CHEMSMART Modules
- chemsmart package
- tests package
- Submodules
- tests.conftest module
Ni_def2tzvp_PCHOSi_svp_text_file()Ni_def2tzvp_PCHOSi_svp_txt_file()acetylene_molecule()blank_element_pdb_file()canonical_3b_file()canonical_3b_permuted_file()canonical_3b_trans_rot_file()canonical_formaldehyde_file()canonical_formaldehyde_perturbed_file()canonical_formaldehyde_trans_rot_file()canonical_methane_distorted_file()canonical_methane_file()canonical_methane_trans_rot_file()canonical_r_bromochlorofluoromethane_file()canonical_s_bromochlorofluoromethane_file()canonical_test_directory()capture_log()captured()chemdraw_directory()chemdraw_expected_directory()chemsmart_generated_xyz_file()chemsmart_templates_config()chiral_molecule()co2_molecule()colored_implicit_proton_cdxml_file()colored_proton_cdxml_file()colored_proton_two_molecule_cdxml_file()complex_molecule_cdxml_file()conformers_from_rdkit()constrained_atoms()constrained_pbc_db_file()crest_hexane_failed_outfolder()crest_jobrunner_no_scratch()crest_jobrunner_scratch()crest_octane_outfolder()crest_outputs_directory()crest_styrene_outfolder()crest_test_directory()crest_ts1a_constrained_outfolder()crest_yaml_settings_directory()crest_yaml_settings_gas()crest_yaml_settings_gas_project_name()crest_yaml_settings_solv()crest_yaml_settings_solv_project_name()cube_test_directory()cxsmiles_expected_large_c2_file()cxsmiles_expected_large_c3_file()cxsmiles_large_molecule_c2_file()cxsmiles_large_molecule_c3_file()cxsmiles_normal_file()cxsmiles_r_enantiomer_file()cxsmiles_r_rotamer_file()cxsmiles_s_enantiomer_file()cxsmiles_s_rotamer_file()cxsmiles_test_directory()database_ase_file()database_chemsmart_file()database_chemsmart_xtb_file()database_empty_file()database_test_directory()dlpno_ccsdt_sp_full_print()dna_hybrid_visualized_xyz_file()dummy_yaml_file()empty_pdb_file()esp_cube_file()ethanol_molecule()ethylene_molecule()excel_file()expected_benzene_com()expected_benzene_xyz()expected_complex_molecule_com()expected_imidazole_xyz()expected_methane_com()expected_methane_xyz()expected_two_molecules_1_com()expected_two_molecules_1_xyz()expected_two_molecules_2_com()expected_two_molecules_2_xyz()extended_xyz_file()fake_iterate_jobrunner()fe2_quintet_output()fe2_singlet_output()fe2_triplet_output()fe3_doublet_output()fe3_quartet_output()fe3_sextet_output()gaussian_acetone_opt_outfile()gaussian_benzene_opt_outfile()gaussian_boltzmann_test_directory()gaussian_co2_opt_outfile()gaussian_co2_pressure1p5_outfile()gaussian_co2_pressure3_outfile()gaussian_conformer1_outfile()gaussian_conformer2_outfile()gaussian_dna_link_sp_outputfile()gaussian_dppeFeCl2_link_opt_failed_outputfile()gaussian_dppeFeCl2_link_opt_outputfile()gaussian_failed_link_output()gaussian_failed_modred_outfile()gaussian_failed_scan_outfile()gaussian_frozen_opt_inputfile()gaussian_frozen_opt_outfile()gaussian_full_gen_outfile()gaussian_full_genecp_outfile()gaussian_he_opt_outfile()gaussian_hirshfeld_outfile()gaussian_inputs_genecp_directory()gaussian_inputs_test_directory()gaussian_jobrunner_no_scratch()gaussian_jobrunner_scratch()gaussian_koh_linear_opt_outfile()gaussian_koh_opt_outfile()gaussian_link_failed_outfile()gaussian_link_inputs_test_directory()gaussian_link_modred_output()gaussian_link_opt_input()gaussian_link_opt_outfile()gaussian_link_opt_outputfile()gaussian_link_outputs_test_directory()gaussian_link_sp_input()gaussian_link_sp_outfile()gaussian_link_sp_outputfile()gaussian_link_ts_input()gaussian_link_ts_outputfile()gaussian_modred_inputfile()gaussian_modred_with_custom_basis_for_all_atoms_from_api()gaussian_mp2_outputfile()gaussian_oniom_outputfile()gaussian_opt_genecp_inputfile()gaussian_opt_inputfile()gaussian_outputs_test_directory()gaussian_ozone_opt_outfile()gaussian_pKa_A_optimization_outputfile()gaussian_pKa_A_single_point_outputfile()gaussian_pKa_B_optimization_outputfile()gaussian_pKa_B_single_point_outputfile()gaussian_pKa_HA_optimization_outputfile()gaussian_pKa_HA_single_point_outputfile()gaussian_pKa_HB_optimization_outputfile()gaussian_pKa_HB_single_point_outputfile()gaussian_pbc_1d_inputfile()gaussian_pbc_2d_outputfile()gaussian_pbc_3d_outputfile()gaussian_pbc_inputs_test_directory()gaussian_pbc_outputs_test_directory()gaussian_pbc_test_directory()gaussian_pd_insertion_ts_r_outfile()gaussian_project_config_dir()gaussian_qmmm_input_test_directory()gaussian_qmmm_inputfile_2layer()gaussian_qmmm_inputfile_3layer()gaussian_quintet_opt_outfile()gaussian_rc_hirshfeld_outfile()gaussian_scan_inputfile()gaussian_semiempirical_pm6_output_file()gaussian_semiempirical_test_directory()gaussian_singlet_opt_outfile()gaussian_smd_generic_outfile()gaussian_test_directory()gaussian_thermochem_test_directory()gaussian_triplet_opt_outfile()gaussian_ts_genecp_outfile()gaussian_written_files_directory()gaussian_written_modred_file()gaussian_written_opt_file()gaussian_written_opt_file_with_route()gaussian_written_opt_from_graphite_2d_pbc_log()gaussian_written_pm6_opt_file()gaussian_written_qmmm_file()gaussian_written_qmmm_log_file()gaussian_written_scan_multiple_degrees_of_freedom_file()gaussian_written_scan_multiple_degrees_of_freedom_with_constraints_file()gaussian_written_scan_single_degree_of_freedom_file()gaussian_written_sp_from_nhc_singlet_log_with_custom_basis_file()gaussian_written_sp_from_nhc_singlet_log_with_custom_basis_from_api_file()gaussian_written_sp_from_nhc_singlet_log_with_custom_basis_from_api_file_v2()gaussian_written_sp_from_nhc_singlet_log_with_custom_solvent_file()gaussian_written_sp_from_nhc_singlet_log_with_solvent_file()gaussian_written_ts_file()gaussian_written_ts_from_nhc_singlet_log_file()gaussian_yaml_settings_defaults()gaussian_yaml_settings_directory()gaussian_yaml_settings_gas_solv()gaussian_yaml_settings_gas_solv_project_name()gaussian_yaml_settings_qmmm()gaussian_yaml_settings_qmmm_project_name()gaussian_yaml_settings_solv()gen_text_file_from_web()gen_txt_file_from_web()genecp_text_file_from_web()genecp_txt_file_from_web()gtoint_errfile()hf_com_filepath()hirshfeld_full_print()hydrogen_molecule()inchikey_large_molecule_c2_file()inchikey_large_molecule_c3_file()inchikey_normal_file()inchikey_r_enantiomer_file()inchikey_s_enantiomer_file()inchikey_test_directory()inpfile_path()invoke_config_server()invoke_folder_command()invoke_mol_cli()invoke_mol_with_visualize()invoke_update_configs()invoke_update_projects()io_test_directory()iterate_configs_directory()iterate_expected_output_directory()iterate_expected_output_file()iterate_input_directory()iterate_integration_config_file()iterate_invalid_skeleton_link_index_config_file()iterate_jobrunner()iterate_template_file()iterate_test_directory()iterate_timeout_config_file()legacy_server_yaml()make_cli_ctx_obj()make_thermochemistry_mock()metal_ligand_molecules_cdxml_file()methane_molecule()methanol_and_ethanol()methanol_molecule()methanol_molecules()methyl3hexane_molecule()mock_popen()modred_gen_inputfile()modred_genecp_custom_solvent_inputfile()modred_genecp_inputfile()multi_model_pdb_file()multi_molecule_cdxml_file()multiple_molecules_xyz_file()nciplot_jobrunner_no_scratch()nciplot_jobrunner_scratch()orca_co2_output()orca_dias_directory()orca_epr_solv()orca_errors_directory()orca_faulty_solv()orca_fixed_atoms()orca_fixed_bonds_and_angles()orca_fixed_dihedral()orca_he_output_freq()orca_he_output_freq_new()orca_input_nebts_file()orca_input_nebts_product_xyz_file()orca_input_nebts_reactant_xyz_file()orca_input_nebts_ts_xyz_file()orca_inputs_directory()orca_inputs_xyz_directory()orca_jobrunner_no_scratch()orca_jobrunner_scratch()orca_koh_output()orca_neb_output_file()orca_outputs_directory()orca_qmmm_input_file()orca_sn2_ts_output()orca_test_directory()orca_two_layer_qmmmm_output_file()orca_written_files_directory()orca_written_he_monoatomic_opt_file()orca_written_modred_file()orca_written_neb_file()orca_written_opt_file()orca_written_opt_file_with_route()orca_written_scan_multiple_degrees_of_freedom_file()orca_written_scan_multiple_degrees_of_freedom_with_constraints_file()orca_written_scan_single_degree_of_freedom_file()orca_written_sp_from_nhc_singlet_log_with_solvent_file()orca_written_ts_file()orca_written_ts_from_nhc_singlet_log_file()orca_yaml_settings_custom_solv_cosmors_project_name()orca_yaml_settings_custom_solv_project_name()orca_yaml_settings_defaults()orca_yaml_settings_directory()orca_yaml_settings_gas_solv()orca_yaml_settings_gas_solv_project_name()orca_yaml_settings_neb_project_name()orca_yaml_settings_orca_project_name()orca_yaml_settings_solv()orca_yaml_settings_solv_project_name()outputs_test_directory()pbs_server()pka_scale_cdxml_file()pymol_align_jobrunner()pymol_hybrid_visualization_jobrunner()pymol_ircmovie_jobrunner()pymol_mo_jobrunner()pymol_movie_jobrunner()pymol_scientific_style_visualization_jobrunner()pymol_visualization_jobrunner()qmmm_written_xyz_file()qmmm_written_xyz_only_file()read_yaml_file()reference_genecp_txt_file_from_api()run_gaussian_and_capture_settings()run_orca_and_capture_settings()run_thermochemistry_and_capture_settings()run_thermochemistry_with_directory()sdf_file()server_yaml_file()session_mocker()single_atom_molecule()single_model_pdb_file()single_molecule_cdx_file_imidazole()single_molecule_cdxml_file_benzene()single_molecule_cdxml_file_methane()single_molecule_xyz_file()smd_TBME_solvent_parameters_text_file()smd_TBME_solvent_parameters_txt_file()spin_cube_file()structure_test_directory()td_outputfile()tddft_test_directory()temp_folder_with_files()temp_text_file()temporary_working_dir()test_data_directory()tests_logger()tetrahydrofuran_molecule()text_directory()ts_conformers_log_directory()two_rotated_molecules_xyz_file()txt_path()utils_test_directory()visualized_1_mer_xyz_file()water_engrad_path()water_molecule()water_opt_input_path()water_output_gas_path()water_sp_gas_input_path()water_sp_gas_path()water_sp_input_path()water_sp_solv_input_path()water_sp_solv_path()water_with_metadata_molecule()wbi_outputfile()write_server_yaml()write_text_file()xtb_acetaldehyde_outfolder()xtb_co2_outfolder()xtb_cyclopentadienyl_anion_outfolder()xtb_default_inputfile()xtb_he_outfolder()xtb_inputs_directory()xtb_jobrunner_no_scratch()xtb_jobrunner_scratch()xtb_optimized_xyz_file()xtb_outputs_directory()xtb_p_benzyne_opt_outfolder()xtb_p_benzyne_sp_outfolder()xtb_sp_alpb_inputfile()xtb_test_directory()xtb_water_outfolder()xyz_directory()
