CHEMSMART Modules
- chemsmart package
- tests package
- Submodules
- tests.conftest module
- 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_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
- tests.test_YAMLIO module
- tests.test_converter module
- tests.test_groupers module
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()
Test_BasicRMSD_grouper_and_basic_functionalityTest_BasicRMSD_grouper_and_basic_functionality.NUM_PROCSTest_BasicRMSD_grouper_and_basic_functionality.pytestmarkTest_BasicRMSD_grouper_and_basic_functionality.test_num_groups_parameter()Test_BasicRMSD_grouper_and_basic_functionality.test_pick_the_lowestenergy_conformers()Test_BasicRMSD_grouper_and_basic_functionality.test_rmsd_grouper()Test_BasicRMSD_grouper_and_basic_functionality.test_rmsd_grouper_for_crest_conformers()Test_BasicRMSD_grouper_and_basic_functionality.test_rmsd_grouper_for_crest_conformers_ignore_Hs()Test_BasicRMSD_grouper_and_basic_functionality.test_rmsd_grouper_for_rotated_molecules()
Test_EnergyGrouperTest_EnergyGrouper.NUM_PROCSTest_EnergyGrouper.pytestmarkTest_EnergyGrouper.test_energy_extraction_from_ts_log_files()Test_EnergyGrouper.test_energy_extraction_from_xyz_file()Test_EnergyGrouper.test_energy_grouper_for_crest_conformers()Test_EnergyGrouper.test_energy_grouper_for_log_conformers()Test_EnergyGrouper.test_energy_grouper_raises_error_for_missing_energy()Test_EnergyGrouper.test_gibbs_energy_extraction_function()
Test_HungarianRMSD_grouperTest_IRMSD_grouperTest_PymolRMSD_grouperTest_PymolRMSD_grouper.NUM_PROCSTest_PymolRMSD_grouper.pytestmarkTest_PymolRMSD_grouper.setup_class()Test_PymolRMSD_grouper.teardown_class()Test_PymolRMSD_grouper.teardown_method()Test_PymolRMSD_grouper.test_ignore_hydrogen()Test_PymolRMSD_grouper.test_pymol_grouper_rejects_multiproc()Test_PymolRMSD_grouper.test_pymolrmsd_grouper_for_crest_molecules()Test_PymolRMSD_grouper.test_pymolrmsd_grouper_for_rotated_molecules()
Test_SpyRMSD_grouperTest_Tanimoto_similarity_grouperTest_TorsionFingerprint_grouperTest_TorsionFingerprint_grouper.NUM_PROCSTest_TorsionFingerprint_grouper.pytestmarkTest_TorsionFingerprint_grouper.test_count_groups_matches_complete_linkage_iteration_order()Test_TorsionFingerprint_grouper.test_torsionfingerprint_grouper_for_crest_molecules()Test_TorsionFingerprint_grouper.test_torsionfingerprint_grouper_for_rotated_molecules()Test_TorsionFingerprint_grouper.test_use_maxdev_parameter()Test_TorsionFingerprint_grouper.test_use_weights_parameter()
Test_conformer_ids_functionalityTest_edge_casesTest_edge_cases.pytestmarkTest_edge_cases.test_different_formulas_always_separate()Test_edge_cases.test_num_groups_equals_num_molecules()Test_edge_cases.test_num_groups_exceeds_num_molecules()Test_edge_cases.test_rmsd_infinity_for_different_molecules()Test_edge_cases.test_two_molecules_grouping()Test_edge_cases.test_very_high_threshold()Test_edge_cases.test_very_low_threshold()
Test_energy_extraction_functionTest_grouper_complete_linkageTest_grouper_utility_functionsTest_label_and_append_labelTest_label_and_append_label.NUM_PROCSTest_label_and_append_label.pytestmarkTest_label_and_append_label.test_different_labels_create_different_outputs()Test_label_and_append_label.test_get_label_function()Test_label_and_append_label.test_label_in_group_xyz_files()Test_label_and_append_label.test_label_in_output_directory()Test_label_and_append_label.test_label_with_num_groups()
Test_other_groupersTest_other_groupers.NUM_PROCSTest_other_groupers.pytestmarkTest_other_groupers.test_base_record_template_method()Test_other_groupers.test_connectivity_grouper()Test_other_groupers.test_connectivity_grouper_for_crest_conformers()Test_other_groupers.test_formula_grouper()Test_other_groupers.test_rdkit_isomorphism_grouper()Test_other_groupers.test_record_writes_formula_outputs_with_headers()Test_other_groupers.test_record_writes_rmsd_matrix_with_headers()
Test_output_file_generationTestfactory
- 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_molecular_geometry()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()
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