testsuite.MDAnalysisTests.analysis.test_align.TestRotationMatrix.test_exception ... ok testsuite.MDAnalysisTests.analysis.test_align.TestRotationMatrix.test_list_args ... ok testsuite.MDAnalysisTests.analysis.test_align.TestRotationMatrix.test_no_solution_no_weights ... ok testsuite.MDAnalysisTests.analysis.test_align.TestRotationMatrix.test_no_solution_with_weights ... ok testsuite.MDAnalysisTests.analysis.test_align.TestRotationMatrix.test_wrong_dtype ... ok test align.fasta2select() on aligned FASTA (Issue 112) ... ok MDAnalysis.analysis.align: test fasta2select() with ClustalW (Issue 113) ... ok testsuite.MDAnalysisTests.analysis.test_align.test_sequence_alignment ... ok testsuite.MDAnalysisTests.analysis.test_base.TestAnalysisBase.test_incomplete_defined_analysis ... ok testsuite.MDAnalysisTests.analysis.test_base.test_filter_baseanalysis_kwargs ... ok testsuite.MDAnalysisTests.analysis.test_base.TestAnalysisBase.test_default ... ok testsuite.MDAnalysisTests.analysis.test_base.TestAnalysisBase.test_old_api ... ok testsuite.MDAnalysisTests.analysis.test_base.TestAnalysisBase.test_start_stop_step_conversion ... ok testsuite.MDAnalysisTests.analysis.test_base.TestAnalysisBase.test_start ... ok testsuite.MDAnalysisTests.analysis.test_base.TestAnalysisBase.test_verbose ... ok testsuite.MDAnalysisTests.analysis.test_base.TestAnalysisBase.test_step ... ok testsuite.MDAnalysisTests.analysis.test_base.TestAnalysisBase.test_stop ... ok test_end_zero: TestContactAnalysis1: stop frame 0 is not ignored ... ok testsuite.MDAnalysisTests.analysis.test_base.test_analysis_class ... ok testsuite.MDAnalysisTests.analysis.test_contacts.test_soft_cut_q ... ok testsuite.MDAnalysisTests.analysis.test_contacts.TestContacts.test_non_callable_method ... ok testsuite.MDAnalysisTests.analysis.test_base.test_AnalysisFromFunction ... ok testsuite.MDAnalysisTests.analysis.test_contacts.test_hard_cut_q ... ok testsuite.MDAnalysisTests.analysis.test_contacts.test_radius_cut_q ... ok testsuite.MDAnalysisTests.analysis.test_contacts.TestContacts.test_hard_cut_method ... ok testsuite.MDAnalysisTests.analysis.test_contacts.test_contact_matrix ... ok testsuite.MDAnalysisTests.analysis.test_contacts.TestContacts.test_own_method ... ok testsuite.MDAnalysisTests.analysis.test_contacts.TestContacts.test_own_method_no_array_cast ... ok test_absence_griddata (testsuite.MDAnalysisTests.analysis.test_density.TestGridImport) ... ok test_presence_griddata (testsuite.MDAnalysisTests.analysis.test_density.TestGridImport) ... ok test_check_set_unit_attributeError (testsuite.MDAnalysisTests.analysis.test_density.TestDensity) ... ok test_check_set_unit_keyerror (testsuite.MDAnalysisTests.analysis.test_density.TestDensity) ... ok test_check_set_unit_nolength (testsuite.MDAnalysisTests.analysis.test_density.TestDensity) ... ok test_delta (testsuite.MDAnalysisTests.analysis.test_density.TestDensity) ... ok test_edges (testsuite.MDAnalysisTests.analysis.test_density.TestDensity) ... ok test_grid (testsuite.MDAnalysisTests.analysis.test_density.TestDensity) ... ok test_midpoints (testsuite.MDAnalysisTests.analysis.test_density.TestDensity) ... ok test_origin (testsuite.MDAnalysisTests.analysis.test_density.TestDensity) ... ok test_shape (testsuite.MDAnalysisTests.analysis.test_density.TestDensity) ... ok testsuite.MDAnalysisTests.analysis.test_contacts.TestContacts.test_save ... ok testsuite.MDAnalysisTests.analysis.test_contacts.TestContacts.test_slicing ... ok test_startframe: TestContactAnalysis1: start frame set to 0 (resolution of ... ok testsuite.MDAnalysisTests.analysis.test_contacts.test_soft_cut_q_folded ... ok testsuite.MDAnalysisTests.analysis.test_contacts.test_soft_cut_q_unfolded ... ok testsuite.MDAnalysisTests.analysis.test_contacts.test_new_selection ... ok testsuite.MDAnalysisTests.analysis.test_contacts.test_q1q2 ... ok test_box_numpy (testsuite.MDAnalysisTests.analysis.test_distances.TestContactMatrix) ... ok test_box_sparse (testsuite.MDAnalysisTests.analysis.test_distances.TestContactMatrix) ... ok test_np (testsuite.MDAnalysisTests.analysis.test_distances.TestContactMatrix) ... ok test_sparse (testsuite.MDAnalysisTests.analysis.test_distances.TestContactMatrix) ... ok testsuite.MDAnalysisTests.analysis.test_diffusionmap.TestDiffusionmap.test_dist_weights ... ERROR testsuite.MDAnalysisTests.analysis.test_contacts.TestContacts.test_villin_folded ... ok testsuite.MDAnalysisTests.analysis.test_contacts.TestContacts.test_villin_unfolded ... ok test_one (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreClusteringSklearn) ... ok Test MDAnalysis.analysis.distances.between() for ... ok testsuite.MDAnalysisTests.analysis.test_diffusionmap.TestDiffusionmap.test_eg ... ok testsuite.MDAnalysisTests.analysis.test_diffusionmap.TestDiffusionmap.test_different_steps ... ok testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreImportWarnings.test_import_warnings('MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod',) ... ok testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreImportWarnings.test_import_warnings('MDAnalysis.analysis.encore.clustering.ClusteringMethod',) ... ok test_get_distance_matrix (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreConfDistMatrix) ... ok testsuite.MDAnalysisTests.analysis.test_gnm.TestGNM.test_closeContactGNMAnalysis_default_weights_is_size ... ok testsuite.MDAnalysisTests.analysis.test_diffusionmap.TestDiffusionmap.test_transform ... ok testsuite.MDAnalysisTests.analysis.test_gnm.TestGNM.test_closeContactGNMAnalysis_deprecated_MassWeight_False ... ok testsuite.MDAnalysisTests.analysis.test_gnm.TestGNM.test_closeContactGNMAnalysis_deprecated_MassWeight_True ... ok testsuite.MDAnalysisTests.analysis.test_density.TestNotWithin.test_not_within ... ok testsuite.MDAnalysisTests.analysis.test_density.TestNotWithin.test_within ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysis.test_acceptor_OC1_OC2 ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysis.test_atoms_too_far ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysis.test_count_by_time ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysis.test_count_by_type ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysis.test_generate_table ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysis.test_helix_backbone ... ok testsuite.MDAnalysisTests.analysis.test_gnm.TestGNM.test_generate_kirchoff ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysis.test_zero_vs_1based ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_check_static_selections ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_check_static_selections ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_check_static_selections ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_check_static_selections(, , 'protein', 'resname ALA and not backbone', 'donor') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_check_static_selections(, , 'protein', 'resname ALA and not backbone', 'acceptor') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_check_static_selections(, , 'protein', 'resname ALA and not backbone', 'both') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_check_static_selections(, , 'resname ALA and not backbone', 'protein', 'donor') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_check_static_selections(, , 'resname ALA and not backbone', 'protein', 'acceptor') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_check_static_selections(, , 'resname ALA and not backbone', 'protein', 'both') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_check_static_selections(, , 'resname ALA and not backbone', 'resname ALA and not backbone', 'donor') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_check_static_selections(, , 'resname ALA and not backbone', 'resname ALA and not backbone', 'acceptor') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_check_static_selections(, , 'resname ALA and not backbone', 'resname ALA and not backbone', 'both') ... ok testsuite.MDAnalysisTests.analysis.test_gnm.TestGNM.test_gnm_run_step ... ok testsuite.MDAnalysisTests.analysis.test_gnm.TestGNM.test_gnm ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeavy.test_acceptor_OC1_OC2 ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeavy.test_atoms_too_far ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeavy.test_count_by_time ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeavy.test_count_by_type ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeavy.test_generate_table ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeavy.test_helix_backbone ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeavy.test_zero_vs_1based ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeavyFail.test_acceptor_OC1_OC2 ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeavyFail.test_atoms_too_far ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_run_empty_selections('protein', 'protein', 'donor') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_run_empty_selections('protein', 'protein', 'acceptor') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_run_empty_selections('protein', 'protein', 'both') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_run_empty_selections('protein', 'resname ALA and not backbone', 'donor') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_run_empty_selections('protein', 'resname ALA and not backbone', 'acceptor') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_run_empty_selections('protein', 'resname ALA and not backbone', 'both') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_run_empty_selections('resname ALA and not backbone', 'protein', 'donor') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_run_empty_selections('resname ALA and not backbone', 'protein', 'acceptor') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_run_empty_selections('resname ALA and not backbone', 'protein', 'both') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_run_empty_selections('resname ALA and not backbone', 'resname ALA and not backbone', 'donor') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_run_empty_selections('resname ALA and not backbone', 'resname ALA and not backbone', 'acceptor') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisChecking.test_run_empty_selections('resname ALA and not backbone', 'resname ALA and not backbone', 'both') ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeavyFail.test_count_by_time ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeavyFail.test_count_by_type ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeavyFail.test_generate_table ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeavyFail.test_helix_backbone ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeavyFail.test_zero_vs_1based ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeuristic.test_acceptor_OC1_OC2 ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeuristic.test_atoms_too_far ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeuristic.test_count_by_time ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeuristic.test_count_by_type ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeuristic.test_generate_table ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeuristic.test_helix_backbone ... ok A ValueError should be raised if the two atomgroups ... ok Test that offsets fed to dist() are correctly calculated. ... ok Ensure that pairwise distances between atoms are ... ok Test that feeding in offsets to dist() doesn't alter ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeuristic.test_zero_vs_1based ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisTIP3P.test_table_atoms ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisTIP3P.test_timeseries ... ok test_AlignTraj (testsuite.MDAnalysisTests.analysis.test_align.TestAlign) ... ok test_AlignTraj_custom_mass_weights (testsuite.MDAnalysisTests.analysis.test_align.TestAlign) ... ok test_AlignTraj_custom_weights (testsuite.MDAnalysisTests.analysis.test_align.TestAlign) ... ok test_AlignTraj_in_memory (testsuite.MDAnalysisTests.analysis.test_align.TestAlign) ... ok test_AlignTraj_partial_fit (testsuite.MDAnalysisTests.analysis.test_align.TestAlign) ... ok test_AlignTraj_weighted (testsuite.MDAnalysisTests.analysis.test_align.TestAlign) ... ok test_AlignTraj_weights_deprecated (testsuite.MDAnalysisTests.analysis.test_align.TestAlign) ... ok Testing that alignto() fails if selections do not ... ok test_alignto_partial_universe (testsuite.MDAnalysisTests.analysis.test_align.TestAlign) ... ok Testing align.rms_fit_trj() for all atoms (Issue 58) ... ok test_rms_fit_trj_defaultfilename (testsuite.MDAnalysisTests.analysis.test_align.TestAlign) ... ok test_rmsd (testsuite.MDAnalysisTests.analysis.test_align.TestAlign) ... ok test_rmsd_custom_mass_weights (testsuite.MDAnalysisTests.analysis.test_align.TestAlign) ... ok test_rmsd_custom_weights (testsuite.MDAnalysisTests.analysis.test_align.TestAlign) ... ok test_rmsd_deprecated (testsuite.MDAnalysisTests.analysis.test_align.TestAlign) ... ok testsuite.MDAnalysisTests.analysis.test_helanal.test_helanal_main ... ok testing MDAnalysis.analysis.helanal xtc striding: Check for resolution of Issue #188. ... ok test_density_from_Universe (testsuite.MDAnalysisTests.analysis.test_density.Test_density_from_Universe) ... ok test_density_from_Universe_notwithin (testsuite.MDAnalysisTests.analysis.test_density.Test_density_from_Universe) ... ok test_density_from_Universe_sliced (testsuite.MDAnalysisTests.analysis.test_density.Test_density_from_Universe) ... ok test_density_from_Universe_update_selection (testsuite.MDAnalysisTests.analysis.test_density.Test_density_from_Universe) ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysis.test_true_traj ... ok testsuite.MDAnalysisTests.analysis.test_helanal.test_helanal_trajectory ... ok testsuite.MDAnalysisTests.analysis.test_hydrogenbondautocorrel.TestHydrogenBondAutocorrel.test_bond_type_VE ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeavy.test_true_traj ... ok testsuite.MDAnalysisTests.analysis.test_hydrogenbondautocorrel.TestHydrogenBondAutocorrel.test_continuous ... ok test_dimensionality_reduction_PCA_direct (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreDimensionalityReduction) ... ok test_dimensionality_reduction_SPENative_direct (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreDimensionalityReduction) ... ok test_dimensionality_reduction_different_method (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreDimensionalityReduction) ... ok test_dimensionality_reduction_one_ensemble (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreDimensionalityReduction) ... ok test_dimensionality_reduction_specified_dimension (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreDimensionalityReduction) ... ok test_dimensionality_reduction_three_ensembles_two_identical (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreDimensionalityReduction) ... ok test_dimensionality_reduction_two_different_methods (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreDimensionalityReduction) ... ok test_dimensionality_reduction_two_ensembles (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreDimensionalityReduction) ... ok test_dimensionality_reduction_two_methods (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreDimensionalityReduction) ... ok testsuite.MDAnalysisTests.analysis.test_hydrogenbondautocorrel.TestHydrogenBondAutocorrel.test_exclusions ... ok testsuite.MDAnalysisTests.analysis.test_hydrogenbondautocorrel.TestHydrogenBondAutocorrel.test_continuous_excl ... ok testsuite.MDAnalysisTests.analysis.test_hydrogenbondautocorrel.TestHydrogenBondAutocorrel.test_intermittent ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeavyFail.test_true_traj ... ok testsuite.MDAnalysisTests.analysis.test_hydrogenbondautocorrel.TestHydrogenBondAutocorrel.test_intermittent_excl ... ok testsuite.MDAnalysisTests.analysis.test_hydrogenbondautocorrel.TestHydrogenBondAutocorrel.test_repr ... ok testsuite.MDAnalysisTests.analysis.test_hydrogenbondautocorrel.TestHydrogenBondAutocorrel.test_intermittent_timecut ... ok testsuite.MDAnalysisTests.analysis.test_hydrogenbondautocorrel.TestHydrogenBondAutocorrel.test_save_without_run_VE ... ok testsuite.MDAnalysisTests.analysis.test_hydrogenbondautocorrel.TestHydrogenBondAutocorrel.test_save ... ok testsuite.MDAnalysisTests.analysis.test_hydrogenbondautocorrel.TestHydrogenBondAutocorrel.test_solve_continuous ... ok testsuite.MDAnalysisTests.analysis.test_hydrogenbondautocorrel.TestHydrogenBondAutocorrel.test_solve_before_run_VE ... ok test_clustering_AffinityPropagationNative_direct (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreClustering) ... ok test_clustering_AffinityPropagation_direct (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreClustering) ... ok test_clustering_DBSCAN_direct (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreClustering) ... ok test_clustering_KMeans_direct (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreClustering) ... ok test_clustering_method_w_no_distance_matrix (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreClustering) ... ok test_clustering_one_ensemble (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreClustering) ... ok test_clustering_three_ensembles_two_identical (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreClustering) ... ok test_clustering_two_different_methods (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreClustering) ... ok test_clustering_two_ensembles (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreClustering) ... ok test_clustering_two_methods (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreClustering) ... ok test_clustering_two_methods_one_w_no_distance_matrix (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreClustering) ... ok test_sklearn_affinity_propagation (testsuite.MDAnalysisTests.analysis.test_encore.TestEncoreClustering) ... ok testsuite.MDAnalysisTests.analysis.test_hydrogenbondautocorrel.TestHydrogenBondAutocorrel.test_unslicable_traj_VE ... ok testsuite.MDAnalysisTests.analysis.test_hydrogenbondautocorrel.TestHydrogenBondAutocorrel.test_solve_intermittent ... ok test_serial (testsuite.MDAnalysisTests.analysis.test_lineardensity.TestLinearDensity) ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_hydroxyl_1 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_hydroxyl_2 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_major_pair_1 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_major_pair_2 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_minor_pair_1 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_minor_pair_2 ... ok testsuite.MDAnalysisTests.analysis.test_hydrogenbondautocorrel.TestHydrogenBondAutocorrel.test_wronglength_DA ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_phase_as_1 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_phase_cp_1 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_phase_cp_2 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_phase_as_2 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_pseudo_dihe_baseflip_2 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_pseudo_dihe_baseflip_1 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_tors_1 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_tors_alpha_1 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_tors_2 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_tors_alpha_2 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_tors_beta_1 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_tors_chi_2 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_tors_chi_1 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_tors_delta_1 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_tors_beta_2 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_tors_delta_2 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_tors_eps_1 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_tors_eps_2 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_tors_gamma_2 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_tors_zeta_1 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_tors_gamma_1 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_tors_zeta_2 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_wc_pair_1 ... ok testsuite.MDAnalysisTests.analysis.test_nuclinfo.TestNuclinfo.test_wc_pair_2 ... ok testsuite.MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeuristic.test_true_traj ... ok test_leaflet_finder (testsuite.MDAnalysisTests.analysis.test_leaflet.TestLeafletFinder) ... ok test_optimize_cutoff (testsuite.MDAnalysisTests.analysis.test_leaflet.TestLeafletFinder) ... ok test_string_vs_atomgroup_proper (testsuite.MDAnalysisTests.analysis.test_leaflet.TestLeafletFinder) ... ok test open file descriptors are closed (MDAnalysisTests.analysis.test_hole.TestHoleModule): Issue 129 ... ok test_HOLE (testsuite.MDAnalysisTests.analysis.test_hole.TestHOLE) ... ok test_vmd_surface (testsuite.MDAnalysisTests.analysis.test_hole.TestHOLE) ... ok testsuite.MDAnalysisTests.analysis.test_pca.TestPCA.test_different_steps ... ok testsuite.MDAnalysisTests.analysis.test_persistencelength.TestFitExponential.test_fit_noisy ... ok testsuite.MDAnalysisTests.analysis.test_persistencelength.TestFitExponential.test_fit_simple ... ok testsuite.MDAnalysisTests.analysis.test_persistencelength.TestPersistenceLength.test_ag_VE ... ok testsuite.MDAnalysisTests.analysis.test_pca.TestPCA.test_cum_var ... ok testsuite.MDAnalysisTests.analysis.test_pca.TestPCA.test_cov ... ok testsuite.MDAnalysisTests.analysis.test_persistencelength.TestPersistenceLength.test_fit ... ok testsuite.MDAnalysisTests.analysis.test_pca.TestPCA.test_pcs ... ok test_discrete_Frechet_concentric_circles (testsuite.MDAnalysisTests.analysis.test_psa.DiscreteFrechetDistance) ... ok Test to ensure that increasing N points in one of the paths ... ok Test that the undirected Hausdorff ... ok Ensure that the undirected (symmetric) ... ok Test that the undirected Hausdorff ... ok Ensure that the undirected (symmetric) ... ok Test that ValueError is raised when i or j are ... ok Test that ValueError is raised when i == j or i,j == N ... ok Test that ValueError is raised when i or j or both are ... ok Test that ValueError is raised when ... ok Test that KeyError is caught by ... ok Ensure that a NoDataError is raised if ... ok Test to ensure that increasing N points in one of the paths ... ok Test that the undirected Hausdorff ... ok Ensure that the undirected (symmetric) ... ok testsuite.MDAnalysisTests.analysis.test_rdf.TestInterRDF.test_count ... ok testsuite.MDAnalysisTests.analysis.test_rdf.TestInterRDF.test_count_sum ... ok testsuite.MDAnalysisTests.analysis.test_rdf.TestInterRDF.test_double_run ... ok testsuite.MDAnalysisTests.analysis.test_rdf.TestInterRDF.test_exclusion ... ok testsuite.MDAnalysisTests.analysis.test_rdf.TestInterRDF.test_nbins ... ok testsuite.MDAnalysisTests.analysis.test_rdf.TestInterRDF.test_range ... ok testsuite.MDAnalysisTests.analysis.test_rms.TestRMSD.test_custom_weighted_and_save ... ok testsuite.MDAnalysisTests.analysis.test_persistencelength.TestPersistenceLength.test_run ... ok testsuite.MDAnalysisTests.analysis.test_pca.TestPCA.test_cosine_content ... ok testsuite.MDAnalysisTests.analysis.test_rms.TestRMSD.test_mass_weighted_and_save ... ok testsuite.MDAnalysisTests.analysis.test_rms.TestRMSD.test_mass_mismatches ... ok testsuite.MDAnalysisTests.analysis.test_rms.TestRMSD.test_group_selections_unequal_len ... ok testsuite.MDAnalysisTests.analysis.test_rms.TestRMSD.test_mass_weighted_and_save_deprecated ... ok testsuite.MDAnalysisTests.analysis.test_pca.TestPCA.test_transform_mismatch ... ok testsuite.MDAnalysisTests.analysis.test_rms.TestRMSD.test_rmsd_group_selections ... ok testsuite.MDAnalysisTests.analysis.test_rms.TestRMSD.test_progress_meter ... ok testsuite.MDAnalysisTests.analysis.test_rms.TestRMSD.test_rmsd ... ok testsuite.MDAnalysisTests.analysis.test_pca.TestPCA.test_transform ... ok testsuite.MDAnalysisTests.analysis.test_rms.TestRMSD.test_ref_length_unequal_len ... ok Ensure that a matplotlib axis object is ... ok testsuite.MDAnalysisTests.analysis.test_rms.TestRMSD.test_rmsd_single_frame ... ok testsuite.MDAnalysisTests.analysis.test_rms.TestRMSD.test_save_before_run ... ok testsuite.MDAnalysisTests.analysis.test_rms.Testrmsd.test_list ... ok testsuite.MDAnalysisTests.analysis.test_rms.Testrmsd.test_no_center ... ok testsuite.MDAnalysisTests.analysis.test_rms.Testrmsd.test_superposition ... ok testsuite.MDAnalysisTests.analysis.test_rms.Testrmsd.test_center ... ok testsuite.MDAnalysisTests.analysis.test_pca.TestPCA.test_transform_universe ... ok testsuite.MDAnalysisTests.analysis.test_rms.Testrmsd.test_unequal_shape ... ok testsuite.MDAnalysisTests.analysis.test_rms.Testrmsd.test_weights ... ok test_HOLEtraj (testsuite.MDAnalysisTests.analysis.test_hole.TestHOLEtraj) ... ok test_min_radius (testsuite.MDAnalysisTests.analysis.test_hole.TestHOLEtraj) ... ok test_plot (testsuite.MDAnalysisTests.analysis.test_hole.TestHOLEtraj) ... ok test_plot3D (testsuite.MDAnalysisTests.analysis.test_hole.TestHOLEtraj) ... ok test_plot3D_rmax (testsuite.MDAnalysisTests.analysis.test_hole.TestHOLEtraj) ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_bad_represent_raises_ValueError ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_changing_n_col_raises_ValueError ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_data_selector ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_data_selector_out_of_range_raises_ValueError ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_dt ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_first_step ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_get_auxreader_for ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_get_description ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_initial_time ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_invalid_step_to_time_raises_ValueError ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_iter ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_iter_list ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_iter_slice ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_iterate_as_auxiliary_from_trajectory ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_iterate_through_trajectory ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_last_step ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_load_from_description ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_move_to_invalid_step_raises_IndexError ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_move_to_step ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_n_steps ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_next ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_next_past_last_step_raises_StopIteration ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_no_constant_dt ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_read_higher_freq_timestep ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_read_lower_freq_timestep ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_read_offset_timestep ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_reopen ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_represent_as_average ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_represent_as_average_with_cutoff ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_represent_as_closest_with_cutoff ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_rewind ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_slice_non_int_raises_TypeError ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_slice_out_of_range_raises_IndexError ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_slice_start_after_stop_raises_IndexError ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_time_selector ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_time_selector_out_of_range_raises_ValueError ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGFileReader.test_update_ts_without_auxname_raises_ValueError ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_bad_represent_raises_ValueError ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_changing_n_col_raises_ValueError ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_data_selector ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_data_selector_out_of_range_raises_ValueError ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_dt ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_first_step ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_get_auxreader_for ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_get_description ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_initial_time ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_invalid_step_to_time_raises_ValueError ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_iter ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_iter_list ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_iter_slice ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_iterate_as_auxiliary_from_trajectory ... ok testsuite.MDAnalysisTests.analysis.test_rms.Testrmsd.test_weights_and_superposition_1 ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_iterate_through_trajectory ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_load_from_description ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_last_step ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_move_to_invalid_step_raises_IndexError ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_move_to_step ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_n_steps ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_next ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_next_past_last_step_raises_StopIteration ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_read_higher_freq_timestep ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_read_lower_freq_timestep ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_no_constant_dt ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_read_offset_timestep ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_represent_as_average_with_cutoff ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_represent_as_average ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_represent_as_closest_with_cutoff ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_rewind ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_slice_non_int_raises_TypeError ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_slice_out_of_range_raises_IndexError ... ok testsuite.MDAnalysisTests.analysis.test_rms.Testrmsd.test_with_superposition_smaller ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_slice_start_after_stop_raises_IndexError ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_time_selector ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_time_selector_out_of_range_raises_ValueError ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.TestXVGReader.test_update_ts_without_auxname_raises_ValueError ... ok testsuite.MDAnalysisTests.analysis.test_rms.Testrmsd.test_with_superposition_equal ... ok test_AngularDistribution (testsuite.MDAnalysisTests.analysis.test_waterdynamics.TestWaterdynamics) ... ok test_HydrogenBondLifetimes (testsuite.MDAnalysisTests.analysis.test_waterdynamics.TestWaterdynamics) ... ok test_MeanSquareDisplacement (testsuite.MDAnalysisTests.analysis.test_waterdynamics.TestWaterdynamics) ... ok test_MeanSquareDisplacement_zeroMolecules (testsuite.MDAnalysisTests.analysis.test_waterdynamics.TestWaterdynamics) ... ok test_SurvivalProbability (testsuite.MDAnalysisTests.analysis.test_waterdynamics.TestWaterdynamics) ... ok test_SurvivalProbability_zeroMolecules (testsuite.MDAnalysisTests.analysis.test_waterdynamics.TestWaterdynamics) ... ok test_WaterOrientationalRelaxation (testsuite.MDAnalysisTests.analysis.test_waterdynamics.TestWaterdynamics) ... ok test_WaterOrientationalRelaxation_zeroMolecules (testsuite.MDAnalysisTests.analysis.test_waterdynamics.TestWaterdynamics) ... ok testsuite.MDAnalysisTests.analysis.test_rms.Testrmsd.test_weights_and_superposition_2 ... ok testsuite.MDAnalysisTests.auxiliary.test_xvg.test_xvg_bz2 ... ok testsuite.MDAnalysisTests.analysis.test_rms.Testrmsd.test_wrong_weights ... ok testsuite.MDAnalysisTests.core.test_atom.TestAtom.test_attributes_names ... ok testsuite.MDAnalysisTests.core.test_atom.TestAtom.test_add_AG ... ok testsuite.MDAnalysisTests.core.test_atom.TestAtom.test_attributes_positions ... ok testsuite.MDAnalysisTests.core.test_atom.TestAtom.test_atom_selection ... ok testsuite.MDAnalysisTests.core.test_atom.TestAtom.test_bad_add ... ok testsuite.MDAnalysisTests.core.test_atom.TestAtom.test_hierarchy ... ok testsuite.MDAnalysisTests.core.test_atom.TestAtom.test_bonded_atoms ... ok testsuite.MDAnalysisTests.core.test_atom.TestAtomNoForceNoVel.test_force_fail ... ok testsuite.MDAnalysisTests.core.test_atom.TestAtomNoForceNoVel.test_force_set_fail ... ok testsuite.MDAnalysisTests.core.test_atom.TestAtomNoForceNoVel.test_velocity_fail ... ok testsuite.MDAnalysisTests.core.test_atom.TestAtomNoForceNoVel.test_velocity_set_fail ... ok testsuite.MDAnalysisTests.core.test_atom.TestAtom.test_no_velo ... ok testsuite.MDAnalysisTests.core.test_atom.TestAtom.test_setting_attribute_type ... ok testsuite.MDAnalysisTests.core.test_atom.TestAtom.test_setting_attribute_mass ... ok testsuite.MDAnalysisTests.core.test_atom.TestAtom.test_setting_attribute_name ... ok testsuite.MDAnalysisTests.core.test_atom.TestAtom.test_undefined_occupancy ... ok testsuite.MDAnalysisTests.core.test_atom.TestAtom.test_setting_attributes_charge ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_angle ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_angle_ValueError ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_atom_order ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_bad_add_AG ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_bad_make ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_asphericity ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_bond ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_bond_ValueError ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_bond_pbc ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_bool_IE ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_bool_true ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_bool_false ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_boolean_indexing ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_boolean_indexing_2 ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_center_of_mass ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_center_of_geometry ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_charges ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_charges_ndarray ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_coordinates ... ok test that AtomGroup.dihedral() raises ValueError if not exactly ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_dihedral_equals_improper ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_getitem_IE ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_getitem_int ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_getitem_slice ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_getitem_slice2 ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_getitem_str ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_improper ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_index_advancedslice ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_index_integer ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_index_slice ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_index_slice_empty ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_indices ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_indices_ndarray ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_masses ... ok testing that len(atomgroup) == atomgroup.n_atoms ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_masses_ndarray ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_n_atoms ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_n_residues ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_n_segments ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_names ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_nonexistent_instantselector_raises_AttributeError ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_names_ndarray ... ok test