from __future__ import absolute_import, division, print_function from libtbx import test_utils import libtbx.load_env from libtbx import easy_run import libtbx.load_env general_tests = [ "$D/suitename/unit-test/FullTest.py", # "$D/regression/tst_sampled_model_density.py", # pair interaction "$D/pair_interaction/tst_00.py", "$D/pair_interaction/tst_01.py", "$D/pair_interaction/tst_02.py", "$D/pair_interaction/tst_03.py", "$D/pair_interaction/tst_04.py", "$D/pair_interaction/tst_05.py", # ions SVM "$D/ions/svm/tst_classifier.py", "$D/ions/tst_pick_ca_svm.py", "$D/ions/tst_pickle.py", # ion picking "$D/ions/tst_parameters.py", "$D/ions/tst_pick_ca.py", "$D/ions/tst_pick_mg.py", "$D/ions/tst_pick_approx_zn.py", "$D/ions/tst_validate_ca.py", "$D/ions/tst_validate_mg.py", "$D/ions/tst_symmetry_axis.py", "$D/ions/tst_utils.py", # TLS "$D/regression/tls/tst_tls.py", "$D/regression/tls/tst_tls_analysis.py", "$D/regression/tls/tst_tls_utils.py", "$D/regression/tls/tst_tls_optimise_amplitudes.py", "$D/regression/tls/tst_get_t_scheme.py", ["$D/regression/tls/tst_tls_refinement_fft.py", "--comprehensive", "--random_seed=2679941"], "$D/regression/tls/tst_u_tls_vs_u_ens_00.py", "$D/regression/tls/tst_u_tls_vs_u_ens_01.py", "$D/regression/tls/tst_u_tls_vs_u_ens_02.py", "$D/regression/tls/tst_u_tls_vs_u_ens_03.py", "$D/regression/tls/tst_u_tls_vs_u_ens_04.py", "$D/regression/tls/tst_tls_as_xyz.py", "$D/regression/tls/tst_formula_t_S_10_vs_11_2igd.py", "$D/regression/tls/tst_formula_t_S_10_vs_11_4muy.py", # "$D/regression/tst_angle.py", "$D/rotamer/tst_rotamer_eval.py", "$D/rotamer/tst_geostd_vs_sidechain_angles_props.py", "$D/monomer_library/tst_idealized_aa.py", "$D/regression/tst_ml_estimate.py", "$D/density_modification/tst_density_modification.py", "$D/geometry_restraints/tst_ramachandran.py", "$D/geometry_restraints/tst_manager.py", "$D/geometry_restraints/external.py", "$D/regression/tst_map_type_parser.py", "$D/rsr/tst.py", "$D/polygon/tst.py", "$D/polygon/tst_gui.py", "$D/polygon/tst_polygon_data.py", "$D/chemical_components/tst.py", "$D/regression/tst_add_h_to_water.py", "$D/rotamer/rotamer_eval.py", "$D/wwpdb/tst_standard_geometry_cif.py", "$D/regression/tst_pdbtools.py", "$D/real_space/tst.py", "$D/ias/tst_ias.py", "$D/refinement/tst_fit_rotamers.py", "$D/regression/tst_process_predicted_model.py", "$D/regression/tst_domains_from_pae.py", ["$D/refinement/tst_anomalous_scatterer_groups.py", "P3"], "$D/refinement/tst_rigid_body.py", "$D/refinement/tst_rigid_body_groups_from_pdb_chains.py", "$D/refinement/tst_refinement_flags.py", "$D/geometry_restraints/torsion_restraints/tst_reference_model.py", "$D/geometry_restraints/torsion_restraints/tst_reference_model_ligands.py", # model tests, some more elsewhere in this file "$D/regression/model/tst_model_mtrix.py", "$D/regression/model/tst_model_ncs.py", "$D/regression/model/tst_model_2.py", "$D/regression/model/tst_model_biomt_mtrix.py", "$D/regression/model/tst_model_biomt_mtrix_2.py", "$D/regression/model/tst_model_neutralize_scatterers.py", "$D/regression/model/tst_model_set_hydrogen_bond_length.py", "$D/regression/model/tst_model_cart_ref_restraints.py", "$D/regression/model/tst_model_tors_ref_restraints.py", "$D/regression/model/tst_model_remove_alternative_conformations.py