- tests.test_GaussianGenECP module
TestGaussianGenGenECPTestGaussianGenGenECP.test_gen_fallback_when_heavy_element_does_not_require_ecp()TestGaussianGenGenECP.test_genecp_fallback_when_basis_missing_from_bse()TestGaussianGenGenECP.test_genecp_from_base_api()TestGaussianGenGenECP.test_genecp_from_base_api_accepts_hyphenless_def2_heavy_basis()TestGaussianGenGenECP.test_genecp_from_comfile()TestGaussianGenGenECP.test_genecp_from_modred_gen_comfile()TestGaussianGenGenECP.test_genecp_from_modred_genecp_comfile()TestGaussianGenGenECP.test_genecp_from_modred_genecp_solvent_comfile()
TestGenECPReplacementInRouteTestGenGenECPBasisDeterminationTestGenGenECPBasisDetermination.test_determine_basis_keyword_mixed_elements()TestGenGenECPBasisDetermination.test_determine_basis_keyword_no_heavy_elements()TestGenGenECPBasisDetermination.test_determine_basis_keyword_non_gen_basis()TestGenGenECPBasisDetermination.test_determine_basis_keyword_with_br()TestGenGenECPBasisDetermination.test_determine_basis_keyword_with_i()TestGenGenECPBasisDetermination.test_determine_basis_keyword_with_pd()TestGenGenECPBasisDetermination.test_periodic_table_requires_ecp()
- tests.test_GaussianIO module
TestGaussian16InputTestGaussian16Input.test_oniom_charge_multiplicity()TestGaussian16Input.test_oniom_charge_multiplicity_2layer()TestGaussian16Input.test_oniom_connectivity_only_has_no_mm_parameters()TestGaussian16Input.test_oniom_freeze_flags_are_preserved()TestGaussian16Input.test_oniom_mm_parameters_empty_parts_and_groups()TestGaussian16Input.test_oniom_mm_parameters_extracted_after_connectivity()TestGaussian16Input.test_oniom_mm_parameters_skips_empty_and_non_mm_groups()TestGaussian16Input.test_oniom_model_charge_defaults_when_absent()TestGaussian16Input.test_oniom_negative_charge_line()TestGaussian16Input.test_oniom_partition_recursion_error_is_tolerated()TestGaussian16Input.test_oniom_route_without_layer_labels_returns_plain_molecule()TestGaussian16Input.test_oniom_single_pair_charge_defaults_model()TestGaussian16Input.test_oniom_three_layer_full_charge_line_maps_model()TestGaussian16Input.test_oniom_three_layer_short_charge_line()TestGaussian16Input.test_partition()TestGaussian16Input.test_pbc_1d_input()TestGaussian16Input.test_read_frozen_coords()TestGaussian16Input.test_read_gaussian_input()TestGaussian16Input.test_read_gaussian_link_opt_input()TestGaussian16Input.test_read_gaussian_link_ts_input()TestGaussian16Input.test_read_gausssian_link_sp_input()TestGaussian16Input.test_read_genecp_inputfile()TestGaussian16Input.test_read_modred_inputfile()TestGaussian16Input.test_read_scan_inputfile()
TestGaussian16OutputTestGaussian16Output.test_contribution_percentage_spin_scaling()TestGaussian16Output.test_custom_solvent_smd_generic()TestGaussian16Output.test_energy_extraction_from_gaussian_output_file()TestGaussian16Output.test_normal_termination_semiempirical_pm6_output_file()TestGaussian16Output.test_normal_termination_with_forces_and_frequencies()TestGaussian16Output.test_normal_termination_with_trailing_blank_lines()TestGaussian16Output.test_oldform_redundant_coordinates_atomic_numbers()TestGaussian16Output.test_pd_insertion_ts_r_logfile()TestGaussian16Output.test_quintet_opt_output()TestGaussian16Output.test_read_failed_link_job()TestGaussian16Output.test_read_frozen_opt_outputfile()TestGaussian16Output.test_read_full_gen_outputfile()TestGaussian16Output.test_read_full_genecp_outputfile()TestGaussian16Output.test_read_gaussian_link_modred_output_file()TestGaussian16Output.test_read_gaussian_link_opt_output_file()TestGaussian16Output.test_read_gaussian_link_sp_output_file()TestGaussian16Output.test_read_gaussian_link_ts_output_file()TestGaussian16Output.test_read_genecp_outputfile()TestGaussian16Output.test_read_hirshfeld_charges_outputfile()TestGaussian16Output.test_read_hirshfeld_rc_charges_outputfile()TestGaussian16Output.test_read_modred_outputfile()TestGaussian16Output.test_read_mp2_outputfile()TestGaussian16Output.test_read_oniom_outputfile()TestGaussian16Output.test_read_scan_outputfile()TestGaussian16Output.test_singlet_opt_output()TestGaussian16Output.test_triplet_opt_output()
TestGaussian16pKaOutputTestGaussian16pKaOutput.A_ETestGaussian16pKaOutput.A_GTestGaussian16pKaOutput.A_HTestGaussian16pKaOutput.A_QH_GTestGaussian16pKaOutput.A_QH_HTestGaussian16pKaOutput.A_QH_TSTestGaussian16pKaOutput.A_TSTestGaussian16pKaOutput.A_ZPETestGaussian16pKaOutput.HA_ETestGaussian16pKaOutput.HA_GTestGaussian16pKaOutput.HA_HTestGaussian16pKaOutput.HA_QH_GTestGaussian16pKaOutput.HA_QH_HTestGaussian16pKaOutput.HA_QH_TSTestGaussian16pKaOutput.HA_TSTestGaussian16pKaOutput.HA_ZPETestGaussian16pKaOutput.PKA_COLLIDINE_REFERENCETestGaussian16pKaOutput.test_compute_pka()TestGaussian16pKaOutput.test_compute_pka_direct_scheme()TestGaussian16pKaOutput.test_compute_pka_energy_values()TestGaussian16pKaOutput.test_compute_pka_thermochemistry_ha_and_a()TestGaussian16pKaOutput.test_compute_thermochemistry_ha()TestGaussian16pKaOutput.test_deprotonation_energy_difference()TestGaussian16pKaOutput.test_electronic_energy_a()TestGaussian16pKaOutput.test_electronic_energy_ha()TestGaussian16pKaOutput.test_energy_units_conversion_kcal_mol()TestGaussian16pKaOutput.test_energy_units_conversion_kj_mol()TestGaussian16pKaOutput.test_enthalpy_ha()TestGaussian16pKaOutput.test_gibbs_free_energy_ha()TestGaussian16pKaOutput.test_init_with_custom_settings()TestGaussian16pKaOutput.test_init_with_default_settings()TestGaussian16pKaOutput.test_print_pka_summary()TestGaussian16pKaOutput.test_print_pka_thermochemistry_summary()TestGaussian16pKaOutput.test_qh_enthalpy_ha()TestGaussian16pKaOutput.test_qh_gibbs_free_energy_a()TestGaussian16pKaOutput.test_qh_gibbs_free_energy_ha()TestGaussian16pKaOutput.test_thermochemistry_property_caching()TestGaussian16pKaOutput.test_zero_point_energy_ha()
TestGaussianCubeFileTestGaussianPBCOutputFileTestGaussianWBIOutputTestRouteStringTestRouteString.test_read_additional_route_parameters()TestRouteString.test_read_route_semiempirical()TestRouteString.test_read_route_string_nonstandard()TestRouteString.test_read_route_string_oniom_layer_methods_and_bases()TestRouteString.test_read_route_string_opt_options()TestRouteString.test_read_route_string_standard()TestRouteString.test_read_route_string_standard2()TestRouteString.test_read_route_string_standard3a()TestRouteString.test_read_route_string_standard3b()TestRouteString.test_read_route_string_standard4()TestRouteString.test_read_route_string_standard5()TestRouteString.test_read_route_string_standard6()TestRouteString.test_read_route_string_standard7()TestRouteString.test_solvent_in_route()
- tests.test_GaussianSettings module
TestGaussianJobFromComFileTestGaussianJobFromComFile.test_cli_group_remove_solvent_overrides_project_settings()TestGaussianJobFromComFile.test_cli_group_solvent_options_propagate_to_opt()TestGaussianJobFromComFile.test_cli_group_solvent_options_propagate_to_td()TestGaussianJobFromComFile.test_include_solvent()TestGaussianJobFromComFile.test_reads_com_file()TestGaussianJobFromComFile.test_update_solvent()
TestGaussianJobFromLogFileTestGaussianJobFromLogFile.test_accumulates_settings()TestGaussianJobFromLogFile.test_reads_custom_solvent_from_logfile_as_settings_text()TestGaussianJobFromLogFile.test_reads_gaussian_pm6_outfile()TestGaussianJobFromLogFile.test_reads_gaussian_ts_genecp_outfile()TestGaussianJobFromLogFile.test_reads_oldform_redundant_coordinates_with_atomic_numbers()TestGaussianJobFromLogFile.test_reads_pd_insertion_ts_r_logfile()
TestGaussianJobSettingsTestGaussianJobSettings.test_get_settings_from_yaml_gas_solv()TestGaussianJobSettings.test_get_settings_from_yaml_solv()TestGaussianJobSettings.test_merge_dict()TestGaussianJobSettings.test_merge_other_settings()TestGaussianJobSettings.test_read_gaussian_hf_comfile()TestGaussianJobSettings.test_read_gaussian_settings_from_orca_inp()
TestGaussianLinkJobSettingsGuessTestGaussianLinkJobSettingsGuess.test_multiple_guess_options_with_parentheses()TestGaussianLinkJobSettingsGuess.test_pre_parenthesized_input_no_double_wrapping()TestGaussianLinkJobSettingsGuess.test_pre_parenthesized_input_with_whitespace()TestGaussianLinkJobSettingsGuess.test_single_guess_option_no_parentheses()