AtomGroup.pack_into_box(): Tests application of periodic boundary ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_packintobox_badshape ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_packintobox_noshape ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_positions ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_principal_axes ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_repr ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_resids ... ok test_rmsf (testsuite.MDAnalysisTests.analysis.test_rms.TestRMSF) ... ok test_rmsf_identical_frames (testsuite.MDAnalysisTests.analysis.test_rms.TestRMSF) ... ok test_rmsf_old_run (testsuite.MDAnalysisTests.analysis.test_rms.TestRMSF) ... ok test_rmsf_single_frame (testsuite.MDAnalysisTests.analysis.test_rms.TestRMSF) ... ok test_rmsf_weights (testsuite.MDAnalysisTests.analysis.test_rms.TestRMSF) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_resids_dim ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_resids_ndarray ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_residues ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_resnames ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_resnums ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_resnames_ndarray ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_resnums_dim ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_resnums_ndarray ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_segids ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_segids_dim ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_segids_ndarray ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_segments ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupProperties.test_attributes('name', 'names', ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupProperties.test_attributes('name', 'names', ['A', 'B', 'C', 'D', 'E', 'F'], ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupProperties.test_attributes('type', 'types', ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupProperties.test_attributes('type', 'types', ['A', 'B', 'C', 'D', 'E', 'F'], ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupProperties.test_attributes('altLoc', 'altLocs', ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupProperties.test_attributes('altLoc', 'altLocs', ['A', 'B', 'C', 'D', 'E', 'F'], ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupProperties.test_attributes('charge', 'charges', ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupProperties.test_attributes('charge', 'charges', array([ 0.001, 0.002, 0.003, 0.005, 0.012, 0.025], dtype=float32), ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupProperties.test_attributes('mass', 'masses', ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupProperties.test_attributes('mass', 'masses', array([ 0.001, 0.002, 0.003, 0.005, 0.012, 0.025], dtype=float32), ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupProperties.test_attributes('radius', 'radii', ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupProperties.test_attributes('radius', 'radii', array([ 0.001, 0.002, 0.003, 0.005, 0.012, 0.025], dtype=float32), ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupProperties.test_attributes('bfactor', 'bfactors', ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupProperties.test_attributes('bfactor', 'bfactors', array([ 0.001, 0.002, 0.003, 0.005, 0.012, 0.025], dtype=float32), ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupProperties.test_attributes('occupancy', 'occupancies', ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupProperties.test_attributes('occupancy', 'occupancies', array([ 0.001, 0.002, 0.003, 0.005, 0.012, 0.025], dtype=float32), ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_set_resnum_single ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_set_resname_single ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_set_names ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupTimestep.test_partial_timestep ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_shape_parameter ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_total_mass ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroup.test_total_charge ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupToTopology.test_angle ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupToTopology.test_dihedral ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupToTopology.test_bond ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupToTopology.test_improper ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupTransformations.test_transform_rotation_only ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupTransformations.test_transform_translation_and_rotation ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupWriting.test_bogus_kwarg_pdb ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupWriting.test_write_coordinates ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupWriting.test_raises ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestCenter.test_center_1 ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestCenter.test_center_2 ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestCenter.test_center_wrong_length ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestCenter.test_center_wrong_shape ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupTransformations.test_rotate ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestCrossUniverse.test_adding_empty_ags ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestCrossUniverse.test_add_mixed_universes(, ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestCrossUniverse.test_add_mixed_universes(, ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestCrossUniverse.test_add_mixed_universes(, ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestCrossUniverse.test_add_mixed_universes(, ) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDeprecationWarnings.test_old_AtomGroup_init_warns ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDeprecationWarnings.test_old_AtomGroup_init_works ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupTransformations.test_rotateby ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDeprecationWarnings.test_old_ResidueGroup_init_warns ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDeprecationWarnings.test_old_ResidueGroup_init_works ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDeprecationWarnings.test_old_SegmentGroup_init_warns ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDeprecationWarnings.test_old_SegmentGroup_init_works ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupToTopology.test_VEs('bond',) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupToTopology.test_VEs('angle',) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupToTopology.test_VEs('dihedral',) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupToTopology.test_VEs('improper',) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDeprecationWarnings.test_AtomGroupUniverse_usage_warning ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupWriting.test_write_selection ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDihedralSelections.test_ch1_sel_fail ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDihedralSelections.test_dihedral_chi1 ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDihedralSelections.test_chi1_selection ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupTransformations.test_transform_translation_only ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDihedralSelections.test_dihedral_phi ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDihedralSelections.test_dihedral_omega ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDihedralSelections.test_dihedral_psi ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDihedralSelections.test_omega_sel_fail ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestOrphans.test_atom ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestOrphans.test_atomgroup ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDihedralSelections.test_phi_sel_fail ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDihedralSelections.test_omega_selection ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDihedralSelections.test_phi_selection ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDihedralSelections.test_psi_selection ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestDihedralSelections.test_psi_sel_fail ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestPBCFlag.test_flag ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestPBCFlag.test_default ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestPBCFlag.test_pbcflag ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestPBCFlag.test_usepbc_flag ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestPBCFlag.test_override_flag ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestSplit.test_split_VE ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWrap.test_wrap_atoms ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestSplit.test_split_residues ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestSplit.test_split_atoms ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestSplit.test_split_segments ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWrap.test_wrap_box_fail ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWrap.test_wrap_cent_fail ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWrap.test_wrap_comp_fail ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWrap.test_wrap_group ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWrap.test_wrap_residues ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWrap.test_wrap_segments ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupTransformations.test_translate ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWriteGRO.test_flag_convert_length ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWriteGRO.test_write_ResidueGroup ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWriteGRO.test_write_Residue ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWriteGRO.test_write_Segment ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWriteGRO.test_write_empty_atomgroup ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWriteGRO.test_write_selection ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWritePDB.test_write_Residue ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWriteGRO.test_write_Universe ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestAtomGroupWriting.test_write_no_args ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWriteGRO.test_write_atoms ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWritePDB.test_write_empty_atomgroup ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWritePDB.test_write_ResidueGroup ... ok Test that instant selections work, even for residues that are also termini (Issue 70) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestICodeSelection.test_missing_icodes_VE ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestICodeSelection.test_missing_icodes_range_VE ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestBondedSelection.test_nobonds_warns ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestICodeSelection.test_select_icode ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWritePDB.test_write_selection ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestICodeSelection.test_select_icode_range_1 ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestICodeSelection.test_select_icode_range_2 ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestBondedSelection.test_bonded_1 ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestICodeSelection.test_select_icode_range_3 ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestICodeSelection.test_select_icode_range_4 ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestICodeSelection.test_select_icode_range_5 ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestICodeSelection.test_select_resid_implicit_icode ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_string_selections('name NameABA or name NameACA or name NameADA', 'name NameABA NameACA NameADA') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_string_selections('type TypeE or type TypeD or type TypeB', 'type TypeE TypeD TypeB') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_string_selections('resname RsC or resname RsY', 'resname RsC RsY') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_string_selections('name NameAB* or name NameACC', 'name NameAB* NameACC') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_string_selections('(name NameABC or name NameABB) and (resname RsD or resname RsF)', 'name NameABC NameABB and resname RsD RsF') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_string_selections('segid SegA or segid SegC', 'segid SegA SegC') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_range_selections('resid 1 or resid 2', 'resid 1 2') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_range_selections('resid 1:10 or resid 22', 'resid 1:10 22') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_range_selections('resid 1:10 or resid 20:30', 'resid 1:10 20:30') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_range_selections('resid 1-5 or resid 7', 'resid 1-5 7') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_range_selections('resid 1-5 or resid 7:10 or resid 12', 'resid 1-5 7:10 12') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_range_selections('resid 1 or resid 3 or resid 5:10', 'resid 1 3 5:10') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_range_selections('resnum 1 or resnum 2', 'resnum 1 2') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_range_selections('resnum 1:10 or resnum 22', 'resnum 1:10 22') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_range_selections('resnum 1:10 or resnum 20:30', 'resnum 1:10 20:30') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_range_selections('resnum 1-5 or resnum 7', 'resnum 1-5 7') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_range_selections('resnum 1-5 or resnum 7:10 or resnum 12', 'resnum 1-5 7:10 12') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_range_selections('resnum 1 or resnum 3 or resnum 5:10', 'resnum 1 3 5:10') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_range_selections('bynum 1 or bynum 2', 'bynum 1 2') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_range_selections('bynum 1:10 or bynum 22', 'bynum 1:10 22') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_range_selections('bynum 1:10 or bynum 20:30', 'bynum 1:10 20:30') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_range_selections('bynum 1-5 or bynum 7', 'bynum 1-5 7') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_range_selections('bynum 1-5 or bynum 7:10 or bynum 12', 'bynum 1-5 7:10 12') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestImplicitOr.test_range_selections('bynum 1 or bynum 3 or bynum 5:10', 'bynum 1 3 5:10') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestOrthogonalDistanceSelections.test_cyzone('distmat', True) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestOrthogonalDistanceSelections.test_cyzone('distmat', False) ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWrap.test_wrap_fragments ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', , '<') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', , '>') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', , '<=') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', , '>=') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', , '==') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', , '!=') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', , '<') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', , '>') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', , '<=') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', , '>=') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', , '==') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('mass', , '!=') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', , '<') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', , '>') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', , '<=') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', , '>=') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', , '==') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', , '!=') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', , '<') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', , '>') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', , '<=') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', , '>=') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', , '==') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestPropSelection.test_props('charge', , '!=') ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestOrthogonalDistanceSelections.test_point('kdtree', False) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestOrthogonalDistanceSelections.test_point('distmat', True) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestOrthogonalDistanceSelections.test_point('distmat', False) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionErrors.test_expected_errors('name and H',) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionErrors.test_expected_errors('name )',) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionErrors.test_expected_errors('resid abcd',) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionErrors.test_expected_errors('resnum 7a7',) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionErrors.test_expected_errors('resid 1-',) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionErrors.test_expected_errors('prop chicken == tasty',) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionErrors.test_expected_errors('prop chicken <= 7.4',) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionErrors.test_expected_errors('prop mass ^^ 12.0',) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionErrors.test_expected_errors('same this as resid 1',) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionErrors.test_expected_errors('same resid resname mass 5.0',) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionErrors.test_expected_errors('name H and',) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionErrors.test_expected_errors('naem H',) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionErrors.test_expected_errors('resid and name C',) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionErrors.test_expected_errors('resnum ',) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionErrors.test_expected_errors('bynum or protein',) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionErrors.test_expected_errors('prop mass < 4.0 hello',) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionErrors.test_expected_errors('prop mass > 10. and group this',) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionErrors.test_expected_errors('prop mass > 10. and fullgroup this',) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestOrthogonalDistanceSelections.test_spherical_layer('kdtree', False) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestOrthogonalDistanceSelections.test_spherical_layer('distmat', True) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestOrthogonalDistanceSelections.test_spherical_layer('distmat', False) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsAMBER.test_backbone ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsAMBER.test_protein ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsAMBER.test_type ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestOrthogonalDistanceSelections.test_around('kdtree', False) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestOrthogonalDistanceSelections.test_around('distmat', True) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestOrthogonalDistanceSelections.test_around('distmat', False) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_and ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_around ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_atom ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_atom_empty ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestOrthogonalDistanceSelections.test_spherical_zone('kdtree', False) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestOrthogonalDistanceSelections.test_spherical_zone('distmat', True) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestOrthogonalDistanceSelections.test_spherical_zone('distmat', False) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_backbone ... ok Tests the bynum selection, also from AtomGroup instances (Issue 275) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_byres ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_concatenated_selection ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_cylayer ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_cyzone ... ok Test that empty selection can be processed (see Issue 12) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_fullselgroup ... ok Test the `global` modifier keyword (Issue 268) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_name ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWritePDB.test_write_Segment ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWritePDB.test_write_Universe ... ok Test that no space is needed around parentheses (Issue 43). ... ok testsuite.MDAnalysisTests.core.test_atomgroup.TestWritePDB.test_write_atoms ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_not ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_or ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_empty_same ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_parenthesized_expression ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_point ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_prop ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_protein ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_resid_range ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_resid_single ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_segid ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_resnum_range ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_resnum_single ... ok Test the 'same ... as' construct (Issue 217) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_resname ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_selgroup ... ok Test the 'same ... as' construct (Issue 217) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_sphlayer ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_type ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsNAMD.test_protein ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsCHARMM.test_sphzone ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsNAMD.test_resid_single ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsNAMD.test_type ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsNucleicAcids.test_nucleic ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsNucleicAcids.test_nucleic_all ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsNucleicAcids.test_nucleicbackbone ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsNucleicAcids.test_nucleicbase ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsNucleicAcids.test_nucleicsugar ... ok Cylinder layer selections with tricilinic periodicity (Issue 274) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsGRO.test_resid_single ... ok Cylinder zone selections with tricilinic periodicity (Issue 274) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsGRO.test_backbone ... ok Test the 'same ... as' construct (Issue 217) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestSelectionsGRO.test_protein ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestTriclinicSelections.test_point_2 ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestTriclinicSelections.test_around ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestTriclinicSelections.test_point_1 ... ok testsuite.MDAnalysisTests.core.test_atomselections.test_segid_and_resid ... ok testsuite.MDAnalysisTests.core.test_fragments.TestFragments.test_atom_fragment_nobonds_NDE ... ok testsuite.MDAnalysisTests.core.test_fragments.TestFragments.test_atomgroup_fragments_nobonds_NDE ... ok testsuite.MDAnalysisTests.core.test_fragments.TestFragments.test_fragments(,) ... ok testsuite.MDAnalysisTests.core.test_fragments.TestFragments.test_fragments(,) ... ok testsuite.MDAnalysisTests.core.test_fragments.TestFragments.test_fragments(,) ... ok testsuite.MDAnalysisTests.core.test_fragments.TestFragments.test_fragments(,) ... ok testsuite.MDAnalysisTests.core.test_fragments.TestFragments.test_fragments(,) ... ok testsuite.MDAnalysisTests.core.test_fragments.TestFragments.test_fragments(,) ... ok testsuite.MDAnalysisTests.core.test_fragments.TestFragments.test_fragments(,) ... ok testsuite.MDAnalysisTests.core.test_fragments.TestFragments.test_fragments(,) ... ok testsuite.MDAnalysisTests.core.test_fragments.TestFragments.test_fragments(,) ... ok testsuite.MDAnalysisTests.core.test_fragments.TestFragments.test_fragments(,) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupForces.test_forces ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupForces.test_get_forces ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupForces.test_set_forces ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupTrajAccess.test_all(, True) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupVelocities.test_get_velocities ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestTriclinicSelections.test_sphlayer ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestTriclinicSelections.test_sphzone ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupVelocities.test_set_velocities ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtomGroupVelocities.test_velocities ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestTriclinicDistanceSelections.test_around('kdtree', False) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestTriclinicDistanceSelections.test_around('distmat', True) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestTriclinicDistanceSelections.test_around('distmat', False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtom_ForceVelocity.test_atom_force_set ... ERROR testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtom_ForceVelocity.test_atom_force_get ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtom_ForceVelocity.test_atom_velocity_get ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtom_ForceVelocity.test_atom_velocity_set ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestGROVelocities.testParse_velocities ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestTriclinicDistanceSelections.test_point('kdtree', False) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestTriclinicDistanceSelections.test_point('distmat', True) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestTriclinicDistanceSelections.test_point('distmat', False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtom_ForceVelocity.test_for_iteration ... ok testsuite.MDAnalysisTests.core.test_groups.TestAtomGroup.test_PDB_atom_repr ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestComponentComparisons.test_comparions(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(,) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(,) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(,) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(,) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(,) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(,) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupAddition.test_addition(, ) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestTriclinicDistanceSelections.test_spherical_layer('kdtree', False) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestTriclinicDistanceSelections.test_spherical_layer('distmat', True) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestTriclinicDistanceSelections.test_spherical_layer('distmat', False) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestTriclinicDistanceSelections.test_spherical_zone('kdtree', False) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestTriclinicDistanceSelections.test_spherical_zone('distmat', True) ... ok testsuite.MDAnalysisTests.core.test_atomselections.TestTriclinicDistanceSelections.test_spherical_zone('distmat', False) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtom_ForceVelocity.test_pos_iteration ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level(, 'invalid') ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_only_same_level_different_universes ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_groupbase_operators_duplicated_and_scrambled(, , , , ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBy.test_groupby_float ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBy.test_groupby_string ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBy.test_groupby_int ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupHash.test_hash_diff_cross_universe(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupHash.test_hash_diff_cross_universe(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupHash.test_hash_diff_cross_universe(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupHash.test_hash_difference(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupHash.test_hash_difference(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupHash.test_hash_difference(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupHash.test_hash_equality(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupHash.test_hash_equality(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupHash.test_hash_equality(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupHash.test_hash_difference_cross(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupHash.test_hash_difference_cross(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupHash.test_hash_difference_cross(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupHash.test_hash_difference_cross(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupHash.test_hash_difference_cross(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupHash.test_hash_difference_cross(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupHash.test_hash_exists(,) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupHash.test_hash_exists(,) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupHash.test_hash_exists(,) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_atom_to_residue ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_atom_to_segment ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_atomgroup_to_atomgroup ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_atomgroup_to_residuegroup ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_atomgroup_to_residuegroup_unique ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_atomgroup_to_segmentgroup ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_atomgroup_to_segmentgroup_unique ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_atomgroup_unique ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_residue_to_atomgroup ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_residue_to_segment ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_residuegroup_to_atomgroup ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_residuegroup_to_atomgroup_listcomp ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_shortcut_overriding(, 'concatenate', 'atoms') ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_shortcut_overriding(, 'concatenate', 'residues') ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_shortcut_overriding(, 'concatenate', 'segments') ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_shortcut_overriding(, 'difference', 'atoms') ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_shortcut_overriding(, 'difference', 'residues') ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_shortcut_overriding(, 'difference', 'segments') ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_shortcut_overriding(, 'intersection', 'atoms') ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_shortcut_overriding(, 'intersection', 'residues') ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_shortcut_overriding(, 'intersection', 'segments') ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_shortcut_overriding(, 'union', 'atoms') ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_shortcut_overriding(, 'union', 'residues') ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_shortcut_overriding(, 'union', 'segments') ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_shortcut_overriding(, 'symmetric_difference', 'atoms') ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_shortcut_overriding(, 'symmetric_difference', 'residues') ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupBaseOperators.test_shortcut_overriding(, 'symmetric_difference', 'segments') ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_residuegroup_to_residuegroup ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_residuegroup_to_segmentgroup ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_residuegroup_to_segmentgroup_unique ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_residuegroup_unique ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_segment_to_residuegroup ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_segment_to_atomgroup ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_segmentgroup_to_atomgroup ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_segmentgroup_to_atomgroup_listcomp ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_segmentgroup_to_residuegroup_listcomp ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_segmentgroup_to_segmentgroup ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_segmentgroup_to_residuegroup ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupLevelTransition.test_segmentgroup_unique ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupProperties.test_dimensions ... ok testsuite.MDAnalysisTests.core.test_groups.TestInstantSelectorDeprecationWarnings.test_AtomGroup_nowarn_getitem_index ... ok testsuite.MDAnalysisTests.core.test_groups.TestInstantSelectorDeprecationWarnings.test_AtomGroup_warn_getattr ... ok testsuite.MDAnalysisTests.core.test_groups.TestInstantSelectorDeprecationWarnings.test_AtomGroup_nowarn_segids_attribute ... ok testsuite.MDAnalysisTests.core.test_groups.TestInstantSelectorDeprecationWarnings.test_AtomGroup_warn_getitem ... ok testsuite.MDAnalysisTests.core.test_groups.TestInstantSelectorDeprecationWarnings.test_SegmentGroup_nowarn_getitem ... ok testsuite.MDAnalysisTests.core.test_groups.TestInstantSelectorDeprecationWarnings.test_ResidueGroup_warn_getattr_resname ... ok testsuite.MDAnalysisTests.core.test_groups.TestInstantSelectorDeprecationWarnings.test_SegmentGroup_warn_getattr ... ok testsuite.MDAnalysisTests.core.test_groups.TestMetaclassMagic.test_new_class ... ok testsuite.MDAnalysisTests.core.test_groups.TestInstantSelectorDeprecationWarnings.test_Segment_warn_getattr_rRESNUM ... ok testsuite.MDAnalysisTests.core.test_groups.TestInstantSelectorDeprecationWarnings.test_Segment_warn_getattr_resname ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, 125) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, 125) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(,) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(,) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(,) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, 25) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, 25) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(,) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(,) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(,) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, 5) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, 5) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(,) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(,) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(,) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), slice(0, 10, None)) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), slice(0, 2, None)) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), slice(1, 3, None)) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), slice(0, 2, 2)) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), slice(0, -1, None)) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), slice(5, 