validate_pka_table_entries() (tests.test_utils.TestPKaTableParsing method) test_validation_errors() (tests.test_ORCAIO.TestORCANEBJobSettings method) test_variable_bond_cutoffs() (tests.test_structures.TestGraphFeatures method) test_vdw_volume_and_pbc() (tests.test_structures.TestStructureCoverageBoost method) test_vectorized_bond_add() (tests.test_structures.TestStructureCoverageBoost method) test_very_high_threshold() (tests.test_groupers.Test_edge_cases method) test_very_low_threshold() (tests.test_groupers.Test_edge_cases method) test_vibrationally_displaced() (tests.test_structures.TestStructureCoverageBoost method) test_vibrationally_displaced_negative_index() (tests.test_structures.TestStructureCoverageBoost method) test_volume() (tests.test_structures.TestChemicalFeatures method) test_volumes() (tests.test_structures.TestStructureCoverageBoost 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_coordinates_programs() (tests.test_structures.TestStructureCoverageBoost method) test_write_cosmorsxyz_via_write() (tests.test_structures.TestStructureCoverageBoost method) test_write_extxyz_bad_forces_ignored() (tests.test_structures.TestStructureCoverageBoost method) test_write_extxyz_forces_shape_mismatch() (tests.test_structures.TestStructureCoverageBoost method) test_write_extxyz_with_forces_and_energy() (tests.test_structures.TestStructureCoverageBoost method) test_write_gaussian_connectivity_and_frozen_mm_labels() (tests.test_structures.TestQMMMMolecule method) test_write_gaussian_input_from_pbc_logfile() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_gaussian_with_frozen() (tests.test_structures.TestStructureCoverageBoost 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_pdb_file() (tests.test_structures.TestMoleculeAdvanced method) test_write_pdb_rejects_kwargs() (tests.test_structures.TestStructureCoverageBoost method) test_write_pdb_rejects_unexpected_keyword_argument() (tests.test_structures.TestMoleculeAdvanced method) test_write_qmmm_amber_from_oniom_com_without_sidecar_files() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_qmmm_amber_incomplete_mm_atom_info_raises() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_qmmm_amber_requires_mm_atom_info() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_qmmm_amber_with_mm_atom_info() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_qmmm_auto_assigns_link_atoms_for_cut_bonds() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_qmmm_genecp_follows_conventional_basis_path() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_qmmm_inherits_layers_from_molecule() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_qmmm_input_from_logfile() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_qmmm_job() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_qmmm_job_with_scale_factors() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_qmmm_link_atoms_share_high_boundary() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_qmmm_missing_mm_parameters_file_raises() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_qmmm_mm_parameters_file_overrides_molecule_params() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_qmmm_pm6_skips_connectivity_section() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_qmmm_rejects_multiple_link_atoms_on_same_atom() (tests.test_GaussianWriter.TestGaussianInputWriter method) test_write_qmmm_uses_layers_from_oniom_com() (tests.test_GaussianWriter.TestGaussianInputWriter 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_write_via_openbabel_fallback() (tests.test_structures.TestStructureCoverageBoost method) test_writes_gaussian_input_from_pbc_comfile() (tests.test_GaussianSettings.TestGaussianPBCJob method) test_xtb_executable() (tests.test_server.TestServer method) test_xtb_missing_section_error_message() (tests.test_server.TestMissingProgramSectionFallback method) test_xtb_missing_section_raises() (tests.test_server.TestMissingProgramSectionFallback method) test_zero_point_energy_ha() (tests.test_GaussianIO.TestGaussian16pKaOutput method) TestCDXFile (class in tests.test_structures) TestChemicalFeatures (class in tests.test_structures) TestConformerIdExtraction (class in tests.test_groupers) 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) TestGaussian16pKaOutput (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) TestGaussianpKaJobSettings (class in tests.test_GaussianSettings) 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) TestInChI (class in tests.test_structures) TestInChIKey (class in tests.test_structures) TestIOUtilities (class in tests.test_utils) TestMissingProgramSectionFallback (class in tests.test_server) TestMoleculeAdvanced (class in tests.test_structures) TestMoleculeAndStructureIdentifiers (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) TestORCApKaOutput (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) TestpKaCDXFile (class in tests.test_structures) TestPKaTableParsing (class in tests.test_utils) TestQMMMinMolecule (class in tests.test_structures) TestQMMMMolecule (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.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_server module tests.test_structures module tests.test_utils module tests.test_YAMLIO module TestSDFFile (class in tests.test_structures) TestServer (class in tests.test_server) TestString2Index1Based (class in tests.test_utils) TestStructureCoverageBoost (class in tests.test_structures) TestStructures (class in tests.test_structures) TestStructuresFromGaussianInput (class in tests.test_structures) TestUtils (class in tests.test_utils) TestYAMLFile (class in tests.test_YAMLIO) ts_settings() (chemsmart.settings.gaussian.GaussianProjectSettings method) (chemsmart.settings.gaussian.YamlGaussianProjectSettings method) (chemsmart.settings.orca.ORCAProjectSettings method) (chemsmart.settings.orca.YamlORCAProjectSettings method)

U

update() (chemsmart.cli.update.ConfigurationUpdater method) (chemsmart.cli.update.DependencyUpdater method) (chemsmart.cli.update.ProjectsUpdater method) (chemsmart.cli.update.Updater method) (chemsmart.cli.update.VersionUpdater method) update_pyproject_toml() (chemsmart.cli.update.DependencyUpdater method) update_version_number() (chemsmart.cli.update.VersionUpdater 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_crest_settings_dir (chemsmart.settings.user.CHEMSMARTUserSettings property) 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_xtb_settings_dir (chemsmart.settings.user.CHEMSMARTUserSettings property) USER_YAML_FILE (chemsmart.settings.user.CHEMSMARTUserSettings attribute), [1] uses_builtin_mm() (chemsmart.jobs.gaussian.settings.GaussianQMMMJobSettings method)

V

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

version_file_path (chemsmart.cli.update.VersionUpdater property) VersionUpdater (class in chemsmart.cli.update)

W

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) write_array_job() (chemsmart.settings.submitters.Submitter method)

X

xtb_project_yaml_files (chemsmart.settings.user.CHEMSMARTUserSettings property)

XTBExecutable (class in chemsmart.settings.executable)

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)