TestGaussianPBCJobTestGaussianQMMMJobSettingsTestGaussianQMMMJobSettings.test_builtin_mm_helpers()TestGaussianQMMMJobSettings.test_qmmm_additional_opt_options_in_route()TestGaussianQMMMJobSettings.test_qmmm_additional_route_parameters()TestGaussianQMMMJobSettings.test_qmmm_settings()TestGaussianQMMMJobSettings.test_qmmm_settings_for_atoms()TestGaussianQMMMJobSettings.test_qmmm_settings_for_charge_and_multiplicity()
TestGaussianRouteTestGaussianpKaJobSettingsTestGaussianpKaJobSettings.test_conjugate_base_job_property()TestGaussianpKaJobSettings.test_conjugate_base_molecule_method()TestGaussianpKaJobSettings.test_conjugate_base_molecule_property()TestGaussianpKaJobSettings.test_conjugate_pair_job_settings_method()TestGaussianpKaJobSettings.test_conjugate_pair_molecules_method()TestGaussianpKaJobSettings.test_create_conjugate_base_molecule()TestGaussianpKaJobSettings.test_create_conjugate_base_molecule_custom_charge()TestGaussianpKaJobSettings.test_create_conjugate_base_molecule_invalid_index()TestGaussianpKaJobSettings.test_create_conjugate_base_molecule_no_proton_index()TestGaussianpKaJobSettings.test_create_conjugate_base_molecule_not_hydrogen()TestGaussianpKaJobSettings.test_create_job_settings()TestGaussianpKaJobSettings.test_create_molecules()TestGaussianpKaJobSettings.test_default_scheme()TestGaussianpKaJobSettings.test_direct_cycle_custom_delta_g()TestGaussianpKaJobSettings.test_direct_cycle_no_reference()TestGaussianpKaJobSettings.test_gas_phase_optimization_settings()TestGaussianpKaJobSettings.test_get_reference_conjugate_base_molecule()TestGaussianpKaJobSettings.test_get_reference_molecule()TestGaussianpKaJobSettings.test_init_custom_values()TestGaussianpKaJobSettings.test_init_invalid_settings_type()TestGaussianpKaJobSettings.test_init_no_proton_index()TestGaussianpKaJobSettings.test_job_init_valid_settings()TestGaussianpKaJobSettings.test_job_labels()TestGaussianpKaJobSettings.test_pka_jobs_property()TestGaussianpKaJobSettings.test_proton_exchange_with_reference_file()TestGaussianpKaJobSettings.test_proton_exchange_without_reference_file()TestGaussianpKaJobSettings.test_protonated_charge_multiplicity_properties()TestGaussianpKaJobSettings.test_protonated_job_property()TestGaussianpKaJobSettings.test_protonated_molecule_property()TestGaussianpKaJobSettings.test_reference_gas_phase_job_settings()TestGaussianpKaJobSettings.test_reference_solution_phase_sp_settings()TestGaussianpKaJobSettings.test_reference_validation()TestGaussianpKaJobSettings.test_reference_validation_missing_proton_index()TestGaussianpKaJobSettings.test_solution_phase_sp_settings()
- tests.test_GaussianWriter module
TestGaussianInputWriterTestGaussianInputWriter.test_append_mm_parameters_skips_plain_molecule()TestGaussianInputWriter.test_write_gaussian_input_from_pbc_logfile()TestGaussianInputWriter.test_write_modred_job()TestGaussianInputWriter.test_write_modred_with_custom_basis_for_all_elements_in_structure_using_api()TestGaussianInputWriter.test_write_opt_input_from_logfile()TestGaussianInputWriter.test_write_opt_job()TestGaussianInputWriter.test_write_opt_job_with_route()TestGaussianInputWriter.test_write_qmmm_amber_from_oniom_com_without_sidecar_files()TestGaussianInputWriter.test_write_qmmm_amber_incomplete_mm_atom_info_raises()TestGaussianInputWriter.test_write_qmmm_amber_requires_mm_atom_info()TestGaussianInputWriter.test_write_qmmm_amber_with_mm_atom_info()TestGaussianInputWriter.test_write_qmmm_auto_assigns_link_atoms_for_cut_bonds()TestGaussianInputWriter.test_write_qmmm_genecp_follows_conventional_basis_path()TestGaussianInputWriter.test_write_qmmm_inherits_layers_from_molecule()TestGaussianInputWriter.test_write_qmmm_input_from_logfile()TestGaussianInputWriter.test_write_qmmm_job()TestGaussianInputWriter.test_write_qmmm_job_with_scale_factors()TestGaussianInputWriter.test_write_qmmm_link_atoms_share_high_boundary()TestGaussianInputWriter.test_write_qmmm_missing_mm_parameters_file_raises()TestGaussianInputWriter.test_write_qmmm_mm_parameters_file_overrides_molecule_params()TestGaussianInputWriter.test_write_qmmm_pm6_skips_connectivity_section()TestGaussianInputWriter.test_write_qmmm_rejects_multiple_link_atoms_on_same_atom()TestGaussianInputWriter.test_write_qmmm_uses_layers_from_oniom_com()TestGaussianInputWriter.test_write_scan_job_multiple_degrees_of_freedom()TestGaussianInputWriter.test_write_scan_job_multiple_degrees_of_freedom_with_constraints()TestGaussianInputWriter.test_write_scan_job_single_degree_of_freedom()TestGaussianInputWriter.test_write_semiempirical_opt_job()TestGaussianInputWriter.test_write_sp_input_with_solvation_from_logfile()TestGaussianInputWriter.test_write_sp_with_custom_solvation_from_logfile()TestGaussianInputWriter.test_write_ts_job()TestGaussianInputWriter.test_write_ts_with_custom_basis_from_logfile()TestGaussianInputWriter.test_write_ts_with_custom_basis_using_api()
- tests.test_ORCAIO module
TestORCABasisTestORCAEngradTestORCAInputTestORCANEBTestORCANEBInputTestORCANEBInput.test_neb_input_all_properties()TestORCANEBInput.test_neb_input_case_insensitive()TestORCANEBInput.test_neb_input_charge_and_multiplicity()TestORCANEBInput.test_neb_input_ending_xyzfile()TestORCANEBInput.test_neb_input_inherits_from_orca_input()TestORCANEBInput.test_neb_input_nimages()TestORCANEBInput.test_neb_input_pre_optimization_false()TestORCANEBInput.test_neb_input_restarting_allxyzfile_none()TestORCANEBInput.test_neb_input_starting_xyzfile()TestORCANEBInput.test_neb_input_ts_xyzfile()TestORCANEBInput.test_neb_input_with_preopt_true()TestORCANEBInput.test_neb_input_with_restart_file()TestORCANEBInput.test_neb_input_without_ts_file()TestORCANEBInput.test_read_neb_input_basic()
TestORCANEBJobSettingsTestORCANEBJobSettings.test_equality_different_intermediate_xyzfile()TestORCANEBJobSettings.test_equality_different_joboption()TestORCANEBJobSettings.test_equality_different_nimages()TestORCANEBJobSettings.test_equality_different_parent_attributes()TestORCANEBJobSettings.test_equality_different_preopt_ends()TestORCANEBJobSettings.test_equality_different_restarting_xyzfile()TestORCANEBJobSettings.test_equality_different_semiempirical()TestORCANEBJobSettings.test_equality_identical_settings()TestORCANEBJobSettings.test_equality_includes_all_neb_attributes()TestORCANEBJobSettings.test_inheritance()TestORCANEBJobSettings.test_init_default()TestORCANEBJobSettings.test_init_with_parameters()TestORCANEBJobSettings.test_neb_block_basic()TestORCANEBJobSettings.test_route_string_generation()TestORCANEBJobSettings.test_validation_errors()
TestORCAOutputTestORCAOutput.test_fe2_quintet_orbital_properties()TestORCAOutput.test_fe2_singlet_orbital_properties()TestORCAOutput.test_fe2_triplet_orbital_properties()TestORCAOutput.test_fe3_doublet_orbital_properties()TestORCAOutput.test_fe3_quartet_orbital_properties()TestORCAOutput.test_fe3_sextet_orbital_properties()TestORCAOutput.test_get_constrained_atoms()TestORCAOutput.test_get_constrained_bond_lengths_and_angles()TestORCAOutput.test_get_constrained_dihedral_angles()TestORCAOutput.test_gtoint_errfile()TestORCAOutput.test_he_freq_output()TestORCAOutput.test_read_hirshfeld_full_print_output()TestORCAOutput.test_read_sp_full_print_output()TestORCAOutput.test_read_sp_output()TestORCAOutput.test_read_water_output()TestORCAOutput.test_sn2_ts_orca_output()TestORCAOutput.test_water_optimized_output()
TestORCAQMMMTestORCAQMMMJobSettingsTestORCAQMMMJobSettings.test_charge_and_multiplicity_population()TestORCAQMMMJobSettings.test_embedding_type_helpers()TestORCAQMMMJobSettings.test_partition_string_empty_and_none()TestORCAQMMMJobSettings.test_partition_string_qm_and_qm2()TestORCAQMMMJobSettings.test_partition_string_single_and_list_input()TestORCAQMMMJobSettings.test_qmmm_block_uses_orca_keywords()TestORCAQMMMJobSettings.test_qmmm_xyz_line_does_not_fall_back_to_total_charge()TestORCAQMMMJobSettings.test_qmmm_xyz_line_uses_charge_high_not_total()TestORCAQMMMJobSettings.test_route_string_without_parent_jobtype()
TestORCARouteTestORCApKaOutputTestORCApKaOutput.EXPECTED_DG_AUTestORCApKaOutput.EXPECTED_DG_KCALTestORCApKaOutput.L2_A_ETestORCApKaOutput.L2_A_QH_GTestORCApKaOutput.L2_A_SP_ETestORCApKaOutput.L2_HA_ETestORCApKaOutput.L2_HA_QH_GTestORCApKaOutput.L2_HA_SP_ETestORCApKaOutput.PHENOL_B_ETestORCApKaOutput.PHENOL_B_QH_GTestORCApKaOutput.PHENOL_B_SP_ETestORCApKaOutput.PHENOL_HB_ETestORCApKaOutput.PHENOL_HB_QH_GTestORCApKaOutput.PHENOL_HB_SP_ETestORCApKaOutput.test_compute_pka_thermochemistry_ha_and_a()TestORCApKaOutput.test_compute_pka_uses_requested_files()TestORCApKaOutput.test_electronic_energy_and_qh_gibbs_match_combined_dat()TestORCApKaOutput.test_init_with_default_settings()
- tests.test_PyMOLJobs module
TestPyMOLCLIFolderOptionsTestPyMOLFileProcessingUsesSourceFilenameTestPyMOLFileProcessingUsesSourceFilename.test_generate_fchk_uses_source_basename_not_label()TestPyMOLFileProcessingUsesSourceFilename.test_nci_uses_source_basename_for_cube_loading_and_command()TestPyMOLFileProcessingUsesSourceFilename.test_spin_cli_custom_label_uses_source_basename_and_exact_output_name()TestPyMOLFileProcessingUsesSourceFilename.test_spin_cubegen_uses_source_basename_fchk()