1, -1)) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), slice(10, 0, -2)) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), [0, 1]) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), [0, 0, 0, 1]) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), [3, 2, 1]) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), [-1, -2, -3]) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), []) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), array([0, 1])) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), array([0, 0, 0, 1])) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), array([3, 2, 1])) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), array([-1, -2, -3])) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), array([], dtype=int64)) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), 0, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), 1, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), -1, ) ... ok testsuite.MDAnalysisTests.core.test_groups.TestGroupSlicing.test_groups(, array([0, 1, 2, 3, 4]), -2, ) ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtom_ForceVelocity.test_vel_iteration ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestTRRForces.testForces ... ok testsuite.MDAnalysisTests.core.test_groups.TestReprs.test_atomgroup_str_long ... ok testsuite.MDAnalysisTests.core.test_groups.TestReprs.test_atom_repr ... ok testsuite.MDAnalysisTests.core.test_groups.TestReprs.test_atomgroup_repr ... ok testsuite.MDAnalysisTests.core.test_groups.TestReprs.test_atomgroup_str_short ... ok testsuite.MDAnalysisTests.core.test_groups.TestReprs.test_residue_repr ... ok testsuite.MDAnalysisTests.core.test_groups.TestReprs.test_residuegroup_repr ... ok testsuite.MDAnalysisTests.core.test_index_dtype.TestIndexDtype.test_ag_ix ... ok testsuite.MDAnalysisTests.core.test_index_dtype.TestIndexDtype.test_atom_ix_array ... ok testsuite.MDAnalysisTests.core.test_index_dtype.TestIndexDtype.test_atomgroup_indices ... ok testsuite.MDAnalysisTests.core.test_index_dtype.TestIndexDtype.test_atomgroup_residue_upshift ... ok testsuite.MDAnalysisTests.core.test_index_dtype.TestIndexDtype.test_atomgroup_segment_upshift ... ok testsuite.MDAnalysisTests.core.test_index_dtype.TestIndexDtype.test_residue_ix_array ... ok testsuite.MDAnalysisTests.core.test_index_dtype.TestIndexDtype.test_residuegroup_atom_downshift ... ok testsuite.MDAnalysisTests.core.test_index_dtype.TestIndexDtype.test_residuegroup_resindices ... ok testsuite.MDAnalysisTests.core.test_index_dtype.TestIndexDtype.test_residuegroup_segment_upshift ... ok testsuite.MDAnalysisTests.core.test_index_dtype.TestIndexDtype.test_rg_ix ... ok testsuite.MDAnalysisTests.core.test_index_dtype.TestIndexDtype.test_segment_ix_array ... ok testsuite.MDAnalysisTests.core.test_index_dtype.TestIndexDtype.test_segmentgroup_atom_downshift ... ok testsuite.MDAnalysisTests.core.test_index_dtype.TestIndexDtype.test_segmentgroup_residue_downshift ... ok testsuite.MDAnalysisTests.core.test_index_dtype.TestIndexDtype.test_segmentgroup_segindices ... ok testsuite.MDAnalysisTests.core.test_index_dtype.TestIndexDtype.test_sg_ix ... ok testsuite.MDAnalysisTests.core.test_requires.TestRequires.test_failure_errormessage ... ok testsuite.MDAnalysisTests.core.test_requires.TestRequires.test_requires_failure_multiple ... ok testsuite.MDAnalysisTests.core.test_requires.TestRequires.test_requires_failure_singular ... ok testsuite.MDAnalysisTests.core.test_requires.TestRequires.test_requires_success ... ok testsuite.MDAnalysisTests.core.test_groups.TestReprs.test_residuegroup_str_long ... ok testsuite.MDAnalysisTests.core.test_groups.TestReprs.test_segment_repr ... ok testsuite.MDAnalysisTests.core.test_groups.TestReprs.test_residuegroup_str_short ... ok testsuite.MDAnalysisTests.core.test_groups.TestReprs.test_segmentgroup_repr ... ok testsuite.MDAnalysisTests.core.test_group_traj_access.TestTRRForcesNativeUnits.testForces ... ok testsuite.MDAnalysisTests.core.test_groups.TestReprs.test_segmentgroup_str ... ok testsuite.MDAnalysisTests.core.test_residue.TestResidue.test_atom_order ... ok testsuite.MDAnalysisTests.core.test_residue.TestResidue.test_index ... ok testsuite.MDAnalysisTests.core.test_residue.TestResidue.test_type ... ok testsuite.MDAnalysisTests.core.test_residuegroup.TestResidueGroup.test_atom_order ... ok testing that len(residuegroup) == residuegroup.n_residues ... ok testsuite.MDAnalysisTests.core.test_residuegroup.TestResidueGroup.test_n_atoms ... ok testsuite.MDAnalysisTests.core.test_residuegroup.TestResidueGroup.test_n_residues ... ok Test the 'same ... as' construct (Issue 217) ... ok test that slicing a ResidueGroup returns a new ResidueGroup ... ok testsuite.MDAnalysisTests.core.test_residuegroup.TestResidueGroup.test_resnums_dim ... ok testsuite.MDAnalysisTests.core.test_residuegroup.TestResidueGroup.test_resids_dim ... ok testsuite.MDAnalysisTests.core.test_residuegroup.TestResidueGroup.test_segids_dim ... ok testsuite.MDAnalysisTests.core.test_residuegroup.TestResidueGroup.test_set_resids_updates_self ... ok testsuite.MDAnalysisTests.core.test_residuegroup.TestResidueGroup.test_set_resnum_many ... ok testsuite.MDAnalysisTests.core.test_residuegroup.TestResidueGroup.test_set_resnum_ValueError ... ok test_set_resid: set ResidueGroup resids on a per-residue basis ... ok testsuite.MDAnalysisTests.core.test_segment.TestSegment.test_advanced_slicing ... ok testsuite.MDAnalysisTests.core.test_segment.TestSegment.test_atom_order ... ok testsuite.MDAnalysisTests.core.test_segment.TestSegment.test_index ... ok testsuite.MDAnalysisTests.core.test_segment.TestSegment.test_slicing ... ok testsuite.MDAnalysisTests.core.test_segment.TestSegment.test_type ... ok testsuite.MDAnalysisTests.core.test_residuegroup.TestResidueGroup.test_set_resnum_single ... ok testsuite.MDAnalysisTests.core.test_residuegroup.TestSequence.test_Seq ... ok testsuite.MDAnalysisTests.core.test_residuegroup.TestSequence.test_SeqRecord ... ok testsuite.MDAnalysisTests.core.test_residuegroup.TestSequence.test_format_TE ... ok Test that a generated residue group always returns a ResidueGroup (Issue 47) ... ok test_sequence_nonIUPACresname: non recognized amino acids raise ... ok testsuite.MDAnalysisTests.core.test_residuegroup.TestSequence.test_string ... ok testsuite.MDAnalysisTests.core.test_segmentgroup.TestSegmentGroup.test_n_atoms ... ok testsuite.MDAnalysisTests.core.test_segmentgroup.TestSegmentGroup.test_n_residues ... ok testsuite.MDAnalysisTests.core.test_segmentgroup.TestSegmentGroup.test_atom_order ... ok testsuite.MDAnalysisTests.core.test_topology.TestAddingResidues.test_add_Residue_NDE_message ... ok testsuite.MDAnalysisTests.core.test_topology.TestAddingResidues.test_add_Residue_NDE_message_2 ... ok testsuite.MDAnalysisTests.core.test_topology.TestAddingResidues.test_add_Residue_ambiguous_segment_NDE ... ok testsuite.MDAnalysisTests.core.test_topology.TestAddingResidues.test_add_Residue_missing_attr_NDE ... ok testsuite.MDAnalysisTests.core.test_topology.TestAddingResidues.test_add_Residue_with_attrs ... ok testsuite.MDAnalysisTests.core.test_topology.TestAddingResidues.test_add_Segment_NDE_message ... ok test that slicing a SegmentGroup returns a new SegmentGroup (Issue 135) ... ok testsuite.MDAnalysisTests.core.test_topology.TestAddingResidues.test_add_residue_no_attrs ... ok testsuite.MDAnalysisTests.core.test_topology.TestAddingResidues.test_add_Segment_with_attr ... ok testsuite.MDAnalysisTests.core.test_topology.TestAddingResidues.test_add_residue_no_attrs_one_segment ... ok testsuite.MDAnalysisTests.core.test_topology.TestAddingResidues.test_add_segment_no_attrs ... ok testsuite.MDAnalysisTests.core.test_topology.TestAddingResidues.test_missing_attr_NDE_Segment ... ok testsuite.MDAnalysisTests.core.test_topology.TestDownshiftArrays.test_contents_ragged ... ok testsuite.MDAnalysisTests.core.test_topology.TestDownshiftArrays.test_contents_square ... ok testsuite.MDAnalysisTests.core.test_topology.TestDownshiftArrays.test_downshift_dtype_square ... ok testsuite.MDAnalysisTests.core.test_topology.TestDownshiftArrays.test_downshift_dtype_ragged ... ok testsuite.MDAnalysisTests.core.test_topology.TestDownshiftArrays.test_missing_end_values ... ok testsuite.MDAnalysisTests.core.test_topology.TestDownshiftArrays.test_missing_end_values_2 ... ok testsuite.MDAnalysisTests.core.test_topology.TestDownshiftArrays.test_missing_intra_values ... ok testsuite.MDAnalysisTests.core.test_topology.TestDownshiftArrays.test_missing_intra_values_2 ... ok testsuite.MDAnalysisTests.core.test_topology.TestDownshiftArrays.test_shape_ragged ... ok testsuite.MDAnalysisTests.core.test_topology.TestDownshiftArrays.test_shape_square ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_atom ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_atom_TE ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_atom_residuegroup_TE ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_atom_residue_list_TE ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_atom_segment_NIE ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_atomgroup_TE ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_atomgroup_list_TE ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_atomgroup_residue_list_VE ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_atomgroup_residue_list ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_atomgroup_residuegroup_VE ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_atomgroup_residuegroup ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_atomgroup_segment_NIE ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_atomgroup_single_residue ... ok testsuite.MDAnalysisTests.core.test_segmentgroup.TestSegmentGroup.test_resids_dim ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_residue ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_residue_TE ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_residue_segmentgroup_TE ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_residue_list_TE ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_residuegroup_TE ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_residuegroup_list_VE ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_residuegroup_list_TE ... ok testsuite.MDAnalysisTests.core.test_segmentgroup.TestSegmentGroup.test_resnums_dim ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_residuegroup_segment_list ... ok testsuite.MDAnalysisTests.core.test_topology.TestTopologyCreation.test_make_topology_no_attrs ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_residuegroup_segmentgroup_VE ... ok testsuite.MDAnalysisTests.core.test_topology.TestTopologyCreation.test_resindex_VE ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_residuegroup_single_segment ... ok testsuite.MDAnalysisTests.core.test_topology.TestLevelMoves.test_move_residuegroup_segmentgroup ... ok testsuite.MDAnalysisTests.core.test_topology.TestTopologyCreation.test_segindex_VE ... ok testsuite.MDAnalysisTests.core.test_topology.TestTopologyGuessed.test_guessed ... ok testsuite.MDAnalysisTests.core.test_topology.TestTopologyGuessed.test_read ... ok testsuite.MDAnalysisTests.core.test_topology.TestTransTable.test_move_atom_simple ... ok testsuite.MDAnalysisTests.core.test_topology.TestTransTable.test_a2r ... ok testsuite.MDAnalysisTests.core.test_topology.TestTransTable.test_move_residue_simple ... ok testsuite.MDAnalysisTests.core.test_topology.TestTransTable.test_r2a_1d ... ok testsuite.MDAnalysisTests.core.test_topology.TestTransTable.test_r2a_2d ... ok testsuite.MDAnalysisTests.core.test_topology.TestTransTable.test_r2s ... ok testsuite.MDAnalysisTests.core.test_topology.TestTransTable.test_s2a_1d ... ok testsuite.MDAnalysisTests.core.test_topology.TestTransTable.test_s2r_1d ... ok testsuite.MDAnalysisTests.core.test_topology.TestTransTable.test_s2a_2d ... ok testsuite.MDAnalysisTests.core.test_topology.TestTransTable.test_s2r_2d ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAtomAttr.test_get_atoms ... ok Unless overriden by child class, this should yield values for all ... ok Unless overriden by child class, this should yield values for all ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAtomAttr.test_len ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAtomAttr.test_set_atoms_VE ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAtomAttr.test_set_atoms_plural ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAtomAttr.test_set_atom_VE ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAtomAttr.test_set_atoms_singular ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAtomids.test_get_atoms ... ok Unless overriden by child class, this should yield values for all ... ok Unless overriden by child class, this should yield values for all ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAtomids.test_len ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAtomids.test_set_atoms_VE ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAtomids.test_set_atoms_plural ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAtomids.test_set_atom_VE ... ok Unless overriden by child class, this should yield values for all ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAtomnames.test_get_atoms ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAtomids.test_set_atoms_singular ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAtomnames.test_len ... ok Unless overriden by child class, this should yield values for all ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAtomnames.test_set_atoms_plural ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAtomnames.test_set_atoms_VE ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAtomnames.test_set_atom_VE ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAtomnames.test_set_atoms_singular ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestCharges.test_get_atoms ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestCharges.test_get_residues ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestCharges.test_get_segment ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestCharges.test_get_segments ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestCharges.test_len ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestCharges.test_set_atom_VE ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestCharges.test_set_atoms_VE ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestCharges.test_set_atoms_plural ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestCharges.test_set_atoms_singular ... ok testsuite.MDAnalysisTests.core.test_segmentgroup.TestSegmentGroup.test_set_segids ... ok testsuite.MDAnalysisTests.core.test_segmentgroup.TestSegmentGroup.test_segids_dim ... ok testsuite.MDAnalysisTests.core.test_segmentgroup.TestSegmentGroup.test_set_segid_updates_self ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(, 'resids') ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(, 'resid') ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(, 'segids') ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(, 'segid') ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(, 'names') ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(, 'segids') ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(, 'segid') ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(, 'names') ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestCrossLevelAttributeSetting.test_set_crosslevel(, 'resids') ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestMasses.test_get_atoms ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestMasses.test_get_residues ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestMasses.test_get_segment ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestMasses.test_get_segments ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestMasses.test_len ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestMasses.test_set_atom_VE ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestMasses.test_set_atoms_VE ... ok testsuite.MDAnalysisTests.core.test_residuegroup.TestSequence.test_SeqRecord_default ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestMasses.test_set_atoms_singular ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestMasses.test_set_atoms_plural ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResids.test_get_atoms ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResids.test_get_residues ... ok Unless overriden by child class, this should yield values for all ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResids.test_len ... ok Setting the resids of atoms changes their residue membership. ... KNOWNFAIL: Test skipped due to expected failure testsuite.MDAnalysisTests.core.test_topologyattrs.TestResids.test_set_residues ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResids.test_set_residue_VE ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResids.test_set_residues_VE ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResids.test_set_residues_plural ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResids.test_set_residues_singular ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResidueAttr.test_get_atoms ... ok Unless overriden by child class, this should yield values for all ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResidueAttr.test_get_residues ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResidueAttr.test_len ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResidueAttr.test_set_residues_VE ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResidueAttr.test_set_residue_VE ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResidueAttr.test_set_residues_plural ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResidueAttr.test_set_residues_singular ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResnames.test_get_atoms ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResnames.test_get_residues ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResnames.test_len ... ok Unless overriden by child class, this should yield values for all ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResnames.test_residuegroup_getattr_AE ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResnames.test_residuegroup_getattr_multiple ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResnames.test_segment_getattr_AE ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResnames.test_residuegroup_getattr_single ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResnames.test_segment_getattr_multiple ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResnames.test_segment_getattr_singular ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResnames.test_set_residues_VE ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResnames.test_set_residues_plural ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResnames.test_set_residue_VE ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestSegmentAttr.test_get_atoms ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestResnames.test_set_residues_singular ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestSegmentAttr.test_get_residues ... ok Unless overriden by child class, this should yield values for all ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestSegmentAttr.test_len ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestSegmentAttr.test_set_segments_VE ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestSegmentAttr.test_set_segment_VE ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestSegmentAttr.test_set_segments_plural ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestSegmentAttr.test_set_segments_singular ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAttr.test_align_principal_axes_with_self ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestIndicesClasses.test_cant_set_segment_indices ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestIndicesClasses.test_cant_set_residue_indices ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAttr.test_principal_axes ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestAttr.test_align_principal_axes_with_x ... ok testsuite.MDAnalysisTests.core.test_topologyattrs.TestIndicesClasses.test_cant_set_atom_indices ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_TG_getitem_fancy ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_TG_getitem_slice ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_TG_getitem_single ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_TG_getitem_bool_IE ... ok Pull bonds from a TG which are at least partially in an AG ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_TG_getitem_bool ... ok Make two identical TGs, ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_add_TO_to_empty_TG ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_add_TopologyGroups ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_add_singleitem ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_add_empty_to_TG ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_add_TG_to_empty_TG ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_add_wrongtype_TopologyGroup ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_angles_contains ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_angle_tg_creation_notype ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_angles_reversal ... ok Pull bonds from TG which are fully in an AG ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_atom2 ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_atom1 ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_atom3 ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_atom3_IE ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_angles_uniqueness ... ok TopologyDict for angles ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_atom4 ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_bad_add_TopologyGroup ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_atom4_IE ... ok Test making a TopologyGroup out of nonsense ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_bond_reversal ... ok Test making a TopologyDict out of nonsense ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_bond_tg_creation_notype ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_bonds_contains ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_bond_uniqueness ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_create_TopologyGroup ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_create_guessed_tg ... ok Tests TopologyDict for bonds ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_create_guessed_tg_2 ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_dihedral_tg_creation_notype ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_dihedrals_contains ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_dihedrals_reversal ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_dihedrals_uniqueness ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup_Cython.test_right_type_angles ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_td_keyerror ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup_Cython.test_right_type_bonds ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_td_iter ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup_Cython.test_right_type_dihedrals ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup_Cython.test_right_type_impropers ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_td_len ... ok TopologyDict for dihedrals ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup_Cython.test_wrong_type_bonds ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup_Cython.test_wrong_type_dihedrals ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyObjects.test_angle ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_td_universe ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyObjects.test_bondrepr ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyObjects.test_bondlength ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyObjects.test_dihedral ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyObjects.test_gt ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyObjects.test_eq ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyObjects.test_indices ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyObjects.test_improper ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyObjects.test_iter ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup_Cython.test_wrong_type_angles ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyObjects.test_len ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyObjects.test_lt ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyGroup.test_tg_creation_bad_btype ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyObjects.test_ne ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyObjects.test_partner ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyObjects.test_partner_VE ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyObjects.test_repr ... ok testsuite.MDAnalysisTests.core.test_universe.TestCustomReaders.test_custom_reader_singleframe ... ok testsuite.MDAnalysisTests.core.test_universe.TestCustomReaders.test_custom_reader_singleframe_2 ... ok testsuite.MDAnalysisTests.core.test_universe.TestGuessBonds.test_atomgroup_guess_bonds_no_vdwradii ... ok Test an atomgroup doing guess bonds ... ok testsuite.MDAnalysisTests.core.test_universe.TestGuessBonds.test_atomgroup_guess_bonds_with_vdwradii ... ok Make a Universe that has atoms with unknown vdwradii. ... ok Test that making a Universe with guess_bonds works ... ok testsuite.MDAnalysisTests.core.test_universe.TestGuessBonds.test_universe_guess_bonds_off ... ok testsuite.MDAnalysisTests.core.test_universe.TestCustomReaders.test_custom_both ... ok Unknown atom types, but with vdw radii here to save the day ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.test_bond_length_pbc ... ok testsuite.MDAnalysisTests.core.test_universe.TestCustomReaders.test_custom_parser ... ok testsuite.MDAnalysisTests.core.test_universe.TestCustomReaders.test_custom_reader ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.TestTopologyObjects.test_hash ... ok testsuite.MDAnalysisTests.core.test_universe.TestInMemoryUniverse.test_existing_universe ... ok testsuite.MDAnalysisTests.core.test_universe.TestInMemoryUniverse.test_slicing_negative_start ... ok testsuite.MDAnalysisTests.core.test_universe.TestInMemoryUniverse.test_reader_w_timeseries_frame_interval ... ok testsuite.MDAnalysisTests.core.test_universe.TestInMemoryUniverse.test_slicing_step_dt ... ok testsuite.MDAnalysisTests.core.test_universe.TestInMemoryUniverse.test_slicing_negative_stop ... ok testsuite.MDAnalysisTests.core.test_universe.TestInMemoryUniverse.test_slicing_step_with_start_stop ... ok testsuite.MDAnalysisTests.core.test_universe.TestInMemoryUniverse.test_reader_w_timeseries ... ok testsuite.MDAnalysisTests.core.test_universe.TestInMemoryUniverse.test_slicing_step_without_start_stop ... ok testsuite.MDAnalysisTests.core.test_universe.TestInMemoryUniverse.test_slicing_with_start_stop ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverse.test_load_bad_topology ... ok testsuite.MDAnalysisTests.core.test_universe.TestInMemoryUniverse.test_slicing_without_start ... ok testsuite.MDAnalysisTests.core.test_topologyobjects.test_cross_universe_eq ... ok testsuite.MDAnalysisTests.core.test_universe.TestInMemoryUniverse.test_slicing_without_stop ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverse.test_load_new ... ok testsuite.MDAnalysisTests.core.test_universe.TestInMemoryUniverse.test_frame_interval_convention ... ok testsuite.MDAnalysisTests.core.test_universe.TestInMemoryUniverse.test_reader_wo_timeseries_frame_interval ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverseCreation.test_Universe_filename_IE_msg ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverseCreation.test_Universe_invalidfile_IE_msg ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverseCreation.test_Universe_invalidpermissionfile_IE_msg ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverseCreation.test_Universe_no_trajectory_AE ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverseCreation.test_Universe_topology_IE ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverseCreation.test_Universe_topology_IE_msg ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverseCreation.test_Universe_topology_unrecognizedformat_VE ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverseCreation.test_Universe_topology_unrecognizedformat_VE_msg ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverse.test_load_new_TypeError ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverseCreation.test_load_new_VE ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverseCreation.test_load_topology_stringio ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverseCreation.test_load_trajectory_stringio ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverse.test_load_structure ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverseCreation.test_make_universe_no_args ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverseCreation.test_make_universe_stringio_no_format ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverse.test_load_multiple_args ... ok testsuite.MDAnalysisTests.core.test_universe.test_chainid_quick_select ... ok testsuite.MDAnalysisTests.core.test_updating_atomgroup.TestDynamicUAG.test_driveby ... ok testsuite.MDAnalysisTests.core.test_updating_atomgroup.TestDynamicUAG.test_nested_uags ... ok testsuite.MDAnalysisTests.core.test_updating_atomgroup.TestUAGCallCount.test_updated_when_creating ... ok testsuite.MDAnalysisTests.core.test_updating_atomgroup.TestUAGCallCount.test_updated_when_next ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverse.test_pickle_raises_NotImplementedError ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverse.test_set_dimensions ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverseCreation.test_load ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverse.test_load_multiple_list ... ok testsuite.MDAnalysisTests.core.test_universe.TestInMemoryUniverse.test_reader_wo_timeseries ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverseCreation.test_universe_topology_class_with_coords ... ok testsuite.MDAnalysisTests.core.test_universe.TestUniverseCreation.test_universe_kwargs ... ok testsuite.MDAnalysisTests.core.test_updating_atomgroup.test_representations ... ok testsuite.MDAnalysisTests.core.test_updating_atomgroup.test_empty_UAG ... ok testsuite.MDAnalysisTests.coordinates.test_amber_inpcrd.TestINPCRDReader.test_reader ... ok testsuite.MDAnalysisTests.core.test_updating_atomgroup.TestUpdatingSelectionNotraj.test_update ... ok testsuite.MDAnalysisTests.coordinates.test_amber_inpcrd.TestINPCRDReader.test_universe_inpcrd ... ok testsuite.MDAnalysisTests.coordinates.test_amber_inpcrd.TestINPCRDReader.test_universe_restrt ... ok testsuite.MDAnalysisTests.core.test_updating_atomgroup.TestUpdatingSelection.test_chained_update ... ok testsuite.MDAnalysisTests.core.test_updating_atomgroup.TestUpdatingSelection.test_kwarg_check ... ok testsuite.MDAnalysisTests.core.test_updating_atomgroup.TestUpdatingSelection.test_chained_update2 ... ok testsuite.MDAnalysisTests.core.test_updating_atomgroup.TestUpdatingSelection.test_compounded_update ... ok testsuite.MDAnalysisTests.coordinates.test_crd.TestCRDWriter.test_write_EXT ... ok testsuite.MDAnalysisTests.core.test_updating_atomgroup.TestUpdatingSelection.test_update ... ok testsuite.MDAnalysisTests.coordinates.test_crd.TestCRDWriter.test_roundtrip ... ok testsuite.MDAnalysisTests.core.test_updating_atomgroup.TestUpdatingSelection.test_slice_is_static ... ok test_time (testsuite.MDAnalysisTests.coordinates.test_chainreader.TestChainReaderCommonDt) ... ok testsuite.MDAnalysisTests.coordinates.test_crd.TestCRDWriterMissingAttrs.test_crdwriter('tempfactors',) ... ok testsuite.MDAnalysisTests.coordinates.test_crd.TestCRDWriterMissingAttrs.test_crdwriter('tempfactors',) ... ok testsuite.MDAnalysisTests.coordinates.test_crd.TestCRDWriterMissingAttrs.test_crdwriter('resids',) ... ok testsuite.MDAnalysisTests.coordinates.test_crd.TestCRDWriterMissingAttrs.test_crdwriter('resids',) ... ok testsuite.MDAnalysisTests.coordinates.test_crd.TestCRDWriterMissingAttrs.test_crdwriter('resnames',) ... ok testsuite.MDAnalysisTests.coordinates.test_crd.TestCRDWriterMissingAttrs.test_crdwriter('resnames',) ... ok testsuite.MDAnalysisTests.coordinates.test_crd.TestCRDWriterMissingAttrs.test_crdwriter('names',) ... ok testsuite.MDAnalysisTests.coordinates.test_crd.TestCRDWriterMissingAttrs.test_crdwriter('names',) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_array_trajectory ... ok testsuite.MDAnalysisTests.coordinates.test_crd.TestCRDWriter.test_write_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_frame ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_jump_dcd ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_jump_lastframe_dcd ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_list_repeated_trajectory ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_list_reverse_trajectory ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_list_trajectory ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_next_dcd ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_reverse_dcd ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_rewind_dcd ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_slice_dcd ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_time ... ok test_with_statement (testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReaderClass) ... ok test reading of triclinic unitcell (Issue 187) for NAMD or new ... ok test writing of triclinic unitcell (Issue 187) for NAMD or new ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_totaltime ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_allocate_forces ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_allocate_velocities ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_bad_copy_slice(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_bad_copy_slice(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_bad_copy_slice(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_bad_copy_slice(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_bad_copy_slice(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_bad_copy_slice(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_bad_copy_slice(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_change_dt ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_volume ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DCD') ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DCD') ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DCD') ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DCD') ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DCD') ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DCD') ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DCD') ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_check_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_check_mismatched_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_check_mismatched_vels_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_check_vels_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_check_wrong_vels_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_check_wrong_forces_equality ... ok testing that reading _x, _y, and _z works as expected ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_coordinate_setter_shortcuts ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy_slice('DCD', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_data_presence ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_delete_dt ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_delete_time ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_dimensions_set_box ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_dt_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_forces_remove ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_from_coordinates(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_from_coordinates(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_from_coordinates(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_from_coordinates(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_from_coordinates(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_from_coordinates(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_from_coordinates(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_from_coordinates ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_from_coordinates_mismatch ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_from_coordinates_nodata ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_from_timestep(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_from_timestep(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_from_timestep(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_from_timestep(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_from_timestep(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_from_timestep(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_from_timestep(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_getitem ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_getitem_TE ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_getitem_ndarray ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_getitem_neg ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_getitem_neg_IE ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_getitem_pos_IE ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_getitem_slice ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_getitem_slice2 ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_len ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_n_atoms_presence ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_n_atoms_readonly ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_redefine_dt ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_repr ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_set_triclinic_vectors ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_supply_dt ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_supply_time_offset ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_time ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_time_overrides_dt_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_time_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_triclinic_vectors ... ok Check that users can hack in a custom unitcell order ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_unitcell_presence ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_velocities_remove ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_volume ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_wrong_class_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_wrong_frame_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_wrong_n_atoms_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_wrong_pos_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy('DCD', < Timestep 0 with unit cell dimensions [ 0. 