", "$D/regression/model/tst_model_get_vdw_radii.py", "$D/regression/model/tst_model_dedeuterate.py", "$D/regression/model/tst_model_utils_merge_models.py", # "$D/regression/tst_fmodel.py", "$D/regression/tst_utils.py", "$D/regression/tst_alignment.py", ["$D/regression/tst_fmodel_fd.py", "P31"], "$D/maps/tst_composite_omit_map.py", "$D/maps/tst_composite_omit_map_2.py", "$D/maps/tst_composite_omit_map_3.py", "$D/maps/tst_correlation.py", "$D/maps/tst_map_model_cc_and_vals_per_atom_xtal.py", "$D/regression/ncs/tst_ncs_utils.py", "$D/regression/ncs/tst_ncs_restraints_group_list.py", "$D/regression/ncs/tst_ncs_search.py", "$D/regression/ncs/tst_ncs_search_flips.py", "$D/regression/ncs/tst_restraints.py", "$D/regression/tst_geometry_minimization.py", "$D/regression/tst_special_term_at_end.py", ["$D/ncs/ncs.py", "exercise"], "$D/regression/tst_adp_restraints.py", "$D/regression/tst_metal_link_1.py", # Xtriage "$D/scaling/tst_scaling.py", "$D/scaling/tst_outlier.py", "$D/scaling/tst_absences.py", "$D/scaling/tst_xtriage.py", "$D/scaling/tst_xtriage_twin_analyses.py", "$D/scaling/matthews.py", "$D/scaling/absence_likelihood.py", ["$D/scaling/thorough_outlier_test.py", "P21"], "$D/twinning/probabalistic_detwinning.py", #"$D/scaling/tst_xtriage_massage_data.py", # monomer library "$D/monomer_library/tst_rna_sugar_pucker_analysis.py", "$D/monomer_library/tst_cif_types.py", "$D/monomer_library/tst_motif.py", "$D/monomer_library/tst_cif_triage.py", "$D/monomer_library/tst_rotamer_utils.py", "$D/monomer_library/tst_selection.py", "$D/monomer_library/tst_tyr_from_gly_and_bnz.py", "$D/monomer_library/tst_pdb_interpretation.py", "$D/monomer_library/tst_rna_dna_interpretation.py", "$D/monomer_library/tst_protein_interpretation.py", "$D/monomer_library/tst_pdb_interpretation_ncs_processing.py", "$D/monomer_library/tst_geo_reduce_for_tardy.py", "$D/monomer_library/tst_chg.py", "$D/monomer_library/tst_neutron_distance.py", "$D/monomer_library/tst_carbo_linking.py", "$D/monomer_library/tst_glyco_hand.py", "$D/monomer_library/tst_glyco_coordination.py", "$D/monomer_library/tst_paral_geo.py", # "$D/regression/tst_altloc_remediate.py", "$D/hydrogens/build_hydrogens.py", "$D/hydrogens/tst.py", "$D/hydrogens/tst_add_hydrogen.py", "$D/hydrogens/tst_add_hydrogen_2.py", "$D/hydrogens/tst_validate_H.py", "$D/hydrogens/tst_connectivity.py", "$D/hydrogens/tst_riding_coefficients.py", "$D/hydrogens/tst_riding_manager.py", "$D/hydrogens/tst_parameterization_1.py", "$D/hydrogens/tst_parameterization_2.py", "$D/hydrogens/tst_parameterization_3.py", "$D/hydrogens/tst_parameterization_4.py", "$D/hydrogens/tst_parameterization_5.py", "$D/hydrogens/tst_parameterization_6.py", "$D/hydrogens/tst_parameterization_7.py", "$D/hydrogens/tst_parameterization_8.py", "$D/hydrogens/tst_parameterization_9.py", "$D/hydrogens/tst_riding_fd_1.py", "$D/hydrogens/tst_riding_fd_2.py", "$D/hydrogens/tst_riding_fd_3.py", "$D/hydrogens/tst_riding_fd_4.py", "$D/hydrogens/tst_riding_fd_5.py", "$D/hydrogens/tst_riding_minimize.py", "$D/max_lik/tst_maxlik.py", "$D/masks/tst_masks.py", "$D/masks/tst_asu_mask.py", "$D/max_lik/tst_max_lik.py", "$D/dynamics/tst_cartesian_dynamics.py", "$D/dynamics/tst_sa.py", # "$D/examples/f_model_manager.py", # Bulk solvent "$D/bulk_solvent/tst_bulk_solvent_and_scaling.py", "$D/bulk_solvent/tst_fit_kexpb_to_ktotal.py", "$D/bulk_solvent/tst_scaler.py", "$D/bulk_solvent/tst_flat_nonuniform.py", "$D/bulk_solvent/tst_aniso_scaler.py", "$D/bulk_solvent/tst_kb_sol_u_star_fd.py", "$D/bulk_solvent/tst_mosaic.py", # "$D/invariant_domain.py", # restraints "$D/regression/tst_psi_phi_extraction.py", "$D/secondary_structure/tst.py", "$D/secondary_structure/tst_insertion_codes.py", "$D/secondary_structure/tst_segid.py", "$D/geometry_restraints/tst_reference_coordinate.py", "$D/geometry_restraints/tst_reference_coordinate2.py", "$D/geometry_restraints/tst_c_beta_restraints.py", "$D/geometry_restraints/torsion_restraints/tst_torsion_ncs.py", "$D/conformation_dependent_library/tst_cdl.py", "$D/conformation_dependent_library/tst_cdl_esd.py", "$D/conformation_dependent_library/tst_rdl.py", "$D/conformation_dependent_library/tst_hpdl.py", "$D/conformation_dependent_library/tst_cis_c_n_ca.py", "$D/conformation_dependent_library/cdl_svl_database.py", "$D/conformation_dependent_library/tst_pH_mechanism.py", "$D/conformation_dependent_library/tst_mcl_01.py", "$D/conformation_dependent_library/tst_mcl_02.py", "$D/conformation_dependent_library/tst_mcl_03.py", "$D/regression/tst_find_ss_structure.py", "$D/regression/tst_fix_rotamer_outliers.py", "$D/regression/tst_chain_comparison.py", "$D/regression/tst_regularize_from_pdb.py", "$D/regression/tst_find_ncs.py", "$D/regression/tst_minimize_chain.py", "$D/regression/tst_sequence_validation.py", "$D/regression/tst_prune_model.py", "$D/regression/tst_real_space_correlation.py", "$D/regression/tst_examples.py", "$D/regression/tst_sort_hetatms.py", "$D/regression/tst_schrodinger_interface.py", # real-space tools "$D/refinement/real_space/tst_aa_residue_axes_and_clusters.py", "$D/refinement/real_space/tst_fit_residue_0.py", "$D/refinement/real_space/tst_fit_residue_0H.py", "$D/refinement/real_space/tst_fit_residue_1.py", "$D/refinement/real_space/tst_fit_residue_1H.py", "$D/refinement/real_space/tst_fit_residue_2.py", "$D/refinement/real_space/tst_fit_residue_3.py", "$D/refinement/real_space/tst_fit_residue_4.py", "$D/refinement/real_space/tst_fit_residue_5.py", "$D/refinement/real_space/tst_fit_residue_6.py", "$D/refinement/real_space/tst_fit_residue_7.py", "$D/refinement/real_space/tst_fit_residues_1.py", "$D/refinement/real_space/tst_fit_residues_1H.py", "$D/refinement/real_space/tst_fit_residues_2.py", "$D/refinement/real_space/tst_fit_residues_3.py", "$D/refinement/real_space/tst_fit_residues_4.py", "$D/refinement/real_space/tst_fit_residues_5.py", "$D/refinement/real_space/tst_fit_residues_6.py", "$D/refinement/real_space/tst_fit_residues_selection.py", "$D/refinement/real_space/tst_fit_water.py", "$D/refinement/real_space/tst_flipbase.py", "$D/refinement/real_space/tst_individual_sites_1.py", "$D/refinement/real_space/tst_individual_sites_2.py", "$D/refinement/real_space/tst_individual_sites_3.py", "$D/refinement/real_space/tst_monitor.py", "$D/refinement/real_space/tst_rigid_body.py", "$D/refinement/real_space/tst_weight.py", # "$D/idealized_aa_residues/tst.py", # "$D/regression/tst_dssp.py", "$D/regression/tst_validation_summary.py", "$D/regression/tst_maps_misc.py", "$D/regression/tst_cablam.py", "$D/regression/tst_anomalous_substructure.py", "$D/regression/tst_map_coeffs_simple.py", # "$D/regression/tst_fmodel_no_cryst1.py", "$D/regression/tst_fmodel_misc.py", "$D/regression/tst_isomorphous_difference_misc.py", "$D/regression/tst_dynamics_cli.py", "$D/ligands/tst_xtal_screens.py", "$D/ligands/tst_ready_set_utils.py", "$D/regression/tst_mtz2map.py", # ringer "$D/regression/tst_ringer.py", "$D/ringer/tst_emringer.py", "$D/ringer/tst_em_rscc.py", # validation/molprobity "$D/regression/tst_probe.py", "$D/regression/tst_reduce.py", "$D/validation/regression/tst_molprobity_arguments.py", "$D/validation/regression/tst_waters.py", "$D/validation/regression/tst_keep_hydrogens.py", "$D/validation/regression/tst_mp_geo.py", "$D/validation/regression/tst_rotalyze.py", "$D/validation/regression/tst_ramalyze.py", "$D/validation/regression/tst_ramalyze2.py", "$D/validation/regression/tst_clashscore.py", "$D/validation/regression/tst_clashscore_2.py", "$D/validation/regression/tst_restraints.py", "$D/validation/regression/tst_omegalyze.py", "$D/validation/regression/tst_rna_validate.py", "$D/validation/regression/tst_model_properties.py", "$D/validation/regression/tst_molprobity_2.py", "$D/validation/regression/tst_molprobity_3.py", "$D/validation/regression/tst_hydrogen_addition_clashscore.py", "$D/validation/regression/tst_symmetry_SS.py", "$D/validation/regression/tst_do_flips_clashscore.py", "$D/validation/regression/tst_find_region_max_value.py", # "$D/refinement/tst_select_best_starting_model.py", "$D/regression/tst_refine_anomalous_substructure.py", "$D/regression/tst_helix_sheet_recs_as_pdb_files.py", "$D/regression/tst_command_line_input.py", "$D/regression/tst_cif_as_mtz_wavelengths.py", "$D/building/tst_extend_sidechains.py", "$D/building/tst_extend_sidechains_2.py", # alt confs "$D/disorder/tst.py", "$D/disorder/tst_backbone.py", "$D/disorder/tst_analyze_model.py", # "$D/refinement/tst_group.py", "$D/refinement/tst_group_2.py", "$D/secondary_structure/build/tst_1.py", "$D/secondary_structure/build/tst_2.py", "$D/secondary_structure/build/tst_3.py", "$D/secondary_structure/build/tst_io.py", "$D/secondary_structure/build/tst_ss_id_ncs.py", "$D/regression/tst_loop_closure.py", "$D/regression/model_idealization/tst_nomap_01.py", "$D/regression/model_idealization/tst_nomap_02.py", "$D/regression/model_idealization/tst_nomap_03.py", "$D/regression/model_idealization/tst_nomap_04.py", "$D/regression/model_idealization/tst_withmap_01.py", "$D/regression/model_idealization/tst_withmap_02.py", "$D/regression/model_idealization/tst_withmap_03.py", "$D/regression/model_idealization/tst_withmap_04.py", "$D/regression/model_idealization/tst_withmap_05.py", "$D/regression/model_idealization/tst_withmap_06.py", "$D/regression/model_idealization/tst_ligands.py", "$D/regression/model_idealization/tst_with_mtz.py", "$D/utils/tst_switch_rotamers.py", "$D/refinement/tst_occupancy_selections.py", "$D/regression/ncs/tst_minimization_ncs_constraints.py", "$D/regression/ncs/tst_minimization_ncs_constraints2.py", "$D/regression/ncs/tst_minimization_ncs_constraints3.py", "$D/regression/ncs/tst_minimization_ncs_constraints_real_space.py", "$D/monomer_library/tst_correct_hydrogens.py", "$D/monomer_library/tst_deuterium_terminii.py", # automatic linking "$D/monomer_library/tst_superpose_ideal.py", "$D/monomer_library/tst_iron_sulfur_clusters.py", # "$D/scaling/tst_plan_sad_experiment.py", # "$D/regression/tst_models_to_from_chains.py", # tNCS "$D/regression/tncs/tst_pair.py", "$D/regression/tncs/tst_epsfac_and_radius.py", "$D/regression/tncs/tst_fd.py", "$D/regression/tncs/tst_moments.py", # "$D/regression/tst_rank_scale_map.py", "$D/regression/tst_polder.py", "$D/regression/tst_polder_1.py", "$D/regression/tst_polder_2.py", "$D/regression/tst_polder_3.py", "$D/regression/tst_polder_box.py", "$D/regression/tst_polder_ccs.py", "$D/regression/tst_map_model_cc.py", "$D/regression/tst_model_map.py", # "$D/regression/tst_validate_ligands.py", # "$D/regression/tst_cis_trans_peptide_link.py", "$D/regression/tst_apply_cif_restraints.py", "$D/regression/tst_multi_residue_class.py", "$D/regression/tst_superpose.py", "$D/monomer_library/tst_server.py", # "$D/geometry/tests/tst_altloc.py", "$D/geometry/tests/tst_asa.py", "$D/geometry/tests/tst_clash.py", "$D/geometry/tests/tst_indexing.py", "$D/geometry/tests/tst_shared_types.py", "$D/geometry/tests/tst_sphere_surface_sampling.py", "$D/geometry/tests/tst_topology.py", # "$D/nci/tst_hbond.py", "$D/wwpdb/tst_rcsb_web_services.py", "$D/regression/command_line/tst_find_residue_in_pdb.py", "$D/wwpdb/tst_utils.py", "$D/monomer_library/tst_all_cif_files.py", "$D/refinement/tst_misc.py", "$D/refinement/tst_real_space_simple.py", "$D/scaling/tst_bayesian_estimator.py", "$D/scaling/tst_mean_f_rms_f.py", "$D/scaling/tst_sigmaa.py", "$D/scaling/tst_massage_data.py", "$D/ions/tst_geometries.py", "$D/ions/tst_pick_k.py", "$D/ions/tst_environment.py", "$D/regression/tst_table_one.py", "$D/regression/tst_msa.py", "$D/regression/tst_cc_star.py", "$D/regression/tst_fmodel_2.py", "$D/regression/tst_rigid_bond_test.py", "$D/validation/regression/tst_cablam.py", "$D/building/tst_make_library.py", "$D/regression/real_space_refine_chain/tst_00.py", "$D/regression/real_space_refine_chain/tst_01.py", "$D/conformation_dependent_library/tst_omega_cdl.py", "$D/regression/fix_cablam/tst_basic_cl_operations.py", "$D/regression/fix_cablam/tst_single_outliers_surroundings.py", "$D/regression/fix_cablam/tst_one_resid_rotation.py", "$D/regression/fix_cablam/tst_insertion_codes.py", # "$D/regression/tst_scattering_type_registry.py", "$D/atomic_environment_vectors/tst.py", # "$D/building/ligands/tst_00.py", # Tests that were not in the list and caused us to fail as of 10/6/2021 "$D/regression/tst_ligand_ncs.py", "$D/regression/tst_origin_ids.py", "$D/regression/model/tst_model_ramachandran.py", "$D/regression/model_idealization/tst_ext_map_01.py", "$D/validation/regression/tst_mp_geo_endtoend.py", "$D/validation/regression/tst_mp_geo_chiral_volume_cases.py", "$D/conformation_dependent_library/tst_multi_residue_rna.py", "$D/conformation_dependent_library/tst_cdl_nucleotides.py", "$D/conformation_dependent_library/tst_rna_dna_fragments.py", "$D/conformation_dependent_library/testing_utils.py", "$D/conformation_dependent_library/tst_poly_ca_multi_residue.py", "$D/conformation_dependent_library/tst_mutli_residue.py", ] molprobity_tests = [ "$D/regression/tst_rama_z_01.py", "$D/regression/pdb_interpretation/tst_edits.py", "$D/regression/pdb_interpretation/tst_edits_actions.py", "$D/regression/tst_add_arrows_on_plot.py", "$D/regression/model/tst_model.py", "$D/regression/tst_reduce_timeout.py", "$D/regression/tst_altloc_chain_break.py", "$D/regression/ncs/tst_geometry_minimization_ncs_constraints.py", "$D/regression/tst_clashes.py", "$D/validation/regression/tst_cbetadev.py", "$D/regression/tst_statistics_output.py", "$D/regression/tst_geo_min_restraints_phil.py", "$D/regression/tst_model_vs_map.py", # validation/molprobity "$D/validation/regression/tst_nqh_minimize.py", "$D/validation/regression/tst_molprobity_1.py", "$D/validation/regression/tst_molprobity_4.py", "$D/validation/regression/tst_molprobity_5.py", "$D/validation/regression/tst_experimental.py", "$D/validation/regression/tst_cablam_2.py", # automatic linking ["$D/monomer_library/tst_metal_coordination.py", "1"], ["$D/monomer_library/tst_metal_coordination.py", "2"], ["$D/monomer_library/tst_metal_coordination.py", "3"], ["$D/monomer_library/tst_linking.py", "1"], ["$D/monomer_library/tst_linking.py", "2"], ["$D/monomer_library/tst_linking.py", "3"], ["$D/monomer_library/tst_linking.py", "4"], ["$D/monomer_library/tst_linking.py", "5"], ["$D/monomer_library/tst_linking.py", "6"], ["$D/monomer_library/tst_linking.py", "7"], ["$D/monomer_library/tst_linking.py", "8"], ["$D/monomer_library/tst_linking.py", "9"], ["$D/monomer_library/tst_linking.py", "10"], ["$D/monomer_library/tst_linking.py", "11"], ["$D/monomer_library/tst_linking.py", "12"], ["$D/monomer_library/tst_linking.py", "13"], ["$D/monomer_library/tst_linking.py", "14"], ["$D/monomer_library/tst_linking.py", "15"], ["$D/monomer_library/tst_linking.py", "16"], ["$D/monomer_library/tst_linking.py", "17"], ["$D/monomer_library/tst_linking.py", "18"], ["$D/monomer_library/tst_linking.py", "19"], ["$D/monomer_library/tst_linking.py", "20"], ["$D/monomer_library/tst_linking.py", "21"], ["$D/monomer_library/tst_linking.py", "22"], ["$D/monomer_library/tst_linking.py", "23"], ["$D/monomer_library/tst_linking.py", "24"], ["$D/monomer_library/tst_linking.py", "25"], ["$D/monomer_library/tst_linking.py", "26"], ["$D/monomer_library/tst_linking.py", "27"], ["$D/monomer_library/tst_linking.py", "28"], ["$D/monomer_library/tst_linking.py", "29"], ["$D/monomer_library/tst_linking.py", "30"], ["$D/monomer_library/tst_linking.py", "31"], ["$D/monomer_library/tst_linking.py", "32"], ["$D/monomer_library/tst_linking.py", "33"], ["$D/monomer_library/tst_linking.py", "34"], ["$D/monomer_library/tst_linking.py", "35"], ["$D/monomer_library/tst_linking.py", "36"], ["$D/monomer_library/tst_linking.py", "37"], ["$D/monomer_library/tst_linking.py", "38"], ["$D/monomer_library/tst_linking.py", "39"], ["$D/monomer_library/tst_linking.py", "40"], ] if libtbx.env.has_module(name="probe"): tst_list = tuple(general_tests + molprobity_tests) else: print("Skipping %d MolProbity tests: probe not configured"%len(molprobity_tests)) tst_list = tuple(general_tests) # generally failing tests tst_list_expected_failures = [ "$D/monomer_library/tst_pdb_interpretation_2.py", ] def run(): assert easy_run.call("libtbx.find_untested mmtbx True")==0 build_dir = libtbx.env.under_build("mmtbx") dist_dir = libtbx.env.dist_path("mmtbx") test_utils.run_tests(build_dir, dist_dir, tst_list) if (__name__ == "__main__"): run()