TestPyMOLJobsTestPyMOLJobs.pytestmarkTestPyMOLJobs.test_irc_from_files()TestPyMOLJobs.test_pymol_MO_job_parameters()TestPyMOLJobs.test_pymol_align_job_on_three_files()TestPyMOLJobs.test_pymol_hybrid_visualization_job_custom_light_colors_on_xyz_file()TestPyMOLJobs.test_pymol_hybrid_visualization_job_on_xyz_file()TestPyMOLJobs.test_pymol_hybrid_visualization_job_with_redundant_colors_on_xyz_file()TestPyMOLJobs.test_pymol_irc_movie_job_on_gaussian_log_multiple_structures()TestPyMOLJobs.test_pymol_movie_job_on_gaussian_com_file()TestPyMOLJobs.test_pymol_nci_job_on_gaussian_com_file()TestPyMOLJobs.test_pymol_nci_job_parameters()TestPyMOLJobs.test_pymol_spin_job_on_gaussian_com_file()TestPyMOLJobs.test_pymol_spin_job_parameters()TestPyMOLJobs.test_pymol_visualization_job_on_gaussian_com_file()TestPyMOLJobs.test_pymol_visualization_job_on_gaussian_log_file()TestPyMOLJobs.test_pymol_visualization_job_on_gaussian_log_multiple_structures()TestPyMOLJobs.test_pymol_visualization_job_on_orca_inp_file()TestPyMOLJobs.test_pymol_visualization_job_on_orca_out_file()TestPyMOLJobs.test_pymol_visualization_job_on_pubchem_id()TestPyMOLJobs.test_pymol_visualization_job_on_smiles()
TestPyMOLScientificStyleVisualizationJobsTestPyMOLScientificStyleVisualizationJobs.coordination_bonds_1_merTestPyMOLScientificStyleVisualizationJobs.pytestmarkTestPyMOLScientificStyleVisualizationJobs.test_comic_style_job_on_1_mer_xyz()TestPyMOLScientificStyleVisualizationJobs.test_comic_style_job_with_coordination_bonds_on_1_mer_xyz()TestPyMOLScientificStyleVisualizationJobs.test_editorial_minimal_style_job_on_1_mer_xyz()TestPyMOLScientificStyleVisualizationJobs.test_glossy_style_job_on_1_mer_xyz()TestPyMOLScientificStyleVisualizationJobs.test_soft_ceramic_style_job_on_1_mer_xyz()
TestPyMOLStyleCommandsTestPyMOLStyleCommands.coordination_bonds_1_merTestPyMOLStyleCommands.label_1_merTestPyMOLStyleCommands.test_align_setup_style_cylview_flat()TestPyMOLStyleCommands.test_build_coordination_atoms_uses_geometry_helpers()TestPyMOLStyleCommands.test_comic_metallic_reuses_glossy_palette()TestPyMOLStyleCommands.test_cylview_flat_visualization_job_label_suffix()TestPyMOLStyleCommands.test_derived_styles_hide_distance_value_labels_base_style_keeps_them()TestPyMOLStyleCommands.test_element_category_helpers_are_centralized()TestPyMOLStyleCommands.test_finish_default_runs_finalize_before_camera()TestPyMOLStyleCommands.test_format_pymol_style_command_is_independent_of_coordinates()TestPyMOLStyleCommands.test_hybrid_is_not_a_derived_style()TestPyMOLStyleCommands.test_metal_pymol_selection()TestPyMOLStyleCommands.test_pymol_elem_selection()TestPyMOLStyleCommands.test_scientific_style_registry_matches_classes()TestPyMOLStyleCommands.test_scientific_style_runner_orders_distances_before_render()TestPyMOLStyleCommands.test_select_coordination_uses_command_as_prefix()TestPyMOLStyleCommands.test_setup_style_cylview_flat()TestPyMOLStyleCommands.test_style_wrapper_ignores_pymol_self_kwarg()TestPyMOLStyleCommands.test_zhang_group_scientific_styles_hide_distance_value_labels()TestPyMOLStyleCommands.test_zhang_group_scientific_styles_import_without_pymol()
skip_if_no_pymol()
- tests.test_YAMLIO module
- tests.test_converter module
TestConvertCLITestConvertCLI.test_cli_convert_batch_directory()TestConvertCLI.test_cli_convert_command_object_defaults_to_xyz()TestConvertCLI.test_cli_convert_directory_requires_filetype()TestConvertCLI.test_cli_convert_include_intermediate_structures()TestConvertCLI.test_cli_convert_input_defaults_to_output_filetype()TestConvertCLI.test_cli_convert_input_defaults_to_xyz()TestConvertCLI.test_cli_convert_missing_input_fails()TestConvertCLI.test_cli_convert_mutually_exclusive_input_and_directory()TestConvertCLI.test_cli_convert_output_extension_only()TestConvertCLI.test_cli_convert_output_extension_without_dot()TestConvertCLI.test_cli_convert_output_full_path()TestConvertCLI.test_cli_convert_pdb_to_xyz()TestConvertCLI.test_cli_convert_requires_mode()TestConvertCLI.test_cli_convert_short_flags()TestConvertCLI.test_cli_convert_with_debug_and_stream()TestConvertCLI.test_convert_callback_batch_directory()TestConvertCLI.test_convert_callback_directory_requires_filetype()TestConvertCLI.test_convert_callback_rejects_input_and_directory()TestConvertCLI.test_convert_callback_requires_mode()TestConvertCLI.test_convert_callback_resolves_default_output()TestConvertCLI.test_convert_callback_uses_output_file()
TestConverterTestConverter.test_convert_com_folder_to_xyz()TestConverter.test_convert_log_folder_to_com()TestConverter.test_convert_log_folder_to_xyz()TestConverter.test_convert_single_comfile_to_xyz()TestConverter.test_convert_single_failed_modred_log_file_to_xyz()TestConverter.test_convert_single_failed_oniom_log_file_to_xyz()TestConverter.test_convert_single_link_logfile_to_xyz()TestConverter.test_convert_single_link_opt_logfile_to_com()TestConverter.test_convert_single_link_opt_logfile_to_xyz()TestConverter.test_convert_single_link_sp_logfile_to_xyz()TestConverter.test_convert_single_link_ts_logfile_to_xyz()TestConverter.test_convert_single_logfile_to_com()TestConverter.test_convert_single_opt_log_file_to_xyz()TestConverter.test_convert_single_sp_log_file_to_xyz()TestConverter.test_convert_single_wbi_log_file_to_xyz()TestConverter.test_convert_xyz_folder_to_com()
TestConverterCoverageGapsTestConverterCoverageGaps.test_batch_gaussian_out_to_xyz()TestConverterCoverageGaps.test_batch_gjf_to_xyz()TestConverterCoverageGaps.test_batch_include_intermediate_list_write()TestConverterCoverageGaps.test_batch_orca_inp_to_xyz()TestConverterCoverageGaps.test_batch_orca_out_to_xyz()TestConverterCoverageGaps.test_batch_pdb_to_xyz()TestConverterCoverageGaps.test_batch_sdf_to_xyz()TestConverterCoverageGaps.test_convert_files_neither_directory_nor_filename_raises()TestConverterCoverageGaps.test_convert_out_without_program_raises()TestConverterCoverageGaps.test_convert_unsupported_batch_type_raises()TestConverterCoverageGaps.test_convert_unsupported_single_type_raises()TestConverterCoverageGaps.test_single_gjf_to_xyz()TestConverterCoverageGaps.test_single_include_intermediate_list()TestConverterCoverageGaps.test_single_inp_to_xyz()TestConverterCoverageGaps.test_single_orca_out_to_xyz()TestConverterCoverageGaps.test_single_pdb_to_xyz()TestConverterCoverageGaps.test_single_sdf_to_xyz()TestConverterCoverageGaps.test_single_unknown_program_out_raises()TestConverterCoverageGaps.test_xyz_to_pdb_empty_read_raises()TestConverterCoverageGaps.test_xyz_to_pdb_missing_path_writes_then_converts()
TestConverterTwoWayTestConverterTwoWay.test_convert_file_com_to_xyz()TestConverterTwoWay.test_convert_file_creates_missing_output_dir()TestConverterTwoWay.test_convert_file_empty_list_raises()TestConverterTwoWay.test_convert_file_missing_extension_raises()TestConverterTwoWay.test_convert_file_missing_input_raises()TestConverterTwoWay.test_convert_file_multi_model_pdb_splits()TestConverterTwoWay.test_convert_file_non_list_molecule_wrapped()TestConverterTwoWay.test_convert_file_none_molecules_raises()TestConverterTwoWay.test_convert_file_none_molecules_with_intermediates_raises()TestConverterTwoWay.test_convert_file_pdb_to_com()TestConverterTwoWay.test_convert_file_pdb_to_xyz()TestConverterTwoWay.test_convert_file_single_molecule_with_intermediates()TestConverterTwoWay.test_convert_file_single_structure_without_splitting()TestConverterTwoWay.test_convert_file_xyz_to_com()TestConverterTwoWay.test_convert_file_xyz_to_pdb()TestConverterTwoWay.test_convert_files_routes_to_convert_file_with_output_filepath()TestConverterTwoWay.test_convert_files_routes_with_include_intermediate()
TestOpenBabelReadFallbackTestOpenBabelReadFallback.test_ase_only_cfg_skips_openbabel()TestOpenBabelReadFallback.test_ase_only_cif_skips_openbabel()TestOpenBabelReadFallback.test_ase_only_extensions_constant()TestOpenBabelReadFallback.test_ase_only_traj_skips_openbabel()TestOpenBabelReadFallback.test_batch_xyz_folder_excludes_extxyz()TestOpenBabelReadFallback.test_cli_convert_mol2_to_xyz()TestOpenBabelReadFallback.test_convert_cif_to_xyz_drops_pbc()TestOpenBabelReadFallback.test_convert_file_mol2_to_xyz()TestOpenBabelReadFallback.test_make3d_failure_logs_warning()TestOpenBabelReadFallback.test_missing_openbabel_falls_back_to_ase()TestOpenBabelReadFallback.test_multi_molecule_mol2_index_and_return_list()TestOpenBabelReadFallback.test_numbered_output_warns_on_collision()TestOpenBabelReadFallback.test_obabel_failure_falls_back_to_ase()TestOpenBabelReadFallback.test_read_charged_smiles_propagates_charge()TestOpenBabelReadFallback.test_read_mol2_via_openbabel()TestOpenBabelReadFallback.test_read_neutral_mol2_charge_is_none()TestOpenBabelReadFallback.test_read_smi_via_openbabel_generates_3d()
TestOpenBabelWriteFallbackTestOpenBabelWriteFallback.test_cleanup_false_keeps_temp_xyz()TestOpenBabelWriteFallback.test_cleanup_oserror_on_import_error()TestOpenBabelWriteFallback.test_cleanup_oserror_on_success_is_warned()TestOpenBabelWriteFallback.test_cli_convert_to_mol2()TestOpenBabelWriteFallback.test_convert_file_to_mol2()TestOpenBabelWriteFallback.test_empty_openbabel_read_raises_and_cleans_up()TestOpenBabelWriteFallback.test_missing_openbabel_cleanup_false_keeps_temp()TestOpenBabelWriteFallback.test_missing_openbabel_raises_import_error()TestOpenBabelWriteFallback.test_native_extxyz_via_write()TestOpenBabelWriteFallback.test_native_formats_still_work()TestOpenBabelWriteFallback.test_nonsense_format_raises_value_error()TestOpenBabelWriteFallback.test_temp_xyz_removed_after_success()TestOpenBabelWriteFallback.test_temp_xyz_removed_after_write_failure()TestOpenBabelWriteFallback.test_write_cml_via_openbabel()TestOpenBabelWriteFallback.test_write_cosmorsxyz_is_native()TestOpenBabelWriteFallback.test_write_mol2_via_openbabel()TestOpenBabelWriteFallback.test_write_pdb_pybabel_delegates()TestOpenBabelWriteFallback.test_xyz_to_pdb_existing_file_branch()TestOpenBabelWriteFallback.test_xyz_to_pdb_none_delegates_to_write_pdb_pybabel()