0. 0. 90. 90. 90.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy('DCD', < Timestep 0 with unit cell dimensions [ 0. 0. 0. 90. 90. 90.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy('DCD', < Timestep 0 with unit cell dimensions [ 0. 0. 0. 90. 90. 90.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy('DCD', < Timestep 0 with unit cell dimensions [ 0. 0. 0. 90. 90. 90.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDTimestep.test_copy('DCD', < Timestep 0 with unit cell dimensions [ 0. 0. 0. 90. 90. 90.] >) ... ok test reading of triclinic unitcell (Issue 187) for NAMD or new ... ok test writing of triclinic unitcell (Issue 187) for NAMD or new ... ok test_coordinates (testsuite.MDAnalysisTests.coordinates.test_dcd.TestNCDF2DCD) ... ok NCDFReader: Test that DCDWriter correctly writes the CHARMM ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_backwards_stepping(4, 0, -1) ... KNOWNFAIL: Test skipped due to expected failure -------------------- >> begin captured logging << -------------------- MDAnalysis.topology.PSF: DEBUG: PSF file /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/adk.psf: format STANDARD MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: Universe.load_new(): loading /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/adk_dims.dcd... MDAnalysis.topology.PSF: DEBUG: PSF file /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/adk.psf: format STANDARD MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: Universe.load_new(): loading /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/adk_dims.dcd... --------------------- >> end captured logging << --------------------- testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_backwards_stepping(5, 0, -2) ... KNOWNFAIL: Test skipped due to expected failure -------------------- >> begin captured logging << -------------------- MDAnalysis.topology.PSF: DEBUG: PSF file /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/adk.psf: format STANDARD MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: Universe.load_new(): loading /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/adk_dims.dcd... MDAnalysis.topology.PSF: DEBUG: PSF file /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/adk.psf: format STANDARD MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: Universe.load_new(): loading /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/adk_dims.dcd... --------------------- >> end captured logging << --------------------- testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_backwards_stepping(5, 0, -4) ... KNOWNFAIL: Test skipped due to expected failure -------------------- >> begin captured logging << -------------------- MDAnalysis.topology.PSF: DEBUG: PSF file /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/adk.psf: format STANDARD MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: Universe.load_new(): loading /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/adk_dims.dcd... MDAnalysis.topology.PSF: DEBUG: PSF file /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/adk.psf: format STANDARD MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: Universe.load_new(): loading /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/adk_dims.dcd... --------------------- >> end captured logging << --------------------- Test for Issue 32: 0-size dcds lead to a segfault: now caught with ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigMinimal.test_forces ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigMinimal.test_positions ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigMinimal.test_read_unitcell ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigMinimal.test_velocities ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigOrder.test_forces ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigOrder.test_positions ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigOrder.test_read_unitcell ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigOrder.test_velocities ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigReader.test_forces ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigReader.test_positions ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigReader.test_read ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigReader.test_read_unitcell ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigReader.test_velocities ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigReader2.test_for ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigReader2.test_names ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigReader2.test_number ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigReader2.test_pos ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigReader2.test_vel ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigReaderMinimal2.test_for ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigReaderMinimal2.test_names ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigReaderMinimal2.test_number ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigReaderMinimal2.test_pos ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestConfigReaderMinimal2.test_vel ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistory.test_force ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistory.test_getting ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistory.test_len ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.test_DCDReader_set_dt ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistory.test_position ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistory.test_slicing ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistory.test_unitcell ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistory.test_slicing_2 ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistoryMinimal.test_force ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistoryMinimal.test_getting ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistoryMinimal.test_len ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistory.test_velocity ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistoryMinimal.test_slicing ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistoryMinimal.test_position ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistoryMinimal.test_unitcell ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistoryMinimal.test_slicing_2 ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistoryMinimal.test_velocity ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistoryOrder.test_force ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistoryOrder.test_getting ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistoryOrder.test_len ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistoryOrder.test_position ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistoryOrder.test_slicing ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistoryOrder.test_slicing_2 ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistoryOrder.test_unitcell ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_allocate_forces ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_allocate_velocities ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyHistoryOrder.test_velocity ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_bad_copy_slice(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_bad_copy_slice(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_bad_copy_slice(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_bad_copy_slice(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_bad_copy_slice(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_bad_copy_slice(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_bad_copy_slice(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_change_dt ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_check_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_check_mismatched_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_check_mismatched_vels_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_check_vels_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_check_wrong_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_check_wrong_vels_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DLPoly') ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DLPoly') ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DLPoly') ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DLPoly') ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DLPoly') ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DLPoly') ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DLPoly') ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_coordinate_setter_shortcuts ... ok testing that reading _x, _y, and _z works as expected ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_data_presence ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_delete_dt ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_delete_time ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_dimensions_set_box ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_dt_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_forces_remove ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_from_coordinates(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_from_coordinates(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_from_coordinates(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_from_coordinates(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_from_coordinates(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_from_coordinates(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_from_coordinates(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_from_coordinates ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_from_coordinates_mismatch ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_from_coordinates_nodata ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_from_timestep(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_from_timestep(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_from_timestep(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_from_timestep(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_from_timestep(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_from_timestep(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_from_timestep(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_getitem ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_getitem_TE ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_getitem_ndarray ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_getitem_neg ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_getitem_neg_IE ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_getitem_pos_IE ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_getitem_slice ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_getitem_slice2 ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_len ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_n_atoms_presence ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_n_atoms_readonly ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_redefine_dt ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_repr ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_set_triclinic_vectors ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_supply_dt ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_supply_time_offset ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_copy_slice('DLPoly', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_time ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_time_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_time_overrides_dt_with_offset ... ok test_set_all_format_tuples (testsuite.MDAnalysisTests.coordinates.test_chainreader.TestChainReaderFormats) ... ok test_set_all_formats (testsuite.MDAnalysisTests.coordinates.test_chainreader.TestChainReaderFormats) ... ok test_set_one_format_tuple (testsuite.MDAnalysisTests.coordinates.test_chainreader.TestChainReaderFormats) ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_triclinic_vectors ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_unitcell_presence ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_wrong_class_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_volume ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_wrong_frame_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_velocities_remove ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_wrong_n_atoms_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dlpoly.TestDLPolyTimestep.test_wrong_pos_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_allocate_forces ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_allocate_velocities ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_bad_copy_slice(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_bad_copy_slice(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_bad_copy_slice(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_bad_copy_slice(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_bad_copy_slice(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_bad_copy_slice(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_bad_copy_slice(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_change_dt ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_check_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_check_mismatched_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_check_mismatched_vels_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_check_vels_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_check_wrong_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_check_wrong_vels_equality ... ok testing that reading _x, _y, and _z works as expected ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_coordinate_setter_shortcuts ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DMS') ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DMS') ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DMS') ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DMS') ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DMS') ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DMS') ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on DMS') ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy_slice('DMS', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_data_presence ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_delete_dt ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_delete_time ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_dimensions_set_box ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_dt_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_forces_remove ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_from_coordinates(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_from_coordinates(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_from_coordinates(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_from_coordinates(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_from_coordinates(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_from_coordinates(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_from_coordinates(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_from_coordinates ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_from_coordinates_mismatch ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_from_coordinates_nodata ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_from_timestep(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_from_timestep(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_from_timestep(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_from_timestep(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_from_timestep(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_from_timestep(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_from_timestep(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_getitem ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_getitem_TE ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_getitem_ndarray ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_getitem_neg ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_getitem_neg_IE ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_getitem_pos_IE ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_getitem_slice ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_getitem_slice2 ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_len ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_n_atoms_presence ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_n_atoms_readonly ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_redefine_dt ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_repr ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_set_triclinic_vectors ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_supply_dt ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_supply_time_offset ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_time ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_time_overrides_dt_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_time_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_triclinic_vectors ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_unitcell_presence ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_velocities_remove ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_volume ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_wrong_class_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_wrong_frame_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_wrong_n_atoms_equality ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_wrong_pos_equality ... ok testsuite.MDAnalysisTests.coordinates.test_gms.TestGMSReader.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy('DMS', < Timestep 0 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy('DMS', < Timestep 0 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy('DMS', < Timestep 0 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy('DMS', < Timestep 0 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSTimestep.test_copy('DMS', < Timestep 0 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gms.TestGMSReader.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_gms.TestGMSReader.test_random_access ... ok testsuite.MDAnalysisTests.coordinates.test_gms.TestGMSReader.test_next ... ok testsuite.MDAnalysisTests.coordinates.test_gms.TestGMSReader.test_rewind ... ok testsuite.MDAnalysisTests.coordinates.test_gms.TestGMSReader.test_step5distances ... ok testsuite.MDAnalysisTests.coordinates.test_gms.TestGMSReaderASS.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_gms.TestGMSReaderASS.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_gms.TestGMSReaderASS.test_next ... ok testsuite.MDAnalysisTests.coordinates.test_gms.TestGMSReaderASS.test_random_access ... ok testsuite.MDAnalysisTests.coordinates.test_gms.TestGMSReaderASS.test_step5distances ... ok testsuite.MDAnalysisTests.coordinates.test_gms.TestGMSReaderASS.test_rewind ... ok testsuite.MDAnalysisTests.coordinates.test_gms.TestGMSReaderSO.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_gms.TestGMSReaderSO.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_gms.TestGMSReaderSO.test_next ... ok testsuite.MDAnalysisTests.coordinates.test_gms.TestGMSReaderSO.test_random_access ... ok testsuite.MDAnalysisTests.coordinates.test_gms.TestGMSReaderSO.test_rewind ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_add_same_auxname_raises_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_changing_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_gms.TestGMSReaderSO.test_step5distances ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_double_close ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_first_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_first_frame ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_get_aux_attribute ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_get_writer_1 ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_get_writer_2 ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_iter_as_aux_cutoff ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_iter_auxiliary ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_reload_auxiliaries_from_description ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_remove_auxiliary ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_remove_nonexistant_auxiliary_raises_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_total_time ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_stop_iter ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_ts_dt_matches_reader ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Writer.test_no_container ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Writer.test_write_different_box ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Reader.test_volume ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Writer.test_write_none ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Writer.test_write_not_changing_ts ... ok test_OtherWriter (testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDWriter_Issue59) ... ok Test writing of XTC to DCD (Issue 59) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Writer.test_write_trajectory_timestep ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Writer.test_write_selection ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Writer.test_write_trajectory_atomgroup ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROBZ2Writer.test_write_trajectory_universe ... ok test_frame (testsuite.MDAnalysisTests.coordinates.test_chainreader.TestChainReader) ... ok test_frame_numbering (testsuite.MDAnalysisTests.coordinates.test_chainreader.TestChainReader) ... ok test_full_slice (testsuite.MDAnalysisTests.coordinates.test_chainreader.TestChainReader) ... ok test_iteration (testsuite.MDAnalysisTests.coordinates.test_chainreader.TestChainReader) ... ok test_jump_lastframe_trajectory (testsuite.MDAnalysisTests.coordinates.test_chainreader.TestChainReader) ... ok test_n_atoms (testsuite.MDAnalysisTests.coordinates.test_chainreader.TestChainReader) ... ok test_n_frames (testsuite.MDAnalysisTests.coordinates.test_chainreader.TestChainReader) ... ok test_next_trajectory (testsuite.MDAnalysisTests.coordinates.test_chainreader.TestChainReader) ... ok test_slice_trajectory (testsuite.MDAnalysisTests.coordinates.test_chainreader.TestChainReader) ... ok test_time (testsuite.MDAnalysisTests.coordinates.test_chainreader.TestChainReader) ... ok test that ChainReader written dcd (containing crds) is correct ... ok test_Angle (testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDCorrel) ... ok test_Atom (testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDCorrel) ... ok test_Atom_slicing (testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDCorrel) ... ok test_Bonds (testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDCorrel) ... ok test_CA_COMeqCOG (testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDCorrel) ... ok test_CenterOfGeometry (testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDCorrel) ... ok test_CenterOfMass (testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDCorrel) ... ok test_Dihedral (testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDCorrel) ... ok test_clear (testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDCorrel) ... ok test_correl (testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDCorrel) ... ok test_scalarDistance (testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDCorrel) ... ok test_coords_atom_0 (testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSReader) ... ok test_frame (testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSReader) ... ok test_frame_index_0 (testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSReader) ... ok test_frame_index_1_raises_IndexError (testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSReader) ... ok test_global_cell (testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSReader) ... ok test_n_frames (testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSReader) ... ok test_number_of_coords (testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSReader) ... ok test_time (testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSReader) ... ok test_velocities (testsuite.MDAnalysisTests.coordinates.test_dms.TestDMSReader) ... ok test_OtherWriter (testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDWriter) ... ok test_dt (testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDWriter) ... ok test_single_frame (testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDWriter) ... ok test_with_statement (testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDWriter) ... ok Test writing DCD trajectories (Issue 50) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROLargeWriter.test_write_different_box ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROLargeWriter.test_no_container ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROLargeWriter.test_write_none ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_timeseries_slicing(0, 1, 1) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_timeseries_slicing(1, 1, 1) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_timeseries_slicing(1, 2, 1) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_timeseries_slicing(1, 2, 2) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_timeseries_slicing(1, 4, 2) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_timeseries_slicing(1, 4, 4) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_timeseries_slicing(0, 5, 5) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_timeseries_slicing(3, 5, 1) ... ok testsuite.MDAnalysisTests.coordinates.test_dcd.TestDCDReader.test_timeseries_slicing(None, None, None) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_add_same_auxname_raises_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_changing_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_double_close ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_first_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_first_frame ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_flag_convert_lengths ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_full_slice ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_get_aux_attribute ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_get_writer_1 ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_get_writer_2 ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_iter_as_aux_cutoff ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_iter_auxiliary ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_reload_auxiliaries_from_description ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_remove_auxiliary ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_remove_nonexistant_auxiliary_raises_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_stop_iter ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_time ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_total_time ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_ts_dt_matches_reader ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReader.test_volume ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_add_same_auxname_raises_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_changing_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_double_close ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_first_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_first_frame ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_get_aux_attribute ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_get_writer_1 ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_get_writer_2 ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_iter_as_aux_cutoff ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_iter_auxiliary ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_reload_auxiliaries_from_description ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_remove_auxiliary ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_remove_nonexistant_auxiliary_raises_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_stop_iter ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_total_time ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_ts_dt_matches_reader ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderIncompleteVelocities.test_volume ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_add_same_auxname_raises_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_changing_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_double_close ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_first_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_first_frame ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_get_aux_attribute ... ok test_ces (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_ces_convergence (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_ces_error_estimation (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_ces_error_estimation_ensemble_bootstrap (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_ces_to_self (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_dres (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_dres_convergence (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_dres_error_estimation (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_dres_to_self (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_dres_without_superimposition (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_ensemble_superimposition (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_ensemble_superimposition_to_reference_non_weighted (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_hes (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_hes_align (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_hes_custom_weights (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_hes_error_estimation (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_hes_to_self (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_parallel_calculation (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_rmsd_matrix_with_superimposition (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_rmsd_matrix_with_superimposition_custom_weights (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_rmsd_matrix_without_superimposition (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok test_triangular_matrix (testsuite.MDAnalysisTests.analysis.test_encore.TestEncore) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_get_writer_1 ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_get_writer_2 ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_iter_auxiliary ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_iter_as_aux_cutoff ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_remove_auxiliary ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_reload_auxiliaries_from_description ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_remove_nonexistant_auxiliary_raises_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_stop_iter ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_total_time ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_ts_dt_matches_reader ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversion.test_volume ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversionOld.test_distances ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversionOld.test_coordinates ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROLargeWriter.test_write_not_changing_ts ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversionOld.test_unitcell ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderNoConversionOld.test_volume ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderOld.test_coordinates ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROLargeWriter.test_write_selection ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderOld.test_distances ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderOld.test_flag_convert_lengths ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_allocate_forces ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_allocate_velocities ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_bad_copy_slice(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_bad_copy_slice(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_bad_copy_slice(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_bad_copy_slice(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_bad_copy_slice(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_bad_copy_slice(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_bad_copy_slice(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_change_dt ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on GRO') ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on GRO') ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on GRO') ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on GRO') ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on GRO') ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on GRO') ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on GRO') ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_check_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_check_mismatched_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_check_mismatched_vels_equality ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_check_vels_equality ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_check_wrong_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_check_wrong_vels_equality ... ok testing that reading _x, _y, and _z works as expected ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_coordinate_setter_shortcuts ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderOld.test_load_gro ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROLargeWriter.test_write_trajectory_timestep ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_data_presence ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_delete_dt ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_delete_time ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_dimensions_set_box ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_dt_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_forces_remove ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy_slice('GRO', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_from_coordinates(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_from_coordinates(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_from_coordinates(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_from_coordinates(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_from_coordinates(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_from_coordinates(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_from_coordinates(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_from_coordinates ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_from_coordinates_mismatch ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_from_coordinates_nodata ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_getitem ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_getitem_TE ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_from_timestep(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_from_timestep(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_from_timestep(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_from_timestep(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_from_timestep(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_from_timestep(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_from_timestep(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_getitem_neg ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_getitem_ndarray ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_getitem_neg_IE ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_getitem_pos_IE ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_getitem_slice ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_getitem_slice2 ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_len ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_n_atoms_readonly ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_n_atoms_presence ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_redefine_dt ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_repr ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_set_triclinic_vectors ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_supply_time_offset ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_supply_dt ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_time ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_time_overrides_dt_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_time_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_unitcell_presence ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_triclinic_vectors ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_unitcell_set2 ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_velocities_remove ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_volume ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_wrong_class_equality ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_wrong_frame_equality ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_wrong_n_atoms_equality ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_wrong_pos_equality ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderOld.test_unitcell ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROReaderOld.test_selection ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriter.test_no_container ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriter.test_write_different_box ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriter.test_write_no_resids ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriter.test_write_no_resnames ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriter.test_write_none ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriter.test_write_not_changing_ts ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriter.test_write_selection ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy('GRO', < Timestep 0 with unit cell dimensions [ 80.01700592 80.01700592 80.01702881 60.00000381 60.00000381 90. ] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy('GRO', < Timestep 0 with unit cell dimensions [ 80.01700592 80.01700592 80.01702881 60.00000381 60.00000381 90. ] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy('GRO', < Timestep 0 with unit cell dimensions [ 80.01700592 80.01700592 80.01702881 60.00000381 60.00000381 90. ] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy('GRO', < Timestep 0 with unit cell dimensions [ 80.01700592 80.01700592 80.01702881 60.00000381 60.00000381 90. ] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROTimestep.test_copy('GRO', < Timestep 0 with unit cell dimensions [ 80.01700592 80.01700592 80.01702881 60.00000381 60.00000381 90. ] >) ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriter.test_write_trajectory_atomgroup ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriter.test_write_trajectory_timestep ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriter.test_write_trajectory_universe ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriter.test_write_velocities ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriter.test_writer_no_atom_names ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriterIncompleteVelocities.test_no_container ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriterIncompleteVelocities.test_write_different_box ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriterIncompleteVelocities.test_write_none ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriterIncompleteVelocities.test_write_not_changing_ts ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriterIncompleteVelocities.test_write_selection ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriterIncompleteVelocities.test_write_trajectory_timestep ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriterIncompleteVelocities.test_write_trajectory_atomgroup ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriterNoConversion.test_no_container ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriterIncompleteVelocities.test_write_trajectory_universe ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriterNoConversion.test_write_different_box ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriterNoConversion.test_write_none ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriterNoConversion.test_write_not_changing_ts ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriterNoConversion.test_write_selection ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriterNoConversion.test_write_trajectory_timestep ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriterNoConversion.test_write_trajectory_atomgroup ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROWriterNoConversion.test_write_trajectory_universe ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestDataWriterErrors.test_write_no_masses ... ok testsuite.MDAnalysisTests.coordinates.test_gro.test_growriter_resid_truncation ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestDataWriterErrors.test_write_no_types ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestDataWriterErrors.test_write_non_numerical_types ... ok Test that illegal GRO coordinates (x > 9999.9995 nm) are caught ... ok Test that illegal GRO coordinates (x > 9999.9995 nm) also ... ok Test that illegal GRO coordinates (x <= -999.9995 nm) are caught ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDATAWriter_cnt.test_Writer_dimensions ... ok testsuite.MDAnalysisTests.analysis.test_gnm.TestGNM.test_closeContactGNMAnalysis ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDATAWriter_hyd.test_Writer_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDATAWriter_hyd.test_Writer_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDATAWriter_mini.test_Writer_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDATAWriter_mini.test_Writer_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROLargeWriter.test_write_trajectory_atomgroup ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDCDReader.test_LAMMPSDCDReader_set_dt ... ok Ensure large residue number truncation for ... ok testsuite.MDAnalysisTests.analysis.test_gnm.TestGNM.test_closeContactGNMAnalysis_weights_None ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDCDReader.test_Reader_is_LAMMPS ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDATAWriter_data_partial.test_Writer_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDCDReader.test_Timestep_time ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDCDReader.test_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_gro.TestGROLargeWriter.test_write_trajectory_universe ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDCDReader.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDCDReader.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDATAWriter_data_partial.test_Writer_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDCDReader.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDCDWriterClass.test_Writer_is_LAMMPS ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDCDWriterClass.test_open ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDCDWriterClass.test_wrong_time_unit ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDCDWriterClass.test_wrong_unit ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLammpsDataMini_Coords.test_coords ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLammpsDataMini_Coords.test_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLammpsDataMini_Coords.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLammpsDataMini_Coords.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLammpsDataMini_Coords.test_seek ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLammpsDataMini_Coords.test_seek_2 ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLammpsDataMini_Coords.test_singleframe ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLammpsDataMini_Coords.test_velos ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLammpsDataTriclinic.test_triclinicness ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDCDWriter.test_OtherWriter_is_LAMMPS ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDCDWriter.test_Writer_is_LAMMPS ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDCDReader.test_wrong_time_unit ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDCDReader.test_wrong_unit ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDCDWriter.test_OtherWriter ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDCDWriter.test_Writer ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLammpsData_Coords.test_coords ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLammpsData_Coords.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.test_datareader_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLammpsData_Coords.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLammpsData_Coords.test_seek ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLammpsData_Coords.test_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLammpsData_Coords.test_seek_2 ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLammpsData_Coords.test_singleframe ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_changing_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_double_close ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_add_same_auxname_raises_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_extract_array_acf ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_default_memory_layout ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_extract_array_afc ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLammpsData_Coords.test_velos ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_extract_array_caf ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_extract_array_cfa ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_extract_array_fac ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_extract_array_fca ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_first_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_first_frame ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_filename_transefer_to_memory ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_filename_array ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_frame_jump ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_get_aux_attribute ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_float32 ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_get_writer_1 ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_get_writer_2 ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_go_over_last_frame ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDATAWriter_cnt.test_Writer_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_iter_as_aux_cutoff ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_iter_as_aux_highf ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_iter_as_aux_lowf ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_iter_auxiliary ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_last_frame ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_iteration ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_next_gives_second_frame ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_remove_auxiliary ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDATAWriter_data.test_Writer_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_remove_nonexistant_auxiliary_raises_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_reload_auxiliaries_from_description ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_rename_aux ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_reopen ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_repr ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_stop_iter ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_timeseries_noview ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_timeseries_skip1 ... ok testsuite.MDAnalysisTests.coordinates.test_mmtf.TestMMTFReader.test_forces ... ok testsuite.MDAnalysisTests.coordinates.test_mmtf.TestMMTFReader.test_len ... ok testsuite.MDAnalysisTests.coordinates.test_mmtf.TestMMTFReader.test_read_frame_size ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_timeseries_subarray_view ... ok testsuite.MDAnalysisTests.coordinates.test_mmtf.TestMMTFReader.test_read_positions ... ok testsuite.MDAnalysisTests.coordinates.test_mmtf.TestMMTFReader.test_velocities ... ok testsuite.MDAnalysisTests.coordinates.test_mmtf.TestMMTFReaderGZ.test_forces ... ok testsuite.MDAnalysisTests.coordinates.test_mmtf.TestMMTFReaderGZ.test_len ... ok testsuite.MDAnalysisTests.coordinates.test_mmtf.TestMMTFReaderGZ.test_read_frame_size ... ok testsuite.MDAnalysisTests.coordinates.test_mmtf.TestMMTFReaderGZ.test_read_positions ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_timeseries_skip10 ... ok testsuite.MDAnalysisTests.coordinates.test_mmtf.TestMMTFReaderGZ.test_velocities ... ok testsuite.MDAnalysisTests.coordinates.test_mol2.TestMOL2NoSubstructure.test_load ... ok testsuite.MDAnalysisTests.coordinates.test_mol2.TestMOL2NoSubstructure.test_universe ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_timeseries_view ... ok testsuite.MDAnalysisTests.coordinates.test_mol2.TestMOL2NoSubstructure.test_write_nostructure ... ok testsuite.MDAnalysisTests.coordinates.test_mol2.test_mol2_write_NIE ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_timeseries_view_from_select_all ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_timeseries_view_from_universe_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader.test_amber_proteinselection ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader.test_get_writer ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader.test_get_writer_custom_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader.test_initial_frame_is_0 ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader.test_full_slice ... ok test_jump_lastframe_traj (testsuite.MDAnalysisTests.coordinates.test_mol2.TestMol2_traj) ... ok test_jump_traj (testsuite.MDAnalysisTests.coordinates.test_mol2.TestMol2_traj) ... ok test_n_frames (testsuite.MDAnalysisTests.coordinates.test_mol2.TestMol2_traj) ... ok test_next_traj (testsuite.MDAnalysisTests.coordinates.test_mol2.TestMol2_traj) ... ok test_reverse_traj (testsuite.MDAnalysisTests.coordinates.test_mol2.TestMol2_traj) ... ok test_rewind_traj (testsuite.MDAnalysisTests.coordinates.test_mol2.TestMol2_traj) ... ok test_slice_traj (testsuite.MDAnalysisTests.coordinates.test_mol2.TestMol2_traj) ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader.test_load_prm ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader.test_metadata ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader.test_periodic ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader.test_read_on_closed ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader.test_random_access ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader.test_rewind ... ok Test that coordinate arrays are filled as soon as the trajectory ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader.test_slice_iteration ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader.test_wrong_natoms ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader.test_sum_centres_of_geometry ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_total_time ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_ts_dt_matches_reader ... ok test_dt (testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader2) ... ok Check forces on first frame ... ok Check forces on second frame ... ok Check positions on first frame ... ok Check positions on second frame ... ok Check time on first frame ... ok Check time on second frame ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2.test_amber_proteinselection ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2.test_full_slice ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2.test_get_writer ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2.test_get_writer_custom_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2.test_load_prm ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2.test_metadata ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2.test_initial_frame_is_0 ... ok testsuite.MDAnalysisTests.coordinates.test_memory.TestMemoryReader.test_volume ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2.test_periodic ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2.test_read_on_closed ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterErrors.test_no_ts ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterErrors.test_wrong_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterErrors.test_zero_atoms_VE ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2.test_random_access ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2.test_rewind ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNetCDFImport.test_import_netcdfreader ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNetCDFImport.test_import_netcdfwriter ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2.test_slice_iteration ... ok test_pos (testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterVelsForces) ... ok test_pos_force (testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterVelsForces) ... ok test_pos_vel (testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterVelsForces) ... ok test_pos_vel_force (testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterVelsForces) ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2.test_wrong_natoms ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestIncompletePDB.test_coords ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestIncompletePDB.test_dims ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestIncompletePDB.test_names ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestIncompletePDB.test_natoms ... ok Test that coordinate arrays are filled as soon as the trajectory ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestIncompletePDB.test_reading_trajectory ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestIncompletePDB.test_residues ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestIncompletePDB.test_resnames ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestCrystModelOrder.test_order('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/cryst_then_model.pdb',) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestCrystModelOrder.test_order('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/cryst_then_model.pdb',) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestCrystModelOrder.test_order('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/cryst_then_model.pdb',) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestCrystModelOrder.test_order('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/cryst_then_model.pdb.bz2',) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestCrystModelOrder.test_order('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/cryst_then_model.pdb.bz2',) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestCrystModelOrder.test_order('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/cryst_then_model.pdb.bz2',) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestCrystModelOrder.test_order('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/cryst_then_model.pdb.gz',) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestCrystModelOrder.test_order('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/cryst_then_model.pdb.gz',) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestCrystModelOrder.test_order('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/cryst_then_model.pdb.gz',) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestCrystModelOrder.test_order('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/model_then_cryst.pdb',) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestCrystModelOrder.test_order('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/model_then_cryst.pdb',) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestCrystModelOrder.test_order('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/model_then_cryst.pdb',) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestCrystModelOrder.test_order('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/model_then_cryst.pdb.bz2',) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestCrystModelOrder.test_order('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/model_then_cryst.pdb.bz2',) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestCrystModelOrder.test_order('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/model_then_cryst.pdb.bz2',) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestCrystModelOrder.test_order('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/model_then_cryst.pdb.gz',) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestCrystModelOrder.test_order('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/model_then_cryst.pdb.gz',) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestCrystModelOrder.test_order('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/model_then_cryst.pdb.gz',) ... ok testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2.test_sum_centres_of_geometry ... ok Test that atom numbers are truncated for large ... ok test_coordinates (testsuite.MDAnalysisTests.coordinates.test_pdb.TestExtendedPDBReader) ... ok test_distances (testsuite.MDAnalysisTests.coordinates.test_pdb.TestExtendedPDBReader) ... ok testing that accessing universe.trajectory.dt gives 1.0 ... ok test_frame (testsuite.MDAnalysisTests.coordinates.test_pdb.TestExtendedPDBReader) ... ok test_frame_index_0 (testsuite.MDAnalysisTests.coordinates.test_pdb.TestExtendedPDBReader) ... ok test_frame_index_1_raises_IndexError (testsuite.MDAnalysisTests.coordinates.test_pdb.TestExtendedPDBReader) ... ok test_full_slice (testsuite.MDAnalysisTests.coordinates.test_pdb.TestExtendedPDBReader) ... ok test_last_slice (testsuite.MDAnalysisTests.coordinates.test_pdb.TestExtendedPDBReader) ... ok test_load_file (testsuite.MDAnalysisTests.coordinates.test_pdb.TestExtendedPDBReader) ... ok test_long_resSeq (testsuite.MDAnalysisTests.coordinates.test_pdb.TestExtendedPDBReader) ... ok test_n_atoms (testsuite.MDAnalysisTests.coordinates.test_pdb.TestExtendedPDBReader) ... ok test_n_frames (testsuite.MDAnalysisTests.coordinates.test_pdb.TestExtendedPDBReader) ... ok test_numres (testsuite.MDAnalysisTests.coordinates.test_pdb.TestExtendedPDBReader) ... ok test_time (testsuite.MDAnalysisTests.coordinates.test_pdb.TestExtendedPDBReader) ... ok test_broken_molecule (testsuite.MDAnalysisTests.coordinates.test_mol2.TestMol2) ... ok test_read (testsuite.MDAnalysisTests.coordinates.test_mol2.TestMol2) ... ok test_write (testsuite.MDAnalysisTests.coordinates.test_mol2.TestMol2) ... ok test_write_in_loop (testsuite.MDAnalysisTests.coordinates.test_mol2.TestMol2) ... ok test_write_selection (testsuite.MDAnalysisTests.coordinates.test_mol2.TestMol2) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBXLSerial.test_load ... ok testsuite.MDAnalysisTests.coordinates.test_null.TestNullWriter.test_NullWriter ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBXLSerial.test_serials ... ok test_ENT (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReader) ... ok test_coordinates (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReader) ... ok test_dimensions (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReader) ... ok test_distances (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReader) ... ok testing that accessing universe.trajectory.dt gives 1.0 ... ok test_frame (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReader) ... ok test_frame_index_0 (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReader) ... ok test_frame_index_1_raises_IndexError (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReader) ... ok test_full_slice (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReader) ... ok test_last_slice (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReader) ... ok test_load_file (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReader) ... ok test_n_atoms (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReader) ... ok test_n_frames (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReader) ... ok test_numres (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReader) ... ok test_time (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReader) ... ok test_uses_PDBReader (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReader) ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestWriterAlignments.test_atomname_alignment ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.TestWriterAlignments.test_atomtype_alignment ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.test_deduce_PDB_atom_name(Atom(resname='ASP', name='CA'), ' CA ') ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.test_deduce_PDB_atom_name(Atom(resname='GLU', name='OE1'), ' OE1') ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.test_deduce_PDB_atom_name(Atom(resname='MSE', name='SE'), 'SE ') ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.test_deduce_PDB_atom_name(Atom(resname='CA', name='CA'), 'CA ') ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.test_deduce_PDB_atom_name(Atom(resname='HDD', name='FE'), 'FE ') ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.test_deduce_PDB_atom_name(Atom(resname='PLC', name='P'), ' P ') ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.test_standalone_pdb ... ok testsuite.MDAnalysisTests.coordinates.test_pdb.test_write_pdb_zero_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_pdbqt.TestPDBQT.test_backbone ... ok testsuite.MDAnalysisTests.coordinates.test_pdbqt.TestPDBQT.test_frame ... ok Modify occupancies, write out the file and check ... ok testsuite.MDAnalysisTests.coordinates.test_pdbqt.TestPDBQT.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_pdbqt.TestPDBQT.test_protein ... ok test KDTree-based distance search around query atoms ... ok testsuite.MDAnalysisTests.coordinates.test_pdbqt.TestPDBQT.test_time ... ok testsuite.MDAnalysisTests.coordinates.test_pdbqt.TestPDBQT.test_segid ... ok testsuite.MDAnalysisTests.coordinates.test_pdbqt.TestPDBQTWriter.test_get_writer ... ok testsuite.MDAnalysisTests.coordinates.test_pdbqt.TestPDBQTWriter.test_roundtrip_formatting ... ok testsuite.MDAnalysisTests.coordinates.test_pdbqt.TestPDBQTWriter.test_write_no_chainids_with_segids ... ok testsuite.MDAnalysisTests.coordinates.test_pdbqt.TestPDBQTWriter.test_roundtrip_writing_coords ... ok testsuite.MDAnalysisTests.coordinates.test_pdbqt.TestPDBQTWriter.test_write_no_charges ... ok testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRWriter.test_timestep_not_modified_by_writer ... ok testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRWriter.test_total_charge ... ok testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRWriter.test_write_withChainID ... ok test_OtherWriter (testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriter) ... ok test_TRR2NCDF (testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriter) ... ok test to write NCDF from AtomGroup (Issue 116) ... ok test_write_trajectory (testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriter) ... ok testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRWriterMissingAttrs.test_no_charges_writing ... ok testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRWriterMissingAttrs.test_no_names_writing ... ok testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRWriterMissingAttrs.test_no_radii_writing ... ok testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRWriterMissingAttrs.test_no_resnames_writing ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_array_TE ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_bool_slice([True, False, True, False, True, False, True, False, True, False],) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_bool_slice(array([ True, False, True, False, True, False, True, False, True, False], dtype=bool),) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_bool_slice([True, True, False, False, True, True, False, True, False, True],) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_bool_slice(array([ True, True, False, False, True, True, False, True, False, True], dtype=bool),) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_bool_slice([True, True, True, True, True, True, True, True, True, True],) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_bool_slice(array([ True, True, True, True, True, True, True, True, True, True], dtype=bool),) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_bool_slice([False, False, False, False, False, False, False, False, False, False],) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_bool_slice(array([False, False, False, False, False, False, False, False, False, False], dtype=bool),) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_close ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_context ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_getitem_list_ints([0, 1, 4, 5],) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_getitem_list_ints(array([0, 1, 4, 5]),) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_getitem_list_ints([5, 1, 6, 2, 7, 3, 8],) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_getitem_list_ints(array([5, 1, 6, 2, 7, 3, 8]),) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_getitem_list_ints([0, 1, 1, 1, 0, 0, 2, 3, 4],) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_getitem_list_ints(array([0, 1, 1, 1, 0, 0, 2, 3, 4]),) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_len ... ok testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRWriter.test_writer_noChainID ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_list_TE ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_raises_StopIteration ... ok Test that Reader has the required attributes ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_rewind ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slice_TE_1 ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slice_VE_1 ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestSingleFrameReader.test_close ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestSingleFrameReader.test_context ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestSingleFrameReader.test_getitem ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestSingleFrameReader.test_getitem_2 ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(None, None, None) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(None, 5, None) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(2, None, None) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(2, 5, None) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(None, None, 2) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(None, None, -1) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(0, 10, 1) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(0, 10, 2) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(None, 20, None) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(None, 20, 2) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(0, 5, 2) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(5, None, -1) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(None, 5, -1) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(100, 10, 1) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(-10, None, 1) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(100, None, -1) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(100, 5, -20) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(5, 1, 1) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(1, 5, -1) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(-100, None, None) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(100, None, None) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestMultiFrameReader.test_slices(-2, 10, -2) ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestSingleFrameReader.test_getitem_IE ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestSingleFrameReader.test_getitem_IE_2 ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestSingleFrameReader.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestSingleFrameReader.test_next ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestSingleFrameReader.test_len ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestSingleFrameReader.test_raises_StopIteration ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestSingleFrameReader.test_read_frame ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestSingleFrameReader.test_reopen ... ok Test that Reader has the required attributes ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestSingleFrameReader.test_rewind ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestSingleFrameReader.test_slice_1 ... ok testsuite.MDAnalysisTests.coordinates.test_reader_api.TestSingleFrameReader.test_slice_2 ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_allocate_velocities ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_allocate_forces ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_bad_copy_slice(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_bad_copy_slice(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_bad_copy_slice(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_bad_copy_slice(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_bad_copy_slice(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_bad_copy_slice(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_bad_copy_slice(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_change_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_check_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_check_mismatched_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_check_mismatched_vels_equality ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_check_vels_equality ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_check_wrong_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_check_wrong_vels_equality ... ok testing that reading _x, _y, and _z works as expected ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_coordinate_setter_shortcuts ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on base') ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on base') ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on base') ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on base') ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on base') ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on base') ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on base') ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_data_presence ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_delete_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_delete_time ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_dimensions ... ok test_OtherWriter (testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterTZ2) ... ok test_TRR2NCDF (testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterTZ2) ... ok test to write NCDF from AtomGroup (Issue 116) ... ok test_write_trajectory (testsuite.MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterTZ2) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_dimensions_set_box ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_dt_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_forces_remove ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_from_coordinates_mismatch ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_from_coordinates_nodata ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_from_coordinates(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_from_coordinates(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_from_coordinates(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_from_coordinates(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_from_coordinates(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_from_coordinates(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_from_coordinates(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_from_coordinates ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_getitem ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_getitem_TE ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_from_timestep(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_from_timestep(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_from_timestep(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_from_timestep(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_from_timestep(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_from_timestep(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_from_timestep(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_getitem_neg ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_getitem_ndarray ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_copy_slice('base', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_getitem_pos_IE ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_getitem_neg_IE ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_getitem_slice ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_getitem_slice2 ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_len ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_n_atoms_presence ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_n_atoms_readonly ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_redefine_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_repr ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_set_triclinic_vectors ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_supply_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_time ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_supply_time_offset ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_time_overrides_dt_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_time_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_triclinic_vectors ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_other_timestep(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, "Failed on ") ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_other_timestep(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, "Failed on ") ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_other_timestep(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, "Failed on ") ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_other_timestep(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, "Failed on ") ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_other_timestep(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, "Failed on ") ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_unitcell_presence ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_velocities_remove ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_volume ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_wrong_class_equality ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_wrong_frame_equality ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_wrong_n_atoms_equality ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestBaseTimestep.test_wrong_pos_equality ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestCRD.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestCRD.test_frame ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestDLPConfig.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestDLPConfig.test_frame ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestDLPHistory.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestDLPHistory.test_frame ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestDMS.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestDCD.test_frame ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestDCD.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestGMS.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestGMS.test_frame ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestDMS.test_frame ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestINPCRD.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestINPCRD.test_frame ... ok test_ArgCACharges (testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRReader) ... ok test_ProNCharges (testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRReader) ... ok test_coordinates (testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRReader) ... ok test_distances (testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRReader) ... ok testing that accessing universe.trajectory.dt gives 1.0 ... ok test_frame (testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRReader) ... ok test_frame_index_0 (testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRReader) ... ok test_frame_index_1_raises_IndexError (testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRReader) ... ok test_full_slice (testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRReader) ... ok test_hydrogenCharges (testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRReader) ... ok test_last_slice (testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRReader) ... ok test_load_file (testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRReader) ... ok test_n_atoms (testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRReader) ... ok test_n_frames (testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRReader) ... ok test_numres (testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRReader) ... ok test_time (testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRReader) ... ok test_total_charge (testsuite.MDAnalysisTests.coordinates.test_pqr.TestPQRReader) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestGRO.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestGRO.test_frame ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestLAMMPS.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestMOL2.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestMOL2.test_frame ... ok test_coordinates (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_CRDReader) ... ok test_distances (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_CRDReader) ... ok testing that accessing universe.trajectory.dt gives 1.0 ... ok test_frame (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_CRDReader) ... ok test_frame_index_0 (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_CRDReader) ... ok test_frame_index_1_raises_IndexError (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_CRDReader) ... ok test_full_slice (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_CRDReader) ... ok test_last_slice (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_CRDReader) ... ok test_load_file (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_CRDReader) ... ok test_n_atoms (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_CRDReader) ... ok test_n_frames (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_CRDReader) ... ok test_numres (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_CRDReader) ... ok test_time (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_CRDReader) ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestLAMMPS.test_frame ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestNCDF.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestNCDF.test_frame ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestPDBQT.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestPDB.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestPDB.test_frame ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestPDBQT.test_frame ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestTRJ.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestTRJ.test_frame ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestPQR.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestPQR.test_frame ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestLAMMPSDCD.test_frame ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestLAMMPSDCD.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestTRZ.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestTRZ.test_frame ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReader.test_amber_proteinselection ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReader.test_full_slice ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReader.test_initial_frame_is_0 ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReader.test_load_prm ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReader.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReader.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReader.test_periodic ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReader.test_random_access ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestTRR.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestTRR.test_frame ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReader.test_rewind ... ok Test that coordinate arrays are filled as soon as the trajectory ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReader.test_read_frame_reopens ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestXTC.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReader.test_sum_centres_of_geometry ... ok testsuite.MDAnalysisTests.coordinates.test_timestep_api.TestXTC.test_frame ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReaderPBC.test_amber_proteinselection ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReaderPBC.test_load_prm ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReaderPBC.test_initial_frame_is_0 ... ok test_ENT (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_PDBReader) ... ok test_coordinates (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_PDBReader) ... ok test_dimensions (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_PDBReader) ... ok test_distances (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_PDBReader) ... ok testing that accessing universe.trajectory.dt gives 1.0 ... ok test_frame (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_PDBReader) ... ok test_frame_index_0 (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_PDBReader) ... ok test_frame_index_1_raises_IndexError (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_PDBReader) ... ok test_full_slice (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_PDBReader) ... ok test_last_slice (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_PDBReader) ... ok test_load_file (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_PDBReader) ... ok test_n_atoms (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_PDBReader) ... ok test_n_frames (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_PDBReader) ... ok test_numres (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_PDBReader) ... ok test_time (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_PDBReader) ... ok test_uses_PDBReader (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPSF_PDBReader) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReaderPBC.test_n_atoms ... ok Test write_all_timesteps() of the multiframe writer (selected frames ... ok test_write_atoms (testsuite.MDAnalysisTests.coordinates.test_pdb.TestMultiPDBWriter) ... ok Test if multiframe writer can write selected frames for an ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReaderPBC.test_periodic ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJReader.test_amber_proteinselection ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJReader.test_full_slice ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJReader.test_initial_frame_is_0 ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJReader.test_load_prm ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJReader.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJReader.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJReader.test_periodic ... ok Test that coordinate arrays are filled as soon as the trajectory ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJReader.test_random_access ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJReader.test_read_frame_reopens ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJReader.test_rewind ... ok Test that coordinate arrays are filled as soon as the trajectory ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_allocate_forces ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_allocate_velocities ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_bad_copy_slice(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_bad_copy_slice(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_bad_copy_slice(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_bad_copy_slice(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_bad_copy_slice(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_bad_copy_slice(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_bad_copy_slice(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJReader.test_sum_centres_of_geometry ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_change_dt ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_check_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_check_mismatched_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_check_mismatched_vels_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_check_vels_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_check_wrong_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_check_wrong_vels_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on TRJ') ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on TRJ') ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on TRJ') ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on TRJ') ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on TRJ') ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on TRJ') ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on TRJ') ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_coordinate_setter_shortcuts ... ok testing that reading _x, _y, and _z works as expected ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReaderPBC.test_rewind ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_data_presence ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_delete_dt ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_delete_time ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_dimensions_set_box ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_dt_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_forces_remove ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_from_coordinates(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_from_coordinates(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_from_coordinates(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_from_coordinates(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_from_coordinates(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_from_coordinates(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_from_coordinates(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_from_coordinates ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_from_coordinates_mismatch ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy('TRJ', < Timestep 0 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy('TRJ', < Timestep 0 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy('TRJ', < Timestep 0 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy('TRJ', < Timestep 0 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy('TRJ', < Timestep 0 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_from_coordinates_nodata ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_getitem ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_getitem_TE ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_getitem_ndarray ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_getitem_neg ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_from_timestep(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_from_timestep(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_from_timestep(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_from_timestep(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_from_timestep(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_from_timestep(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_from_timestep(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_getitem_neg_IE ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_getitem_pos_IE ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_getitem_slice ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_copy_slice('TRJ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_getitem_slice2 ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_len ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_n_atoms_presence ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_n_atoms_readonly ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_redefine_dt ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_set_triclinic_vectors ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_repr ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_supply_time_offset ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_supply_dt ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_time ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_time_overrides_dt_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_time_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_triclinic_vectors ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_unitcell_presence ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_wrong_class_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_velocities_remove ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_volume ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_wrong_frame_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_wrong_n_atoms_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestTRJTimestep.test_wrong_pos_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trj.test_trj_no_natoms ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_allocate_velocities ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_allocate_forces ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_bad_copy_slice(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_bad_copy_slice(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_bad_copy_slice(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_bad_copy_slice(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_bad_copy_slice(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_bad_copy_slice(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_bad_copy_slice(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_change_dt ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_check_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_check_mismatched_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_check_mismatched_vels_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_check_vels_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_check_wrong_forces_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_check_wrong_vels_equality ... ok testing that reading _x, _y, and _z works as expected ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_coordinate_setter_shortcuts ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on TRZ') ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on TRZ') ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on TRZ') ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on TRZ') ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on TRZ') ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on TRZ') ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_check_equal(< Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >, 'Failed on TRZ') ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy_slice('TRZ', < Timestep -1 with unit cell dimensions [ 0. 0. 0. 0. 0. 0.] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_data_presence ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_delete_dt ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_delete_time ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_dimensions_set_box ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_dt_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_forces_remove ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy('TRZ', < Timestep 0 with unit cell dimensions [ 55.42282867 55.42282867 55.42282867 90. 90. 90. ] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy('TRZ', < Timestep 0 with unit cell dimensions [ 55.42282867 55.42282867 55.42282867 90. 90. 90. ] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy('TRZ', < Timestep 0 with unit cell dimensions [ 55.42282867 55.42282867 55.42282867 90. 90. 90. ] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy('TRZ', < Timestep 0 with unit cell dimensions [ 55.42282867 55.42282867 55.42282867 90. 90. 90. ] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_copy('TRZ', < Timestep 0 with unit cell dimensions [ 55.42282867 55.42282867 55.42282867 90. 90. 90. ] >) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_from_coordinates_mismatch ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_from_coordinates_nodata ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_from_coordinates(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_from_coordinates(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_from_coordinates(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_from_coordinates(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_from_coordinates(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_from_coordinates(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_from_coordinates(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_from_coordinates ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_getitem ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_getitem_TE ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_getitem_ndarray ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_from_timestep(True, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_from_timestep(True, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_from_timestep(True, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_from_timestep(True, False, False) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_from_timestep(False, True, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_from_timestep(False, True, False) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_from_timestep(False, False, True) ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_getitem_neg ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_getitem_pos_IE ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_getitem_neg_IE ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_getitem_slice ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_getitem_slice2 ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_len ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_n_atoms_readonly ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_n_atoms_presence ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_redefine_dt ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_repr ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_supply_dt ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_set_triclinic_vectors ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_supply_time_offset ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_time ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_time_overrides_dt_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_time_with_offset ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_triclinic_vectors ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_unitcell_presence ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_velocities_remove ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_volume ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_wrong_class_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_wrong_frame_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_wrong_n_atoms_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZTimestep.test_wrong_pos_equality ... ok testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZWriter2.test_writer_trz_from_other ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReaderPBC.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_writer_registration.TestWriterCreation.test_default_multiframe ... ok testsuite.MDAnalysisTests.coordinates.test_writer_registration.TestWriterCreation.test_multiframe_magic2 ... ok testsuite.MDAnalysisTests.coordinates.test_writer_registration.TestWriterCreation.test_singleframe ... ok testsuite.MDAnalysisTests.coordinates.test_writer_registration.TestWriterCreation.test_singleframe_magic2 ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReaderPBC.test_sum_centres_of_geometry ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReaderPBC.test_full_slice ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_add_same_auxname_raises_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_changing_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_trj.TestBzippedTRJReaderPBC.test_random_access ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_double_close ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_first_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_first_frame ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_frame_jump ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_get_aux_attribute ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_get_writer_1 ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_get_writer_2 ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_go_over_last_frame ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_iter_as_aux_cutoff ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_iter_as_aux_lowf ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_iter_as_aux_highf ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_last_frame ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_iter_auxiliary ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_next_gives_second_frame ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_reload_auxiliaries_from_description ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_remove_auxiliary ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_remove_nonexistant_auxiliary_raises_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_rename_aux ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_reopen ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_stop_iter ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_total_time ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_ts_dt_matches_reader ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_2.test_volume ... ok test_long_title (testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZWriter) ... ok test_write_trajectory (testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZWriter) ... ok test_write_trajectory (testsuite.MDAnalysisTests.coordinates.test_trz.TestWrite_Partial_Timestep) ... ok test_coordinates (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRNoConversion) ... ok Test writing Gromacs trajectories from AMBER NCDF (Issue 117) ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRWriter_2.test_lambda ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRWriter_2.test_no_container ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRWriter_2.test_write_different_box ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRWriter_2.test_write_none ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRWriter_2.test_write_not_changing_ts ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRWriter_2.test_write_selection ... ok test_load_new_raises_ValueError (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_Sub) ... ok load solvated trajectory into universe with unsolvated protein. ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRWriter_2.test_write_trajectory_atomgroup ... ok test_offsets (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_offsets) ... ok test_persistent_offsets_ctime_mismatch (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_offsets) ... ok test_persistent_offsets_last_frame_wrong (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_offsets) ... ok test_persistent_offsets_natoms_mismatch (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_offsets) ... ok test_persistent_offsets_readonly (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_offsets) ... ok test_persistent_offsets_size_mismatch (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_offsets) ... ok test_reload_offsets (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_offsets) ... ok test_unsupported_format (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader_offsets) ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRWriter_2.test_write_trajectory_timestep ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRWriter_2.test_write_trajectory_universe ... ok test_with_statement (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReaderClass) ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_add_same_auxname_raises_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_changing_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_double_close ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_first_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_first_frame ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_frame_jump ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_get_aux_attribute ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_get_writer_1 ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_get_writer_2 ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_go_over_last_frame ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_iter_as_aux_cutoff ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_iter_as_aux_highf ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_iter_as_aux_lowf ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_iter_auxiliary ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_last_frame ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_next_gives_second_frame ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_reload_auxiliaries_from_description ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_remove_auxiliary ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_remove_nonexistant_auxiliary_raises_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_rename_aux ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_reopen ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_stop_iter ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_total_time ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_ts_dt_matches_reader ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_2.test_volume ... ok test_coordinates (testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZReader) ... ok test_delta (testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZReader) ... ok test_get_writer (testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZReader) ... ok test_get_writer_2 (testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZReader) ... ok test_load_trz (testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZReader) ... ok test_n_frames (testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZReader) ... ok test_next_trz (testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZReader) ... ok test_rewind_trz (testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZReader) ... ok test_seeking (testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZReader) ... ok test_time (testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZReader) ... ok test_title (testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZReader) ... ok test_unitcell (testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZReader) ... ok test_velocities (testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZReader) ... ok test_volume (testsuite.MDAnalysisTests.coordinates.test_trz.TestTRZReader) ... ok test_offsets (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_offsets) ... ok test_persistent_offsets_ctime_mismatch (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_offsets) ... ok test_persistent_offsets_last_frame_wrong (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_offsets) ... ok test_persistent_offsets_natoms_mismatch (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_offsets) ... ok test_persistent_offsets_readonly (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_offsets) ... ok test_persistent_offsets_size_mismatch (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_offsets) ... ok test_reload_offsets (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_offsets) ... ok test_unsupported_format (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_offsets) ... ok test_coordinates (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCNoConversion) ... ok Test writing Gromacs trajectories from AMBER NCDF (Issue 117) ... ok test_load_new_raises_ValueError (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader_Sub) ... ok load solvated trajectory into universe with unsolvated protein. ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCWriter_2.test_different_precision ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCWriter_2.test_no_container ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCWriter_2.test_write_different_box ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCWriter_2.test_write_none ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCWriter_2.test_write_not_changing_ts ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCWriter_2.test_write_selection ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCWriter_2.test_write_trajectory_atomgroup ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCWriter_2.test_write_trajectory_timestep ... ok testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCWriter_2.test_write_trajectory_universe ... ok Test coordinates.core.triclinic_box() (Issue 61) ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_add_same_auxname_raises_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_changing_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_double_close ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_first_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_first_frame ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_frame_jump ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_get_aux_attribute ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_get_writer_1 ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_get_writer_2 ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_go_over_last_frame ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_iter_as_aux_cutoff ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_iter_as_aux_highf ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_iter_as_aux_lowf ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_iter_auxiliary ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_last_frame ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_next_gives_second_frame ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_reload_auxiliaries_from_description ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_remove_auxiliary ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_remove_nonexistant_auxiliary_raises_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_rename_aux ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_reopen ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_stop_iter ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_total_time ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_ts_dt_matches_reader ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZReader.test_volume ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZWriter.test_no_container ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZWriter.test_no_conversion ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZWriter.test_write_different_box ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZWriter.test_write_different_models_in_trajectory ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZWriter.test_write_none ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZWriter.test_write_not_changing_ts ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZWriter.test_write_selection ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZWriter.test_write_trajectory_atomgroup ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZWriter.test_write_trajectory_timestep ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZWriter.test_write_trajectory_universe ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZWriterNames.test_list_names ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZWriterNames.test_no_names ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.TestXYZWriterNames.test_single_name ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_add_same_auxname_raises_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_changing_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_double_close ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_dt ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_first_dimensions ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_first_frame ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_frame_jump ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_get_aux_attribute ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_get_writer_1 ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_get_writer_2 ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_go_over_last_frame ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_iter ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_iter_as_aux_cutoff ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_iter_as_aux_highf ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_iter_as_aux_lowf ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_iter_auxiliary ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_last_frame ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_n_atoms ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_n_frames ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_next_gives_second_frame ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_reload_auxiliaries_from_description ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_remove_auxiliary ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_remove_nonexistant_auxiliary_raises_ValueError ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_rename_aux ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_reopen ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_stop_iter ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_total_time ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_ts_dt_matches_reader ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZReader.test_volume ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZWriter.test_no_container ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZWriter.test_no_conversion ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZWriter.test_write_different_box ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZWriter.test_write_different_models_in_trajectory ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZWriter.test_write_none ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZWriter.test_write_not_changing_ts ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZWriter.test_write_selection ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZWriter.test_write_trajectory_atomgroup ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZWriter.test_write_trajectory_timestep ... ok testsuite.MDAnalysisTests.coordinates.test_xyz.Test_XYZBZWriter.test_write_trajectory_universe ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_TRRFile.test_iter ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_TRRFile.test_n_atoms ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_TRRFile.test_offset ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_TRRFile.test_open_wrong_mode ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_TRRFile.test_over_seek ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_TRRFile.test_raise_not_existing ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_TRRFile.test_read_closed ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_TRRFile.test_read_write_mode_file ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_TRRFile.test_seek ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_TRRFile.test_seek_overflow ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_TRRFile.test_seek_tell_all ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_TRRFile.test_seek_tell_all_bytes ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_TRRFile.test_seek_tell_largefile ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_TRRFile.test_set_offsets ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_TRRFile.test_tell ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_XTCFile.test_iter ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_XTCFile.test_n_atoms ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_XTCFile.test_offset ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_XTCFile.test_open_wrong_mode ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_XTCFile.test_over_seek ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_XTCFile.test_raise_not_existing ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_XTCFile.test_read_closed ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_XTCFile.test_read_write_mode_file ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_XTCFile.test_seek ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_XTCFile.test_seek_overflow ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_XTCFile.test_seek_tell_all ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_XTCFile.test_seek_tell_all_bytes ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_XTCFile.test_seek_tell_largefile ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_XTCFile.test_set_offsets ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.Test_XTCFile.test_tell ... ok test if we can write different box-sizes for different frames. ... ok test if we can write different box-sizes for different frames. ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.test_write_different_f ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.test_write_different_natoms ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.test_write_different_prec ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.test_write_different_v ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.test_write_different_x_trr ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.test_write_different_x_xtc ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.test_write_prec ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.test_write_trr ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.test_write_xtc ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.test_xtc ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.test_read_multi_frame_xtc ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.test_trr ... ok testsuite.MDAnalysisTests.formats.test_libmdaxdr.test_read_multi_frame_trr ... ok testsuite.MDAnalysisTests.lib.test_util.TestBlocksOf.test_blocks_of_1 ... ok testsuite.MDAnalysisTests.lib.test_util.TestBlocksOf.test_blocks_of_2 ... ok testsuite.MDAnalysisTests.lib.test_util.TestBlocksOf.test_blocks_of_3 ... ok testsuite.MDAnalysisTests.lib.test_util.TestBlocksOf.test_blocks_of_VE ... ok testsuite.MDAnalysisTests.lib.test_util.TestCachedDecorator.test_val1_inject ... ok testsuite.MDAnalysisTests.lib.test_util.TestCachedDecorator.test_val1_lookup ... ok testsuite.MDAnalysisTests.lib.test_util.TestCachedDecorator.test_val2_inject ... ok testsuite.MDAnalysisTests.lib.test_util.TestCachedDecorator.test_val2_lookup ... ok testsuite.MDAnalysisTests.lib.test_util.TestCachedDecorator.test_val3_del ... ok testsuite.MDAnalysisTests.lib.test_util.TestCachedDecorator.test_val3_set ... ok testsuite.MDAnalysisTests.lib.test_util.TestCachedDecorator.test_val4_args ... ok testsuite.MDAnalysisTests.lib.test_util.TestCachedDecorator.test_val5_kwargs ... ok testsuite.MDAnalysisTests.lib.test_util.TestConvFloat.test_float_1 ... ok testsuite.MDAnalysisTests.lib.test_util.TestConvFloat.test_float_2 ... ok testsuite.MDAnalysisTests.lib.test_util.TestConvFloat.test_map_1 ... ok testsuite.MDAnalysisTests.lib.test_util.TestConvFloat.test_map_2 ... ok testsuite.MDAnalysisTests.lib.test_util.TestConvFloat.test_str ... ok testsuite.MDAnalysisTests.lib.test_util.TestFilename.testNamedStream ... ok testsuite.MDAnalysisTests.lib.test_util.TestFilename.testStringExt ... ok testsuite.MDAnalysisTests.lib.test_util.TestFilename.testStringKeep ... ok testsuite.MDAnalysisTests.lib.test_util.TestFilename.testStringNoExt ... ok testsuite.MDAnalysisTests.lib.test_util.TestFilename.testStringRootExt ... ok testsuite.MDAnalysisTests.lib.test_util.TestFilename.testStringRootExtKeep ... ok testsuite.MDAnalysisTests.lib.test_util.TestFixedwidthBins.test_VE ... ok testsuite.MDAnalysisTests.lib.test_util.TestFixedwidthBins.test_keys ... ok testsuite.MDAnalysisTests.lib.test_util.TestFixedwidthBins.test_usage_1 ... ok testsuite.MDAnalysisTests.lib.test_util.TestFixedwidthBins.test_usage_2 ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.testDihedral ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.testNormalNullVector ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.testStp ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleColinear ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleNullVector ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AnglePi ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(0.0,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(0.16534698176788384,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(0.33069396353576769,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(0.4960409453036515,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(0.66138792707153538,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(0.82673490883941925,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(0.99208189060730301,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(1.1574288723751869,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(1.3227758541430708,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(1.4881228359109546,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(1.6534698176788385,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(1.8188167994467224,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(1.984163781214606,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(2.1495107629824899,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(2.3148577447503738,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(2.4802047265182576,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(2.6455517082861415,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(2.8108986900540254,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(2.9762456718219092,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleRange(3.1415926535897931,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleUnitvectors ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_AngleVectors ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_Norm ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormNullVector ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(0.0,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(0.16534698176788384,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(0.33069396353576769,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(0.4960409453036515,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(0.66138792707153538,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(0.82673490883941925,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(0.99208189060730301,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(1.1574288723751869,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(1.3227758541430708,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(1.4881228359109546,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(1.6534698176788385,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(1.8188167994467224,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(1.984163781214606,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(2.1495107629824899,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(2.3148577447503738,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(2.4802047265182576,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(2.6455517082861415,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(2.8108986900540254,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(2.9762456718219092,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_NormRange(3.1415926535897931,) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGeometryFunctions.test_Normal ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_compressed_extension ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_compressed_extension_fail ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('CRD', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('CRD',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('crd', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('crd',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('GRO', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('GRO',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('gro', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('gro',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('MOL2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('MOL2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('mol2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('mol2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('NCDF', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('NCDF', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('ncdf', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('ncdf', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('NULL', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('NULL', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('null', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('null', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('PDBQT', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('PDBQT',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('pdbqt', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('pdbqt',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('PQR', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('PQR',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('pqr', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('pqr',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('TRR', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('TRR', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('trr', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('trr', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('XTC', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('XTC', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('xtc', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('xtc', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('XYZ', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('XYZ', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('xyz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('xyz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('DATA', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('DATA',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('data', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('data',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('DCD', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('DCD', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('dcd', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('dcd', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('LAMMPS', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('LAMMPS', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('lammps', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('lammps', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('TRZ', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('TRZ', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('trz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for('trz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_get_writer_for_pdb ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_missing_extension ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_multiframe_failure ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_multiframe_nonsense ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_no_filename_argument ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_non_string_filename ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_precedence ... ok testsuite.MDAnalysisTests.lib.test_util.TestGetWriterFor.test_wrong_format ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_check_compressed_format_TE ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_format_from_filename_TE ... ok test_timestep_not_modified_by_writer (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCWriter) ... ok Test writing Gromacs trajectories (Issue 38) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_from_ndarray ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_guess_format_stream_VE ... ok testsuite.MDAnalysisTests.lib.test_util.TestIterable.test_arrays ... ok testsuite.MDAnalysisTests.lib.test_util.TestIterable.test_iterator ... ok testsuite.MDAnalysisTests.lib.test_util.TestIterable.test_lists ... ok testsuite.MDAnalysisTests.lib.test_util.TestIterable.test_scalars ... ok Test that iterable() works on any string (Fixed bug) ... ok testsuite.MDAnalysisTests.lib.test_util.TestIterable.test_tuples ... ok testsuite.MDAnalysisTests.lib.test_util.TestMakeWhole.test_double_frag_short_bonds ... ok testsuite.MDAnalysisTests.lib.test_util.TestMakeWhole.test_impossible_solve ... ok testsuite.MDAnalysisTests.lib.test_util.TestMakeWhole.test_no_bonds ... ok testsuite.MDAnalysisTests.lib.test_util.TestMakeWhole.test_not_orthogonal ... ok testsuite.MDAnalysisTests.lib.test_util.TestMakeWhole.test_solve_1 ... ok testsuite.MDAnalysisTests.lib.test_util.TestMakeWhole.test_solve_2 ... ok testsuite.MDAnalysisTests.lib.test_util.TestMakeWhole.test_solve_3 ... ok testsuite.MDAnalysisTests.lib.test_util.TestMakeWhole.test_solve_4 ... ok testsuite.MDAnalysisTests.lib.test_util.TestMakeWhole.test_too_small_box_size ... ok testsuite.MDAnalysisTests.lib.test_util.TestMakeWhole.test_walk_1 ... ok testsuite.MDAnalysisTests.lib.test_util.TestMakeWhole.test_walk_2 ... ok testsuite.MDAnalysisTests.lib.test_util.TestMakeWhole.test_wrong_reference_atom ... ok testsuite.MDAnalysisTests.lib.test_util.TestMakeWhole.test_zero_box_size ... ok testsuite.MDAnalysisTests.lib.test_util.TestNamespace.test_delattr ... ok testsuite.MDAnalysisTests.lib.test_util.TestNamespace.test_delitem ... ok testsuite.MDAnalysisTests.lib.test_util.TestNamespace.test_delitem_AE ... ok testsuite.MDAnalysisTests.lib.test_util.TestNamespace.test_eq ... ok testsuite.MDAnalysisTests.lib.test_util.TestNamespace.test_getattr ... ok testsuite.MDAnalysisTests.lib.test_util.TestNamespace.test_getattr_AE ... ok testsuite.MDAnalysisTests.lib.test_util.TestNamespace.test_getitem ... ok testsuite.MDAnalysisTests.lib.test_util.TestNamespace.test_getitem_KE ... ok testsuite.MDAnalysisTests.lib.test_util.TestNamespace.test_iter ... ok testsuite.MDAnalysisTests.lib.test_util.TestNamespace.test_len ... ok testsuite.MDAnalysisTests.lib.test_util.TestNamespace.test_setattr ... ok testsuite.MDAnalysisTests.lib.test_util.TestNamespace.test_setitem ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_VE_1 ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_VE_2 ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('HIS', 'H') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('HISA', 'H') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('HISB', 'H') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('HSE', 'H') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('HSD', 'H') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('HIS1', 'H') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('HIS2', 'H') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('HIE', 'H') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('HID', 'H') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('LYS', 'K') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('LYSH', 'K') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('LYN', 'K') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('ALA', 'A') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('ASP', 'D') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('ASPH', 'D') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('ASH', 'D') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('GLU', 'E') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('GLUH', 'E') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('GLH', 'E') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('ASN', 'N') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('GLN', 'Q') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('CYS', 'C') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('CYSH', 'C') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('CYS1', 'C') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_long('CYS2', 'C') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_short('H', 'HIS') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_short('K', 'LYS') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_short('A', 'ALA') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_short('D', 'ASP') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_short('E', 'GLU') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_short('N', 'ASN') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_short('Q', 'GLN') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_convert_aa_code_short('C', 'CYS') ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_parse_residue('LYS300:HZ1', ('LYS', 300, 'HZ1')) ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_parse_residue('K300:HZ1', ('LYS', 300, 'HZ1')) ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_parse_residue('K300', ('LYS', 300, None)) ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_parse_residue('LYS 300:HZ1', ('LYS', 300, 'HZ1')) ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_parse_residue('M1:CA', ('MET', 1, 'CA')) ... ok testsuite.MDAnalysisTests.lib.test_util.TestStringFunctions.test_parse_residue_VE ... ok testsuite.MDAnalysisTests.lib.test_util.TestTruncateInteger.test_ltruncate_int((1234, 1), 4) ... ok testsuite.MDAnalysisTests.lib.test_util.TestTruncateInteger.test_ltruncate_int((1234, 2), 34) ... ok testsuite.MDAnalysisTests.lib.test_util.TestTruncateInteger.test_ltruncate_int((1234, 3), 234) ... ok testsuite.MDAnalysisTests.lib.test_util.TestTruncateInteger.test_ltruncate_int((1234, 4), 1234) ... ok testsuite.MDAnalysisTests.lib.test_util.TestTruncateInteger.test_ltruncate_int((1234, 5), 1234) ... ok testsuite.MDAnalysisTests.lib.test_util.TestUniqueRows.test_unique_rows_2 ... ok testsuite.MDAnalysisTests.lib.test_util.TestUniqueRows.test_unique_rows_3 ... ok testsuite.MDAnalysisTests.lib.test_util.TestUniqueRows.test_unique_rows_with_view ... ok testsuite.MDAnalysisTests.lib.test_util.test_greedy_splitext ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CHAIN', 'file.CHAIN') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CHAIN', 'file.CHAIN') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CHAIN', 'file.CHAIN') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CHAIN', 'file.CHAIN.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CHAIN', 'file.CHAIN.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CHAIN', 'file.CHAIN.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CHAIN', 'file.CHAIN.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('chain', 'file.chain') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('chain', 'file.chain') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('chain', 'file.chain') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('chain', 'file.chain.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('chain', 'file.chain.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('chain', 'file.chain.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('chain', 'file.chain.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.chain',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.chain', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.chain.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.chain.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CONFIG', 'file.CONFIG') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CONFIG', 'file.CONFIG') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CONFIG', 'file.CONFIG') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CONFIG', 'file.CONFIG.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CONFIG', 'file.CONFIG.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CONFIG', 'file.CONFIG.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CONFIG', 'file.CONFIG.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('config', 'file.config') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('config', 'file.config') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('config', 'file.config') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('config', 'file.config.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('config', 'file.config.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('config', 'file.config.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('config', 'file.config.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.config', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.config.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.config.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.config', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.config.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.config.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CRD', 'file.CRD') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CRD', 'file.CRD') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CRD', 'file.CRD') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CRD', 'file.CRD.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CRD', 'file.CRD.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CRD', 'file.CRD.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('CRD', 'file.CRD.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('crd', 'file.crd') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('crd', 'file.crd') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('crd', 'file.crd') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('crd', 'file.crd.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('crd', 'file.crd.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('crd', 'file.crd.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('crd', 'file.crd.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.crd', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.crd.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.crd.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.crd', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.crd.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.crd.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DMS', 'file.DMS') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DMS', 'file.DMS') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DMS', 'file.DMS') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DMS', 'file.DMS.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DMS', 'file.DMS.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DMS', 'file.DMS.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DMS', 'file.DMS.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('dms', 'file.dms') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('dms', 'file.dms') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('dms', 'file.dms') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('dms', 'file.dms.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('dms', 'file.dms.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('dms', 'file.dms.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('dms', 'file.dms.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.dms', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.dms.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.dms.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.dms', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.dms.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.dms.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('GMS', 'file.GMS') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('GMS', 'file.GMS') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('GMS', 'file.GMS') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('GMS', 'file.GMS.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('GMS', 'file.GMS.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('GMS', 'file.GMS.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('GMS', 'file.GMS.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('gms', 'file.gms') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('gms', 'file.gms') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('gms', 'file.gms') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('gms', 'file.gms.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('gms', 'file.gms.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('gms', 'file.gms.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('gms', 'file.gms.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.gms', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.gms.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.gms.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.gms', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.gms.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.gms.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('GRO', 'file.GRO') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('GRO', 'file.GRO') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('GRO', 'file.GRO') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('GRO', 'file.GRO.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('GRO', 'file.GRO.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('GRO', 'file.GRO.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('GRO', 'file.GRO.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('gro', 'file.gro') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('gro', 'file.gro') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('gro', 'file.gro') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('gro', 'file.gro.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('gro', 'file.gro.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('gro', 'file.gro.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('gro', 'file.gro.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.gro', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.gro.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.gro.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.gro', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.gro.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.gro.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('HISTORY', 'file.HISTORY') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('HISTORY', 'file.HISTORY') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('HISTORY', 'file.HISTORY') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('HISTORY', 'file.HISTORY.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('HISTORY', 'file.HISTORY.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('HISTORY', 'file.HISTORY.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('HISTORY', 'file.HISTORY.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('history', 'file.history') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('history', 'file.history') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('history', 'file.history') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('history', 'file.history.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('history', 'file.history.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('history', 'file.history.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('history', 'file.history.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.history', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.history.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.history.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.history', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.history.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.history.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('INPCRD', 'file.INPCRD') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('INPCRD', 'file.INPCRD') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('INPCRD', 'file.INPCRD') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('INPCRD', 'file.INPCRD.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('INPCRD', 'file.INPCRD.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('INPCRD', 'file.INPCRD.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('INPCRD', 'file.INPCRD.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('inpcrd', 'file.inpcrd') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('inpcrd', 'file.inpcrd') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('inpcrd', 'file.inpcrd') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('inpcrd', 'file.inpcrd.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('inpcrd', 'file.inpcrd.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('inpcrd', 'file.inpcrd.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('inpcrd', 'file.inpcrd.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.inpcrd',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.inpcrd', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.inpcrd.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.inpcrd.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MDCRD', 'file.MDCRD') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MDCRD', 'file.MDCRD') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MDCRD', 'file.MDCRD') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MDCRD', 'file.MDCRD.