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()capture_log()chemdraw_directory()chemdraw_expected_directory()chemsmart_generated_xyz_file()chemsmart_templates_config()chiral_molecule()co2_molecule()complex_molecule_cdxml_file()conformers_from_rdkit()constrained_atoms()constrained_pbc_db_file()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()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_he_opt_outfile()gaussian_hirshfeld_outfile()gaussian_inputs_genecp_directory()gaussian_inputs_test_directory()gaussian_jobrunner_no_scratch()gaussian_jobrunner_scratch()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_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_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_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()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()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_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_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()pymol_align_jobrunner()pymol_hybrid_visualization_jobrunner()pymol_ircmovie_jobrunner()pymol_mo_jobrunner()pymol_movie_jobrunner()pymol_visualization_jobrunner()qmmm_written_xyz_file()qmmm_written_xyz_only_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()test_data_directory()tests_logger()tetrahydrofuran_molecule()text_directory()ts_conformers_log_directory()two_rotated_molecules_xyz_file()txt_path()utils_test_directory()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()xtb_optimized_xyz_file()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_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_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_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()
TestGaussianCubeFileTestGaussianPBCOutputFileTestGaussianWBIOutputTestRouteStringTestRouteString.test_read_additional_route_parameters()TestRouteString.test_read_route_semiempirical()TestRouteString.test_read_route_string_nonstandard()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_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()
TestGaussianRoute
- tests.test_GaussianWriter module
TestGaussianInputWriterTestGaussianInputWriter.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_input_from_logfile()TestGaussianInputWriter.test_write_qmmm_job()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()
TestORCAQMMMTestORCAQMMMJobSettingsTestORCARoute
- 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_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()
skip_if_no_pymol()
- tests.test_YAMLIO module
- tests.test_converter module
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()
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_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()
- 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_generationTestfactorytemp_working_dir()
- tests.test_organizer module
- tests.test_server module
- 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_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()
TestCoordinateBlockAdvancedTestFileHandlingAdvancedTestGraphFeaturesTestInChIKeyTestInChIKey.EXPECTED_LARGE_C2TestInChIKey.EXPECTED_LARGE_C3TestInChIKey.EXPECTED_NORMALTestInChIKey.EXPECTED_R_ENANTIOMERTestInChIKey.EXPECTED_S_ENANTIOMERTestInChIKey.test_enantiomers_share_connectivity_layer()TestInChIKey.test_large_molecule_c2_inchikey()TestInChIKey.test_large_molecule_c3_inchikey()TestInChIKey.test_large_molecules_differ()TestInChIKey.test_r_enantiomer_inchikey()TestInChIKey.test_regression_inchikey()TestInChIKey.test_s_enantiomer_inchikey()
TestMoleculeAdvancedTestMoleculeAdvanced.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()
TestQMMMinMoleculeTestSDFFileTestStructuresTestStructuresFromGaussianInputTestStructuresFromGaussianInput.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()
- 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()
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