TestPDBFileTestPDBFile.test_atom_names()TestPDBFile.test_blank_element_columns_infer_two_letter_elements()TestPDBFile.test_chain_ids()TestPDBFile.test_convert_cdxml_folder_to_com()TestPDBFile.test_convert_cdxml_folder_to_xyz()TestPDBFile.test_convert_multi_molecule_cdxml_default_writes_last_only()TestPDBFile.test_convert_multi_molecule_cdxml_to_xyz_splits_files()TestPDBFile.test_convert_single_cdx_to_xyz()TestPDBFile.test_convert_single_cdxml_to_com()TestPDBFile.test_convert_single_cdxml_to_xyz()TestPDBFile.test_empty_file_raises_value_error()TestPDBFile.test_filepath_resolves_absolute()TestPDBFile.test_get_molecules_all()TestPDBFile.test_get_molecules_first()TestPDBFile.test_get_molecules_last()TestPDBFile.test_infer_element_ca_is_carbon()TestPDBFile.test_infer_element_cl()TestPDBFile.test_infer_element_digits_only_raises()TestPDBFile.test_infer_element_empty_raises()TestPDBFile.test_infer_element_fe()TestPDBFile.test_infer_element_leading_digit()TestPDBFile.test_infer_element_zn()TestPDBFile.test_info_dict_populated()TestPDBFile.test_init_stores_filename()TestPDBFile.test_molecule_from_filepath_uses_pdbfile()TestPDBFile.test_molecule_property_raises_on_empty()TestPDBFile.test_molecule_property_returns_last_model()TestPDBFile.test_molecule_returns_molecule_object()TestPDBFile.test_num_atoms()TestPDBFile.test_pdb_infer_pdb_element()TestPDBFile.test_pdb_molecule_from_pdb_atom_lines()TestPDBFile.test_pdb_parse_pdb_models()TestPDBFile.test_positions()TestPDBFile.test_raw_lines_preserves_column_whitespace()TestPDBFile.test_raw_lines_strips_trailing_newlines()TestPDBFile.test_record_types()TestPDBFile.test_repr()TestPDBFile.test_residue_names()TestPDBFile.test_residue_numbers()TestPDBFile.test_return_list_wraps_single()TestPDBFile.test_str()TestPDBFile.test_symbols()TestPDBFile.test_write_creates_file()TestPDBFile.test_write_output_contains_atom_records()TestPDBFile.test_write_round_trip_preserves_atom_count()TestPDBFile.test_write_round_trip_preserves_positions()TestPDBFile.test_write_round_trip_preserves_symbols()
TestResolveOutputPathTestResolveOutputPath.test_resolve_output_path_default()TestResolveOutputPath.test_resolve_output_path_extension_with_dot()TestResolveOutputPath.test_resolve_output_path_extension_without_dot()TestResolveOutputPath.test_resolve_output_path_full_path()TestResolveOutputPath.test_resolve_output_path_output_filetype()TestResolveOutputPath.test_resolve_output_path_relative_path_with_extension()TestResolveOutputPath.test_resolve_output_path_subdirectory_path()
- tests.test_groupers module
TestBasicRMSDGrouperAndBasicFunctionalityTestBasicRMSDGrouperAndBasicFunctionality.NUM_PROCSTestBasicRMSDGrouperAndBasicFunctionality.pytestmarkTestBasicRMSDGrouperAndBasicFunctionality.test_calculate_rmsd_pair_wrapper_validation()TestBasicRMSDGrouperAndBasicFunctionality.test_num_groups_parameter()TestBasicRMSDGrouperAndBasicFunctionality.test_pick_the_lowestenergy_conformers()TestBasicRMSDGrouperAndBasicFunctionality.test_rmsd_grouper()TestBasicRMSDGrouperAndBasicFunctionality.test_rmsd_grouper_for_crest_conformers()TestBasicRMSDGrouperAndBasicFunctionality.test_rmsd_grouper_for_crest_conformers_ignore_Hs()TestBasicRMSDGrouperAndBasicFunctionality.test_rmsd_grouper_for_rotated_molecules()
TestCompleteLinkageInputTestCompleteLinkageInput.NUM_PROCSTestCompleteLinkageInput.pytestmarkTestCompleteLinkageInput.test_clustering_submatrix_validates_original_indices()TestCompleteLinkageInput.test_distance_matrix_shape_validation()TestCompleteLinkageInput.test_energy_order_places_invalid_energies_last()TestCompleteLinkageInput.test_explicit_output_directory_is_used()TestCompleteLinkageInput.test_matrix_grouper_rejects_invalid_grouping_configuration()TestCompleteLinkageInput.test_matrix_grouper_rejects_unknown_representative_strategy()TestCompleteLinkageInput.test_num_groups_resolution_validation()TestCompleteLinkageInput.test_singleton_matrix_helpers()TestCompleteLinkageInput.test_threshold_resolution_validation()
TestCompleteLinkageOutputTestCompleteLinkageOutput.NUM_PROCSTestCompleteLinkageOutput.pytestmarkTestCompleteLinkageOutput.test_asymmetric_distance_matrix_raises()TestCompleteLinkageOutput.test_complete_linkage_prevents_chaining()TestCompleteLinkageOutput.test_energy_public_group_by_num_groups_accepts_signed_kcal_output()TestCompleteLinkageOutput.test_energy_public_group_by_threshold_accepts_signed_kcal_output()TestCompleteLinkageOutput.test_grouping_does_not_modify_distance_matrix()TestCompleteLinkageOutput.test_hierarchical_complete_linkage_prevents_chaining()TestCompleteLinkageOutput.test_hierarchical_grouping_is_input_order_independent()TestCompleteLinkageOutput.test_infinite_distance_matrix_skips_minimum_problematic_structures()TestCompleteLinkageOutput.test_infinite_distance_removal_is_iterative()TestCompleteLinkageOutput.test_infinite_pair_removes_one_structure_and_groups_remaining()TestCompleteLinkageOutput.test_infinite_pair_tie_breaking_is_deterministic()TestCompleteLinkageOutput.test_multiple_infinite_pairs_remove_minimum_problematic_structures()TestCompleteLinkageOutput.test_nan_distance_matrix_raises()TestCompleteLinkageOutput.test_negative_distance_raises()TestCompleteLinkageOutput.test_negative_infinity_raises()TestCompleteLinkageOutput.test_nonzero_diagonal_raises()TestCompleteLinkageOutput.test_num_groups_after_skipping_uses_valid_structure_count()TestCompleteLinkageOutput.test_num_groups_keeps_previous_full_linkage_level()TestCompleteLinkageOutput.test_num_groups_uses_exact_level_when_available()TestCompleteLinkageOutput.test_original_indices_are_preserved_after_skipping()TestCompleteLinkageOutput.test_public_group_by_num_groups_reuses_distance_matrix_and_caches_result()TestCompleteLinkageOutput.test_public_group_by_threshold_reuses_distance_matrix_and_caches_result()TestCompleteLinkageOutput.test_tanimoto_public_group_by_num_groups_accepts_recorded_similarity()TestCompleteLinkageOutput.test_tanimoto_public_group_by_threshold_accepts_recorded_similarity()TestCompleteLinkageOutput.test_tanimoto_threshold_uses_similarity_semantics()TestCompleteLinkageOutput.test_tfd_public_group_by_num_groups_accepts_output_distance_matrix()TestCompleteLinkageOutput.test_tfd_public_group_by_threshold_accepts_output_distance_matrix()TestCompleteLinkageOutput.test_threshold_grouping_clears_previous_auto_threshold()TestCompleteLinkageOutput.test_threshold_includes_equal_distance()
TestConformerIdExtractionTestConformerIdExtraction.test_all_files_without_cxx_pattern()TestConformerIdExtraction.test_conformer_id_fallback_to_filename()TestConformerIdExtraction.test_conformer_ids_molecules_correspondence()TestConformerIdExtraction.test_extract_conformer_id_with_pattern()TestConformerIdExtraction.test_extract_conformer_id_without_pattern()TestConformerIdExtraction.test_mixed_pattern_files_correspondence()
TestConformerIdsFunctionalityTestEdgeCasesTestEdgeCases.pytestmarkTestEdgeCases.test_different_formulas_always_separate()TestEdgeCases.test_incompatible_rmsd_structures_are_skipped()TestEdgeCases.test_num_groups_equals_num_molecules()TestEdgeCases.test_num_groups_exceeds_num_molecules()TestEdgeCases.test_rmsd_infinity_for_different_molecules()TestEdgeCases.test_two_molecules_grouping()TestEdgeCases.test_very_high_threshold()TestEdgeCases.test_very_low_threshold()
TestEnergyExtractionFunctionTestEnergyGrouperTestEnergyGrouper.NUM_PROCSTestEnergyGrouper.pytestmarkTestEnergyGrouper.test_calculate_energy_diff_pair_wrapper_validation()TestEnergyGrouper.test_energy_extraction_from_ts_log_files()TestEnergyGrouper.test_energy_extraction_from_xyz_file()TestEnergyGrouper.test_energy_grouper_for_crest_conformers()TestEnergyGrouper.test_energy_grouper_for_log_conformers()TestEnergyGrouper.test_energy_grouper_raises_error_for_missing_energy()TestEnergyGrouper.test_energy_linkage_preserves_other_validation_errors()TestEnergyGrouper.test_energy_linkage_reports_non_finite_energy()TestEnergyGrouper.test_energy_output_matrix_validation()TestEnergyGrouper.test_gibbs_energy_extraction_function()
TestFactoryTestGrouperCliRunnerTestGrouperCliRunner.test_create_grouper_job_forwards_representative()TestGrouperCliRunner.test_grouper_job_stores_output_configuration()TestGrouperCliRunner.test_grouper_runner_creates_tfd_with_representative()TestGrouperCliRunner.test_grouper_runner_preserves_representative_order()TestGrouperCliRunner.test_irmsd_cli_handles_failure_and_timeout()TestGrouperCliRunner.test_irmsd_helpers_and_direct_api_failure()TestGrouperCliRunner.test_irmsd_initialization_selects_api_cli_or_errors()TestGrouperCliRunner.test_isomorphism_grouper_handles_hashing_failure()TestGrouperCliRunner.test_pymol_heavy_atom_xyz_and_repr()TestGrouperCliRunner.test_pymol_rmsd_handles_invalid_and_failed_alignment()TestGrouperCliRunner.test_rmsd_repr_and_explicit_matrix_output()TestGrouperCliRunner.test_spyrmsd_incompatible_inputs_and_payload_handling()TestGrouperCliRunner.test_tfd_cli_forwards_strategy_and_representative()
TestGrouperUtilityFunctionsTestHungarianRMSDGrouperTestIRMSDGrouperTestLabelAndAppendLabelTestLabelAndAppendLabel.NUM_PROCSTestLabelAndAppendLabel.pytestmarkTestLabelAndAppendLabel.test_different_labels_create_different_outputs()TestLabelAndAppendLabel.test_get_label_function()TestLabelAndAppendLabel.test_label_in_group_xyz_files()TestLabelAndAppendLabel.test_label_in_output_directory()TestLabelAndAppendLabel.test_label_with_num_groups()
TestMultiprocessingSupportTestMultiprocessingSupport.pytestmarkTestMultiprocessingSupport.test_basic_rmsd_parallel_single_molecule_no_pair_no_crash()TestMultiprocessingSupport.test_basic_rmsd_progress_logs_all_milestones_parallel()TestMultiprocessingSupport.test_basic_rmsd_progress_logs_all_milestones_serial()TestMultiprocessingSupport.test_basic_rmsd_serial_parallel_equivalent()TestMultiprocessingSupport.test_energy_grouper_progress_logs_all_milestones()TestMultiprocessingSupport.test_formula_grouper_falls_back_to_single_proc()TestMultiprocessingSupport.test_hungarian_rmsd_serial_parallel_equivalent()TestMultiprocessingSupport.test_irmsd_serial_parallel_equivalent()TestMultiprocessingSupport.test_matrix_grouper_log_progress()TestMultiprocessingSupport.test_serial_only_strategy_warns_and_falls_back()TestMultiprocessingSupport.test_spyrmsd_parallel_preserves_isomorphisms()
TestOtherGroupersTestOtherGroupers.NUM_PROCSTestOtherGroupers.pytestmarkTestOtherGroupers.test_base_record_template_method()TestOtherGroupers.test_connectivity_grouper()TestOtherGroupers.test_connectivity_grouper_for_crest_conformers()TestOtherGroupers.test_formula_grouper()TestOtherGroupers.test_rdkit_isomorphism_grouper()TestOtherGroupers.test_record_writes_formula_outputs_with_headers()TestOtherGroupers.test_record_writes_rmsd_matrix_with_headers()TestOtherGroupers.test_thermochemistry_parameters_header_for_qhg_energy_types()TestOtherGroupers.test_thermochemistry_parameters_header_not_written_for_other_energy_types()
TestOutputFileGenerationTestPymolRMSDGrouperTestPymolRMSDGrouper.NUM_PROCSTestPymolRMSDGrouper.pytestmarkTestPymolRMSDGrouper.setup_class()TestPymolRMSDGrouper.teardown_class()TestPymolRMSDGrouper.teardown_method()TestPymolRMSDGrouper.test_ignore_hydrogen()TestPymolRMSDGrouper.test_pymol_grouper_falls_back_to_single_proc()TestPymolRMSDGrouper.test_pymolrmsd_grouper_for_crest_molecules()TestPymolRMSDGrouper.test_pymolrmsd_grouper_for_rotated_molecules()
TestRepresentativeStrategyTestRepresentativeStrategy.DummyDistanceGrouperTestRepresentativeStrategy.pytestmarkTestRepresentativeStrategy.test_center_puts_most_central_member_first()TestRepresentativeStrategy.test_center_strategy_orders_entire_group_by_centrality()TestRepresentativeStrategy.test_center_tie_breaks_by_energy_then_original_index()TestRepresentativeStrategy.test_default_representative_matches_explicit_lowest()TestRepresentativeStrategy.test_default_representative_strategy_is_lowest()TestRepresentativeStrategy.test_groups_table_and_unique_and_xyz_use_representative_first()TestRepresentativeStrategy.test_lowest_strategy_orders_group_by_energy()TestRepresentativeStrategy.test_non_matrix_center_and_top3_raise()TestRepresentativeStrategy.test_non_matrix_grouper_rejects_matrix_representative_strategy()TestRepresentativeStrategy.test_non_matrix_lowest_orders_first_by_energy()TestRepresentativeStrategy.test_representative_strategy_does_not_change_group_membership()TestRepresentativeStrategy.test_top3_falls_back_to_lowest_for_group_size_one()TestRepresentativeStrategy.test_top3_falls_back_to_lowest_for_group_size_two()TestRepresentativeStrategy.test_top3_falls_back_to_lowest_for_two_member_group()TestRepresentativeStrategy.test_top3_strategy_picks_most_central_among_three_lowest_energy()TestRepresentativeStrategy.test_top3_uses_only_three_lowest_energy_candidates()TestRepresentativeStrategy.test_unique_uses_first_group_member_as_representative()
TestSpyRMSDGrouperTestTanimotoSimilarityGrouperTestTanimotoSimilarityGrouper.NUM_PROCSTestTanimotoSimilarityGrouper.pytestmarkTestTanimotoSimilarityGrouper.test_all_failed_molecule_preparations_return_empty_groups()TestTanimotoSimilarityGrouper.test_all_nan_similarity_matrix_has_no_groups()TestTanimotoSimilarityGrouper.test_calculate_tanimoto_pair_wrapper_validation()TestTanimotoSimilarityGrouper.test_pair_returns_nan_when_fingerprint_generation_fails()TestTanimotoSimilarityGrouper.test_per_call_threshold_cannot_exceed_one()TestTanimotoSimilarityGrouper.test_rejects_out_of_range_threshold()TestTanimotoSimilarityGrouper.test_similarity_output_matrix_validation()TestTanimotoSimilarityGrouper.test_supported_topological_fingerprints()TestTanimotoSimilarityGrouper.test_tanimoto_grouper_for_crest_conformers()TestTanimotoSimilarityGrouper.test_tanimoto_num_groups_and_threshold_postprocessing()TestTanimotoSimilarityGrouper.test_tanimoto_num_groups_record_includes_actual_groups()TestTanimotoSimilarityGrouper.test_tanimoto_similarity_grouper()TestTanimotoSimilarityGrouper.test_tanimoto_threshold_boundary_through_group()TestTanimotoSimilarityGrouper.test_topological_fingerprint_can_ignore_hydrogens()TestTanimotoSimilarityGrouper.test_topological_hueckel_retry_handles_unusable_xyz()TestTanimotoSimilarityGrouper.test_topological_preparation_failure_is_skipped()TestTanimotoSimilarityGrouper.test_topological_preparation_handles_unusable_xyz()TestTanimotoSimilarityGrouper.test_topological_preparation_retries_with_hueckel()TestTanimotoSimilarityGrouper.test_topological_preparation_stops_without_hueckel()TestTanimotoSimilarityGrouper.test_unknown_and_failed_fingerprint_generation()TestTanimotoSimilarityGrouper.test_usr_hydrogen_removal_failure_uses_original_molecule()TestTanimotoSimilarityGrouper.test_usr_pair_similarity_and_hydrogen_removal()TestTanimotoSimilarityGrouper.test_usr_preparation_handles_missing_rdkit_molecule()
TestTorsionFingerprintGrouperTestTorsionFingerprintGrouper.NUM_PROCSTestTorsionFingerprintGrouper.pytestmarkTestTorsionFingerprintGrouper.test_calculate_tfd_pair_wrapper_validation()TestTorsionFingerprintGrouper.test_tfd_num_groups_records_actual_group_count()TestTorsionFingerprintGrouper.test_torsionfingerprint_grouper_for_crest_molecules()TestTorsionFingerprintGrouper.test_torsionfingerprint_grouper_for_rotated_molecules()TestTorsionFingerprintGrouper.test_use_maxdev_parameter()TestTorsionFingerprintGrouper.test_use_weights_parameter()
- tests.test_organizer module
- tests.test_server module
TestMissingProgramSectionFallbackTestServerTestServer.test_crest_executable()TestServer.test_gaussian_executable()TestServer.test_orca_executable()TestServer.test_pbs_submitter_writes_extra_scheduler_directives()TestServer.test_server_yaml()TestServer.test_slurm_submitter_writes_extra_scheduler_directives()TestServer.test_xtb_executable()
- tests.test_structures module
TestCDXFileTestCDXFile.test_cdx_molecule_to_graph()TestCDXFile.test_cdx_molecule_to_rdkit_conversion()TestCDXFile.test_cdxfile_get_molecules_index()TestCDXFile.test_molecule_from_filepath_cdx()TestCDXFile.test_molecule_from_filepath_cdxml()TestCDXFile.test_molecule_from_filepath_cdxml_multi_molecules()TestCDXFile.test_molecule_from_filepath_cdxml_pathlib()TestCDXFile.test_molecule_from_filepath_cdxml_return_list()TestCDXFile.test_read_complex_molecule_cdxml_file_()TestCDXFile.test_read_metal_ligand_molecules_cdxml_file_()TestCDXFile.test_read_multi_molecule_cdxml_file()TestCDXFile.test_read_single_molecule_cdx_file_imidazole()TestCDXFile.test_read_single_molecule_cdxml_file_benzene()TestCDXFile.test_read_single_molecule_cdxml_file_methane()
TestCXSMILESTestCXSMILES.EXPECTED_NORMALTestCXSMILES.EXPECTED_R_ENANTIOMERTestCXSMILES.EXPECTED_R_ROTAMERTestCXSMILES.EXPECTED_S_ENANTIOMERTestCXSMILES.EXPECTED_S_ROTAMERTestCXSMILES.test_enantiomers_differ()TestCXSMILES.test_large_molecule_c2_cxsmiles()TestCXSMILES.test_large_molecule_c3_cxsmiles()TestCXSMILES.test_large_molecules_differ()TestCXSMILES.test_r_enantiomer_cxsmiles()TestCXSMILES.test_r_rotamer_cxsmiles()TestCXSMILES.test_regression_cxsmiles()TestCXSMILES.test_rotamers_differ()TestCXSMILES.test_s_enantiomer_cxsmiles()TestCXSMILES.test_s_rotamer_cxsmiles()
TestChemicalFeaturesTestCoordinateBlockTestCoordinateBlock.test_coordinate_block_with_partitions_returns_qmmm_molecule()TestCoordinateBlock.test_coordinate_block_without_partitions_returns_molecule()TestCoordinateBlock.test_read_coordinate_block()TestCoordinateBlock.test_read_gaussian_cb_frozen_atoms()TestCoordinateBlock.test_read_gaussian_cb_with_tv()
TestCoordinateBlockAdvancedTestFileHandlingAdvancedTestGraphFeaturesTestInChITestInChI.EXPECTED_INCHI_NORMALTestInChI.EXPECTED_INCHI_R_ENANTIOMERTestInChI.EXPECTED_INCHI_S_ENANTIOMERTestInChI.EXPECTED_LARGE_C2TestInChI.EXPECTED_LARGE_C3TestInChI.EXPECTED_NORMALTestInChI.EXPECTED_R_ENANTIOMERTestInChI.EXPECTED_S_ENANTIOMERTestInChI.test_enantiomers_share_connectivity_layer()TestInChI.test_large_molecule_c2_inchikey()TestInChI.test_large_molecule_c3_inchikey()TestInChI.test_large_molecules_differ()TestInChI.test_r_enantiomer_inchikey()TestInChI.test_regression_inchikey()TestInChI.test_s_enantiomer_inchikey()
TestInChIKeyTestMoleculeAdvancedTestMoleculeAdvanced.test_charge_and_multiplicity_handling()TestMoleculeAdvanced.test_convert_ase_atoms_with_constraints_to_molecule()TestMoleculeAdvanced.test_distance_calculation()TestMoleculeAdvanced.test_empty_molecule_handling()TestMoleculeAdvanced.test_from_pdb_file_infers_uppercase_two_letter_elements_when_blank()TestMoleculeAdvanced.test_from_pdb_file_preserves_atom_and_residue_metadata()TestMoleculeAdvanced.test_from_pdb_file_supports_model_index_selection()TestMoleculeAdvanced.test_frozen_atoms_manipulation()TestMoleculeAdvanced.test_infer_pdb_element_from_uppercase_atom_names()TestMoleculeAdvanced.test_invalid_molecule_creation()TestMoleculeAdvanced.test_is_aromatic_non_aromatic_molecules()TestMoleculeAdvanced.test_molecule_from_db_with_pbc_and_constraints()TestMoleculeAdvanced.test_molecule_graph_generation()TestMoleculeAdvanced.test_molecule_to_rdkit_conversion()TestMoleculeAdvanced.test_pbc_handling()TestMoleculeAdvanced.test_pdb_with_different_flavors()TestMoleculeAdvanced.test_pdb_with_no_bonds()TestMoleculeAdvanced.test_to_ase_energy_unit_conversion()TestMoleculeAdvanced.test_to_ase_energy_with_none_forces()TestMoleculeAdvanced.test_to_ase_forces_unit_conversion()TestMoleculeAdvanced.test_to_ase_none_energy_and_forces()TestMoleculeAdvanced.test_to_ase_none_energy_with_forces()TestMoleculeAdvanced.test_to_pdb_conversion()TestMoleculeAdvanced.test_to_pdb_strict_columns_and_final_end_record()TestMoleculeAdvanced.test_to_pdb_uses_molecule_attributes_for_chain_and_residue_metadata()TestMoleculeAdvanced.test_write_generic_method_with_pdb_format()TestMoleculeAdvanced.test_write_pdb_file()TestMoleculeAdvanced.test_write_pdb_rejects_unexpected_keyword_argument()
TestMoleculeAndStructureIdentifiersTestMoleculeAndStructureIdentifiers.test_atom_permutation_preserves_both_ids()TestMoleculeAndStructureIdentifiers.test_different_electronic_state_changes_structure_id_not_molecule_id()TestMoleculeAndStructureIdentifiers.test_different_species_differ_in_both_ids()TestMoleculeAndStructureIdentifiers.test_enantiomers_differ_in_both_ids()TestMoleculeAndStructureIdentifiers.test_geometry_distortion_changes_structure_id_not_molecule_id()TestMoleculeAndStructureIdentifiers.test_ids_are_deterministic()TestMoleculeAndStructureIdentifiers.test_molecule_label_format()TestMoleculeAndStructureIdentifiers.test_rigid_transform_preserves_both_ids_3b()TestMoleculeAndStructureIdentifiers.test_rigid_transform_preserves_both_ids_formaldehyde()TestMoleculeAndStructureIdentifiers.test_rigid_transform_preserves_both_ids_methane()TestMoleculeAndStructureIdentifiers.test_structure_label_format()TestMoleculeAndStructureIdentifiers.test_sub_threshold_perturbation_preserves_both_ids()
TestQMMMMoleculeTestQMMMMolecule.test_auto_assigns_link_atoms_for_cut_covalent_bonds()TestQMMMMolecule.test_mm_atom_info_from_coordinate_lines()TestQMMMMolecule.test_qmmm_helpers_for_uncovered_branches()TestQMMMMolecule.test_qmmm_partition_out_of_range_raises()TestQMMMMolecule.test_qmmm_partition_overlap_raises()TestQMMMMolecule.test_qmmm_string_layer_specs_with_link_atoms()TestQMMMMolecule.test_write_gaussian_connectivity_and_frozen_mm_labels()
TestQMMMinMoleculeTestSDFFileTestStructureCoverageBoostTestStructureCoverageBoost.test_atomic_radii_lists()TestStructureCoverageBoost.test_bond_lengths_helper()TestStructureCoverageBoost.test_bond_orders_and_graphs()TestStructureCoverageBoost.test_chiral_aromatic_ring()TestStructureCoverageBoost.test_coordinate_block_basic()TestStructureCoverageBoost.test_coordinate_block_symbol_token_fallback()TestStructureCoverageBoost.test_coordinate_block_variants()TestStructureCoverageBoost.test_db_neither_chemsmart_nor_ase()TestStructureCoverageBoost.test_delete_atoms_paths()TestStructureCoverageBoost.test_determine_level_from_atom_index()TestStructureCoverageBoost.test_determine_level_on_molecule()TestStructureCoverageBoost.test_empty_filepath_returns_none()TestStructureCoverageBoost.test_energy_and_positions_setters()TestStructureCoverageBoost.test_from_ase_and_copy()TestStructureCoverageBoost.test_from_filepath_missing()TestStructureCoverageBoost.test_from_molecule_copy_dict()TestStructureCoverageBoost.test_from_pubchem_mocked()TestStructureCoverageBoost.test_from_rdkit()TestStructureCoverageBoost.test_geometry_helpers()TestStructureCoverageBoost.test_getitem_and_len()TestStructureCoverageBoost.test_graphs_and_bond_orders_water()TestStructureCoverageBoost.test_has_vibrations_props()TestStructureCoverageBoost.test_inchi_import_error()TestStructureCoverageBoost.test_inchikey_inchi_smiles()TestStructureCoverageBoost.test_init_rejects_empty_symbols()TestStructureCoverageBoost.test_init_validation_branches()TestStructureCoverageBoost.test_is_linear_three_atom_collinear()TestStructureCoverageBoost.test_mass_properties()TestStructureCoverageBoost.test_moments_and_rot_temps()TestStructureCoverageBoost.test_monoatomic_diatomic_linear()TestStructureCoverageBoost.test_monoatomic_moi_and_rot_temps()TestStructureCoverageBoost.test_num_atoms_setter()TestStructureCoverageBoost.test_pbc_property()TestStructureCoverageBoost.test_pbc_write_gaussian_coords()TestStructureCoverageBoost.test_pka_molecule()TestStructureCoverageBoost.test_pka_non_hydrogen_proton_index()TestStructureCoverageBoost.test_qmmm_high_none_raises()TestStructureCoverageBoost.test_qmmm_link_atoms_and_scale()TestStructureCoverageBoost.test_qmmm_overlap_raises()TestStructureCoverageBoost.test_qmmm_partition_levels()TestStructureCoverageBoost.test_qmmm_partition_validation()TestStructureCoverageBoost.test_qmmm_real_charge_sets_state()TestStructureCoverageBoost.test_rdkit_fingerprints()TestStructureCoverageBoost.test_rdkit_vectorized_bond_types()TestStructureCoverageBoost.test_read_chemsmart_db()TestStructureCoverageBoost.test_read_pdb_return_list()TestStructureCoverageBoost.test_read_sdf_and_other_list()TestStructureCoverageBoost.test_read_unsupported_out_and_gaussian_inp_error()TestStructureCoverageBoost.test_repr_str_and_chemical_symbols_none()TestStructureCoverageBoost.test_return_list_from_filepath()TestStructureCoverageBoost.test_to_pymatgen_and_x_data()TestStructureCoverageBoost.test_to_x_data_no_positions_raises()TestStructureCoverageBoost.test_vdw_volume_and_pbc()TestStructureCoverageBoost.test_vectorized_bond_add()TestStructureCoverageBoost.test_vibrationally_displaced()TestStructureCoverageBoost.test_vibrationally_displaced_negative_index()TestStructureCoverageBoost.test_volumes()TestStructureCoverageBoost.test_write_coordinates_programs()TestStructureCoverageBoost.test_write_cosmorsxyz_via_write()TestStructureCoverageBoost.test_write_extxyz_bad_forces_ignored()TestStructureCoverageBoost.test_write_extxyz_forces_shape_mismatch()TestStructureCoverageBoost.test_write_extxyz_with_forces_and_energy()TestStructureCoverageBoost.test_write_gaussian_with_frozen()TestStructureCoverageBoost.test_write_pdb_rejects_kwargs()TestStructureCoverageBoost.test_write_via_openbabel_fallback()
TestStructuresTestStructures.test_angle_is_undefined_for_coincident_points()TestStructures.test_dihedral_for_file_backed_molecule_matches_rdkit()TestStructures.test_dihedral_is_independent_of_central_bond_length()TestStructures.test_dihedral_is_undefined_for_collinear_points()TestStructures.test_documented_geometry_examples()TestStructures.test_geometry_methods_reject_invalid_indices()TestStructures.test_geometry_methods_reject_non_integer_indices()TestStructures.test_get_angle_known_values()TestStructures.test_get_angle_symmetry_and_position_method()TestStructures.test_get_dihedral_known_values()TestStructures.test_get_dihedral_matches_position_method()TestStructures.test_get_distance_known_value_and_symmetry()TestStructures.test_molecular_geometry()TestStructures.test_rdkit_hash_can_ignore_hydrogens()TestStructures.test_rdkit_xyz_conversion_failure()TestStructures.test_read_crest_dynamics_trj_as_xyz()TestStructures.test_read_crestopt_log_as_xyz()TestStructures.test_read_molecule_energy_from_xyz_file()TestStructures.test_read_molecule_from_multiple_molecules_xyz_file()TestStructures.test_read_molecule_from_single_molecule_xyz_file()TestStructures.test_to_rdkit_connectivity_graph()TestStructures.test_to_rdkit_rejects_bondless_rdkit_method()TestStructures.test_to_rdkit_rejects_invalid_bond_method()
TestStructuresFromGaussianInputTestStructuresFromGaussianInput.test_read_molecule_from_gaussian_frozen_opt()TestStructuresFromGaussianInput.test_read_molecule_from_gaussian_modred()TestStructuresFromGaussianInput.test_read_molecule_from_gaussian_opt_input()TestStructuresFromGaussianInput.test_read_molecule_from_gaussian_pbc()TestStructuresFromGaussianInput.test_read_molecule_from_gaussian_scan()TestStructuresFromGaussianInput.test_read_molecule_from_modred_gen()TestStructuresFromGaussianInput.test_read_molecule_from_modred_genecp()TestStructuresFromGaussianInput.test_read_molecule_from_modred_genecp_custom_solvent()TestStructuresFromGaussianInput.test_read_molecule_from_opt_genecp()
TestpKaCDXFileTestpKaCDXFile.test_detect_proton_in_fragment_explicit_h()TestpKaCDXFile.test_detect_proton_in_fragment_uniform_color_raises()TestpKaCDXFile.test_fragment_colors_match_flat_colors()TestpKaCDXFile.test_functional_group_proton_user_color_phenol()TestpKaCDXFile.test_get_colored_proton_index_auto_detect()TestpKaCDXFile.test_get_colored_proton_index_invalid_color_code_raises()TestpKaCDXFile.test_get_colored_proton_index_multiple_atoms_same_color_raises()TestpKaCDXFile.test_get_colored_proton_index_no_hydrogen_raises()TestpKaCDXFile.test_get_colored_proton_index_no_unique_color_raises()TestpKaCDXFile.test_get_colored_proton_index_user_specified()TestpKaCDXFile.test_get_pka_molecule_explicit_proton_index()TestpKaCDXFile.test_get_pka_molecules_auto_implicit_h()TestpKaCDXFile.test_get_pka_molecules_auto_nested_fragment_groups()TestpKaCDXFile.test_get_pka_molecules_auto_single_fragment()TestpKaCDXFile.test_get_pka_molecules_auto_two_fragments()TestpKaCDXFile.test_get_pka_molecules_delegates_to_auto()TestpKaCDXFile.test_get_pka_molecules_with_explicit_proton_index()TestpKaCDXFile.test_implicit_proton_removal_phenol()TestpKaCDXFile.test_parse_cdxml_atom_colors()TestpKaCDXFile.test_parse_cdxml_atom_colors_benzene_no_color()TestpKaCDXFile.test_parse_cdxml_fragment_colors_single_fragment()TestpKaCDXFile.test_parse_cdxml_fragment_colors_two_fragments()TestpKaCDXFile.test_proton_removal_phenol()
- tests.test_utils module
TestDeduplicateStringKeywordsTestDeduplicateStringKeywords.test_args_and_bare_keyword_keeps_args_form()TestDeduplicateStringKeywords.test_bare_and_args_keyword_keeps_args_form()TestDeduplicateStringKeywords.test_bare_keyword_duplicate_keeps_first()TestDeduplicateStringKeywords.test_case_insensitive_matching()TestDeduplicateStringKeywords.test_docstring_example()TestDeduplicateStringKeywords.test_empty_keywords_list_returns_unchanged()TestDeduplicateStringKeywords.test_empty_keywords_returns_unchanged()TestDeduplicateStringKeywords.test_empty_route_string_returns_unchanged()TestDeduplicateStringKeywords.test_keyword_as_list()TestDeduplicateStringKeywords.test_keyword_as_string()TestDeduplicateStringKeywords.test_keyword_as_tuple()TestDeduplicateStringKeywords.test_keyword_not_present_returns_unchanged()TestDeduplicateStringKeywords.test_keyword_with_longer_args_preferred_over_shorter()TestDeduplicateStringKeywords.test_mixed_case_keyword_argument()TestDeduplicateStringKeywords.test_multiple_keywords_deduplicated()TestDeduplicateStringKeywords.test_no_duplicates_returns_unchanged()TestDeduplicateStringKeywords.test_none_route_string_returns_unchanged()TestDeduplicateStringKeywords.test_three_bare_duplicates_keeps_first()TestDeduplicateStringKeywords.test_unrelated_tokens_preserved()
TestGetListFromStringRangeTestIOUtilitiesTestIOUtilities.test_basic_conversion()TestIOUtilities.test_clean_duplicate_structure()TestIOUtilities.test_clean_label()TestIOUtilities.test_conversion_strips_whitespace()TestIOUtilities.test_create_molecule_list()TestIOUtilities.test_header_like_then_data_like()TestIOUtilities.test_line_of_all_integers()TestIOUtilities.test_line_of_integer_followed_by_floats()TestIOUtilities.test_raises_value_error_on_empty_or_invalid_input()TestIOUtilities.test_reject_plain_ints_as_floats()TestIOUtilities.test_trailing_and_leading_spaces()TestIOUtilities.test_trailing_comma_is_ignored()
TestNaturallySortedTestNaturallySorted.test_alphanumeric()TestNaturallySorted.test_empty_list()TestNaturallySorted.test_file_names()TestNaturallySorted.test_large_numbers()TestNaturallySorted.test_mixed_case()TestNaturallySorted.test_mixed_types()TestNaturallySorted.test_no_numbers()TestNaturallySorted.test_numeric_order()TestNaturallySorted.test_single_item()TestNaturallySorted.test_special_characters()
TestPKaTableParsingTestPKaTableParsing.test_discover_pka_reference_companion_outputs()TestPKaTableParsing.test_discover_pka_target_companion_outputs_matches_batch_suffixes()TestPKaTableParsing.test_echo_pka_output_table_results_writes_same_table_to_file()TestPKaTableParsing.test_export_pka_results_table_direct_scheme()TestPKaTableParsing.test_export_pka_results_table_matches_stdout_format()TestPKaTableParsing.test_parse_and_resolve_multi_row_table()TestPKaTableParsing.test_parse_pka_output_table_alias_columns()TestPKaTableParsing.test_parse_pka_output_table_csv()TestPKaTableParsing.test_parse_pka_output_table_empty()TestPKaTableParsing.test_parse_pka_output_table_empty_cells_become_none()TestPKaTableParsing.test_parse_pka_output_table_file_not_found()TestPKaTableParsing.test_parse_pka_table_blank_proton_index_for_cdxml()TestPKaTableParsing.test_parse_pka_table_blank_proton_index_for_xyz_raises()TestPKaTableParsing.test_parse_pka_table_csv()TestPKaTableParsing.test_parse_pka_table_empty_raises()TestPKaTableParsing.test_parse_pka_table_file_not_found()TestPKaTableParsing.test_parse_pka_table_invalid_column_count()TestPKaTableParsing.test_parse_pka_table_invalid_integer()TestPKaTableParsing.test_parse_pka_table_skip_comments_and_empty_lines()TestPKaTableParsing.test_parse_pka_table_txt()TestPKaTableParsing.test_pka_output_table_entry_repr()TestPKaTableParsing.test_pka_output_table_entry_resolve_filenames_gaussian_log()TestPKaTableParsing.test_pka_output_table_entry_resolve_filenames_orca_default_extension()TestPKaTableParsing.test_pka_output_table_entry_resolve_filenames_orca_out()TestPKaTableParsing.test_pka_output_table_entry_to_dict()TestPKaTableParsing.test_pka_output_table_entry_validate_missing_basename()TestPKaTableParsing.test_pka_output_table_entry_validate_missing_file()TestPKaTableParsing.test_pka_output_table_entry_validate_valid()TestPKaTableParsing.test_pka_output_table_prepare_autodetects_files_and_inherits_references()TestPKaTableParsing.test_pka_output_table_run_pka()TestPKaTableParsing.test_pka_output_table_run_pka_direct()TestPKaTableParsing.test_pka_table_entry_alias_resolution()TestPKaTableParsing.test_pka_table_entry_dict_and_kwargs_helpers()TestPKaTableParsing.test_pka_table_entry_from_headers_and_row_dynamic()TestPKaTableParsing.test_pka_table_entry_repr()TestPKaTableParsing.test_pka_table_entry_validate_invalid_multiplicity()TestPKaTableParsing.test_pka_table_entry_validate_invalid_proton_index()TestPKaTableParsing.test_pka_table_entry_validate_missing_file()TestPKaTableParsing.test_resolve_pka_output_references_carry_forward()TestPKaTableParsing.test_resolve_pka_output_references_first_row_blank_raises()TestPKaTableParsing.test_resolve_pka_output_references_partial_carry_forward()TestPKaTableParsing.test_validate_pka_table_entries()
TestParseIndexSpecificationTestParseIndexSpecification.test_ase_style_single_indices()TestParseIndexSpecification.test_ase_style_slices()TestParseIndexSpecification.test_boundary_checking_enabled()TestParseIndexSpecification.test_duplicate_detection_enabled()TestParseIndexSpecification.test_free_format_comma_separated()TestParseIndexSpecification.test_free_format_hyphen_ranges()TestParseIndexSpecification.test_free_format_mixed()TestParseIndexSpecification.test_free_format_with_negative_indices()TestParseIndexSpecification.test_invalid_inputs()TestParseIndexSpecification.test_parse_index_boundary_detection_disabled()TestParseIndexSpecification.test_parse_index_boundary_detection_enabled()TestParseIndexSpecification.test_parse_index_duplicate_detection_disabled()TestParseIndexSpecification.test_parse_index_duplicate_detection_enabled()TestParseIndexSpecification.test_with_actual_lists()
TestReturnObjectsAndIndicesFromStringIndexTestReturnObjectsAndIndicesFromStringIndex.test_empty_list_raises_index_error()TestReturnObjectsAndIndicesFromStringIndex.test_index_zero_raises_value_error()TestReturnObjectsAndIndicesFromStringIndex.test_out_of_range_raises_index_error()TestReturnObjectsAndIndicesFromStringIndex.test_range_with_brackets()TestReturnObjectsAndIndicesFromStringIndex.test_single_index_last()TestReturnObjectsAndIndicesFromStringIndex.test_single_index_middle()TestReturnObjectsAndIndicesFromStringIndex.test_single_index_string()TestReturnObjectsAndIndicesFromStringIndex.test_single_negative_index()TestReturnObjectsAndIndicesFromStringIndex.test_slice_all()TestReturnObjectsAndIndicesFromStringIndex.test_slice_from_beginning()TestReturnObjectsAndIndicesFromStringIndex.test_slice_from_start()TestReturnObjectsAndIndicesFromStringIndex.test_slice_range()TestReturnObjectsAndIndicesFromStringIndex.test_slice_to_end()TestReturnObjectsAndIndicesFromStringIndex.test_slice_with_step()TestReturnObjectsAndIndicesFromStringIndex.test_specified_indices_5_to_8()TestReturnObjectsAndIndicesFromStringIndex.test_user_defined_range()TestReturnObjectsAndIndicesFromStringIndex.test_user_defined_range_complex()TestReturnObjectsAndIndicesFromStringIndex.test_user_defined_range_with_hyphen()TestReturnObjectsAndIndicesFromStringIndex.test_with_integer_objects()TestReturnObjectsAndIndicesFromStringIndex.test_with_mixed_objects()
TestRunCommandTestString2Index1BasedTestUtilsTestUtils.test_cmp_with_ignore_list()TestUtils.test_cmp_with_ignore_string()TestUtils.test_content_blocking()TestUtils.test_get_indices_from_string()TestUtils.test_get_list_from_string_range()TestUtils.test_get_range_from_list()TestUtils.test_is_float()TestUtils.test_iterative_compare_list_of_dicts()TestUtils.test_iterative_compare_list_of_elements()TestUtils.test_iterative_compare_list_of_lists()TestUtils.test_iterative_compare_list_of_string()TestUtils.test_iterative_compare_list_of_tuples()
- Module contents