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MDCRD', 'file.MDCRD.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MDCRD', 'file.MDCRD.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MDCRD', 'file.MDCRD.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mdcrd', 'file.mdcrd') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mdcrd', 'file.mdcrd') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mdcrd', 'file.mdcrd') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mdcrd', 'file.mdcrd.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mdcrd', 'file.mdcrd.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mdcrd', 'file.mdcrd.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mdcrd', 'file.mdcrd.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.mdcrd',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.mdcrd', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.mdcrd.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.mdcrd.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MMTF', 'file.MMTF') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MMTF', 'file.MMTF') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MMTF', 'file.MMTF') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MMTF', 'file.MMTF.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MMTF', 'file.MMTF.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MMTF', 'file.MMTF.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MMTF', 'file.MMTF.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mmtf', 'file.mmtf') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mmtf', 'file.mmtf') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mmtf', 'file.mmtf') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mmtf', 'file.mmtf.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mmtf', 'file.mmtf.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mmtf', 'file.mmtf.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mmtf', 'file.mmtf.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.mmtf', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.mmtf.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.mmtf.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.mmtf', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.mmtf.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.mmtf.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MOL2', 'file.MOL2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MOL2', 'file.MOL2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MOL2', 'file.MOL2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MOL2', 'file.MOL2.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MOL2', 'file.MOL2.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MOL2', 'file.MOL2.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('MOL2', 'file.MOL2.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mol2', 'file.mol2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mol2', 'file.mol2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mol2', 'file.mol2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mol2', 'file.mol2.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mol2', 'file.mol2.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mol2', 'file.mol2.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('mol2', 'file.mol2.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.mol2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.mol2.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.mol2.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.mol2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.mol2.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.mol2.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('NC', 'file.NC') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('NC', 'file.NC') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('NC', 'file.NC') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('NC', 'file.NC.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('NC', 'file.NC.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('NC', 'file.NC.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('NC', 'file.NC.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('nc', 'file.nc') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('nc', 'file.nc') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('nc', 'file.nc') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('nc', 'file.nc.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('nc', 'file.nc.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('nc', 'file.nc.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('nc', 'file.nc.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.nc',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.nc', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.nc.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.nc.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('NCDF', 'file.NCDF') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('NCDF', 'file.NCDF') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('NCDF', 'file.NCDF') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('NCDF', 'file.NCDF.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('NCDF', 'file.NCDF.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('NCDF', 'file.NCDF.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('NCDF', 'file.NCDF.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('ncdf', 'file.ncdf') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('ncdf', 'file.ncdf') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('ncdf', 'file.ncdf') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('ncdf', 'file.ncdf.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('ncdf', 'file.ncdf.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('ncdf', 'file.ncdf.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('ncdf', 'file.ncdf.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.ncdf',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.ncdf', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.ncdf.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.ncdf.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PDB', 'file.PDB') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PDB', 'file.PDB') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PDB', 'file.PDB') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PDB', 'file.PDB.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PDB', 'file.PDB.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PDB', 'file.PDB.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PDB', 'file.PDB.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pdb', 'file.pdb') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pdb', 'file.pdb') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pdb', 'file.pdb') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pdb', 'file.pdb.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pdb', 'file.pdb.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pdb', 'file.pdb.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pdb', 'file.pdb.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.pdb', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.pdb.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.pdb.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.pdb', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.pdb.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.pdb.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PDBQT', 'file.PDBQT') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PDBQT', 'file.PDBQT') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PDBQT', 'file.PDBQT') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PDBQT', 'file.PDBQT.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PDBQT', 'file.PDBQT.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PDBQT', 'file.PDBQT.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PDBQT', 'file.PDBQT.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pdbqt', 'file.pdbqt') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pdbqt', 'file.pdbqt') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pdbqt', 'file.pdbqt') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pdbqt', 'file.pdbqt.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pdbqt', 'file.pdbqt.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pdbqt', 'file.pdbqt.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pdbqt', 'file.pdbqt.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.pdbqt', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.pdbqt.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.pdbqt.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.pdbqt', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.pdbqt.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.pdbqt.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PRMTOP', 'file.PRMTOP') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PRMTOP', 'file.PRMTOP') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PRMTOP', 'file.PRMTOP') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PRMTOP', 'file.PRMTOP.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PRMTOP', 'file.PRMTOP.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PRMTOP', 'file.PRMTOP.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PRMTOP', 'file.PRMTOP.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('prmtop', 'file.prmtop') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('prmtop', 'file.prmtop') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('prmtop', 'file.prmtop') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('prmtop', 'file.prmtop.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('prmtop', 'file.prmtop.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('prmtop', 'file.prmtop.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('prmtop', 'file.prmtop.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.prmtop', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.prmtop.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.prmtop.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.prmtop',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PQR', 'file.PQR') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PQR', 'file.PQR') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PQR', 'file.PQR') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PQR', 'file.PQR.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PQR', 'file.PQR.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PQR', 'file.PQR.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PQR', 'file.PQR.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pqr', 'file.pqr') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pqr', 'file.pqr') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pqr', 'file.pqr') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pqr', 'file.pqr.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pqr', 'file.pqr.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pqr', 'file.pqr.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('pqr', 'file.pqr.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.pqr', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.pqr.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.pqr.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.pqr', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.pqr.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.pqr.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PSF', 'file.PSF') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PSF', 'file.PSF') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PSF', 'file.PSF') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PSF', 'file.PSF.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PSF', 'file.PSF.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PSF', 'file.PSF.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('PSF', 'file.PSF.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('psf', 'file.psf') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('psf', 'file.psf') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('psf', 'file.psf') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('psf', 'file.psf.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('psf', 'file.psf.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('psf', 'file.psf.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('psf', 'file.psf.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.psf', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.psf.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.psf.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.psf',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('RESTRT', 'file.RESTRT') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('RESTRT', 'file.RESTRT') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('RESTRT', 'file.RESTRT') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('RESTRT', 'file.RESTRT.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('RESTRT', 'file.RESTRT.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('RESTRT', 'file.RESTRT.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('RESTRT', 'file.RESTRT.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('restrt', 'file.restrt') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('restrt', 'file.restrt') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('restrt', 'file.restrt') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('restrt', 'file.restrt.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('restrt', 'file.restrt.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('restrt', 'file.restrt.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('restrt', 'file.restrt.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.restrt',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.restrt', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.restrt.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.restrt.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TOP', 'file.TOP') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TOP', 'file.TOP') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TOP', 'file.TOP') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TOP', 'file.TOP.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TOP', 'file.TOP.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TOP', 'file.TOP.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TOP', 'file.TOP.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('top', 'file.top') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('top', 'file.top') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('top', 'file.top') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('top', 'file.top.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('top', 'file.top.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('top', 'file.top.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('top', 'file.top.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.top', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.top.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.top.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.top',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TPR', 'file.TPR') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TPR', 'file.TPR') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TPR', 'file.TPR') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TPR', 'file.TPR.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TPR', 'file.TPR.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TPR', 'file.TPR.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TPR', 'file.TPR.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('tpr', 'file.tpr') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('tpr', 'file.tpr') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('tpr', 'file.tpr') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('tpr', 'file.tpr.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('tpr', 'file.tpr.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('tpr', 'file.tpr.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('tpr', 'file.tpr.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.tpr', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.tpr.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.tpr.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.tpr',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRJ', 'file.TRJ') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRJ', 'file.TRJ') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRJ', 'file.TRJ') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRJ', 'file.TRJ.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRJ', 'file.TRJ.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRJ', 'file.TRJ.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRJ', 'file.TRJ.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trj', 'file.trj') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trj', 'file.trj') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trj', 'file.trj') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trj', 'file.trj.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trj', 'file.trj.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trj', 'file.trj.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trj', 'file.trj.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.trj',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.trj', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.trj.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.trj.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRR', 'file.TRR') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRR', 'file.TRR') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRR', 'file.TRR') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRR', 'file.TRR.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRR', 'file.TRR.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRR', 'file.TRR.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRR', 'file.TRR.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trr', 'file.trr') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trr', 'file.trr') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trr', 'file.trr') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trr', 'file.trr.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trr', 'file.trr.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trr', 'file.trr.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trr', 'file.trr.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.trr',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.trr', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.trr.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.trr.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XML', 'file.XML') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XML', 'file.XML') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XML', 'file.XML') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XML', 'file.XML.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XML', 'file.XML.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XML', 'file.XML.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XML', 'file.XML.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xml', 'file.xml') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xml', 'file.xml') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xml', 'file.xml') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xml', 'file.xml.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xml', 'file.xml.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xml', 'file.xml.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xml', 'file.xml.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xml', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xml.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xml.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xml',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XPDB', 'file.XPDB') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XPDB', 'file.XPDB') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XPDB', 'file.XPDB') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XPDB', 'file.XPDB.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XPDB', 'file.XPDB.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XPDB', 'file.XPDB.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XPDB', 'file.XPDB.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xpdb', 'file.xpdb') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xpdb', 'file.xpdb') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xpdb', 'file.xpdb') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xpdb', 'file.xpdb.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xpdb', 'file.xpdb.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xpdb', 'file.xpdb.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xpdb', 'file.xpdb.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xpdb', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xpdb.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xpdb.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xpdb', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xpdb.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xpdb.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XTC', 'file.XTC') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XTC', 'file.XTC') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XTC', 'file.XTC') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XTC', 'file.XTC.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XTC', 'file.XTC.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XTC', 'file.XTC.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XTC', 'file.XTC.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xtc', 'file.xtc') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xtc', 'file.xtc') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xtc', 'file.xtc') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xtc', 'file.xtc.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xtc', 'file.xtc.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xtc', 'file.xtc.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xtc', 'file.xtc.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xtc',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xtc', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xtc.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xtc.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XYZ', 'file.XYZ') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XYZ', 'file.XYZ') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XYZ', 'file.XYZ') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XYZ', 'file.XYZ.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XYZ', 'file.XYZ.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XYZ', 'file.XYZ.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('XYZ', 'file.XYZ.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xyz', 'file.xyz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xyz', 'file.xyz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xyz', 'file.xyz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xyz', 'file.xyz.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xyz', 'file.xyz.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xyz', 'file.xyz.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('xyz', 'file.xyz.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xyz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xyz.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xyz.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xyz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xyz.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.xyz.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DATA', 'file.DATA') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DATA', 'file.DATA') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DATA', 'file.DATA') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DATA', 'file.DATA.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DATA', 'file.DATA.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DATA', 'file.DATA.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DATA', 'file.DATA.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('data', 'file.data') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('data', 'file.data') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('data', 'file.data') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('data', 'file.data.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('data', 'file.data.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('data', 'file.data.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('data', 'file.data.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.data', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.data.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.data.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.data', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.data.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.data.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DCD', 'file.DCD') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DCD', 'file.DCD') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DCD', 'file.DCD') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DCD', 'file.DCD.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DCD', 'file.DCD.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DCD', 'file.DCD.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('DCD', 'file.DCD.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('dcd', 'file.dcd') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('dcd', 'file.dcd') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('dcd', 'file.dcd') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('dcd', 'file.dcd.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('dcd', 'file.dcd.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('dcd', 'file.dcd.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('dcd', 'file.dcd.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.dcd',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.dcd', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.dcd.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.dcd.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('LAMMPS', 'file.LAMMPS') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('LAMMPS', 'file.LAMMPS') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('LAMMPS', 'file.LAMMPS') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('LAMMPS', 'file.LAMMPS.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('LAMMPS', 'file.LAMMPS.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('LAMMPS', 'file.LAMMPS.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('LAMMPS', 'file.LAMMPS.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('lammps', 'file.lammps') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('lammps', 'file.lammps') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('lammps', 'file.lammps') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('lammps', 'file.lammps.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('lammps', 'file.lammps.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('lammps', 'file.lammps.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('lammps', 'file.lammps.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.lammps',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.lammps', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.lammps.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.lammps.gz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRZ', 'file.TRZ') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRZ', 'file.TRZ') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRZ', 'file.TRZ') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRZ', 'file.TRZ.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRZ', 'file.TRZ.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRZ', 'file.TRZ.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('TRZ', 'file.TRZ.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trz', 'file.trz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trz', 'file.trz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trz', 'file.trz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trz', 'file.trz.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trz', 'file.trz.bz2') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trz', 'file.trz.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('trz', 'file.trz.gz') ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.trz',) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.trz', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.trz.bz2', ) ... ok testsuite.MDAnalysisTests.lib.test_util.TestGuessFormat.test_formats('file.trz.gz', ) ... ok testsuite.MDAnalysisTests.topology.test_crd.TestCRDParser.test_expected_attributes ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_crd.TestCRDParser.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_crd.TestCRDParser.test_mandatory_attributes ... ok Check that the Topology is correctly sized ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPConfigMinimal.test_creates_universe ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPConfigMinimal.test_dlp_names ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPConfigMinimal.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPConfigMinimal.test_guessed_attributes ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPConfigMinimal.test_mandatory_attributes ... ok Testing the call signature ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPConfigOrder.test_dlp_names ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPConfigOrder.test_creates_universe ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPConfigOrder.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPConfigOrder.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPConfigOrder.test_mandatory_attributes ... ok Check that the Topology is correctly sized ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPConfigParser.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPConfigParser.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPConfigParser.test_creates_universe ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPConfigParser.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPConfigParser.test_names ... ok Check that the Topology is correctly sized ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPHistoryMinimal.test_dlp_names ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPHistoryMinimal.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPHistoryMinimal.test_creates_universe ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPHistoryMinimal.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPHistoryMinimal.test_mandatory_attributes ... ok Testing the call signature ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPHistoryOrder.test_dlp_names ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPHistoryOrder.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPHistoryOrder.test_creates_universe ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPHistoryOrder.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPHistoryOrder.test_mandatory_attributes ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok Check that the Topology is correctly sized ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPHistoryParser.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPHistoryParser.test_creates_universe ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPHistoryParser.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPHistoryParser.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_dlpoly.TestDLPHistoryParser.test_names ... ok Testing the call signature ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok test_single_frame_CRD (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRWriterSingleFrame) ... ok test_single_frame_GRO (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRWriterSingleFrame) ... ok test_single_frame_PDB (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRWriterSingleFrame) ... ok testsuite.MDAnalysisTests.topology.test_dms.TestDMSParser.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_dms.TestDMSParser.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_dms.TestDMSParser.test_atomsels ... ok testsuite.MDAnalysisTests.topology.test_dms.TestDMSParser.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_dms.TestDMSParser.test_number_of_bonds ... ok Check that the Topology is correctly sized ... ok Testing the call signature ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_gms.TestGMSASYMOPT.test_expected_attributes ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_gms.TestGMSASYMOPT.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_gms.TestGMSASYMOPT.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_gms.TestGMSASYMOPT.test_names ... ok Check that the Topology is correctly sized ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_gms.TestGMSASYMOPT.test_types ... ok testsuite.MDAnalysisTests.topology.test_gms.TestGMSASYMSURF.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_gms.TestGMSASYMSURF.test_guessed_attributes ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_gms.TestGMSASYMSURF.test_mandatory_attributes ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_gms.TestGMSASYMSURF.test_names ... ok Check that the Topology is correctly sized ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_gms.TestGMSASYMSURF.test_types ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_gms.TestGMSSYMOPT.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_gms.TestGMSSYMOPT.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_gms.TestGMSSYMOPT.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_gms.TestGMSSYMOPT.test_names ... ok Check that the Topology is correctly sized ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_gms.TestGMSSYMOPT.test_types ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_gro.TestGROParser.test_attr_size ... ok testsuite.MDAnalysisTests.topology.test_gro.TestGROParser.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_gro.TestGROParser.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_gro.TestGROParser.test_mandatory_attributes ... ok Check that the Topology is correctly sized ... ok Tests the writing and reading back of TRRs with gaps in any of ... ok test_timestep_not_modified_by_writer (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRWriter) ... ok test_velocities (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRWriter) ... ok Test writing Gromacs trajectories (Issue 38) ... ok testsuite.MDAnalysisTests.topology.test_gro.TestGROWideBox.test_atoms ... ok testsuite.MDAnalysisTests.topology.test_gro.TestGroResidWrapping.test_wrapping_resids ... ok testsuite.MDAnalysisTests.topology.test_gro.TestGroResidWrapping.test_wrapping_resids_0base ... ok testsuite.MDAnalysisTests.topology.test_gro.test_parse_empty_atom_IOerror ... ok testsuite.MDAnalysisTests.topology.test_gro.test_parse_missing_atomname_IOerror ... ok testsuite.MDAnalysisTests.topology.test_gro.test_sameresid_diffresname ... ok testsuite.MDAnalysisTests.topology.test_guessers.TestGuessMasses.test_get_atom_mass ... ok testsuite.MDAnalysisTests.topology.test_guessers.TestGuessMasses.test_get_atom_mass_miss ... ok testsuite.MDAnalysisTests.topology.test_guessers.TestGuessMasses.test_guess_atom_mass ... ok testsuite.MDAnalysisTests.topology.test_guessers.TestGuessMasses.test_guess_masses ... ok testsuite.MDAnalysisTests.topology.test_guessers.TestGuessMasses.test_guess_masses_miss ... ok testsuite.MDAnalysisTests.topology.test_guessers.TestGuessMasses.test_guess_masses_warn ... ok testsuite.MDAnalysisTests.topology.test_guessers.TestGuessTypes.test_guess_atom_element ... ok testsuite.MDAnalysisTests.topology.test_guessers.TestGuessTypes.test_guess_atom_element_1H ... ok testsuite.MDAnalysisTests.topology.test_guessers.TestGuessTypes.test_guess_atom_element_empty ... ok testsuite.MDAnalysisTests.topology.test_guessers.TestGuessTypes.test_guess_atom_element_singledigit ... ok testsuite.MDAnalysisTests.topology.test_guessers.TestGuessTypes.test_guess_types ... ok testsuite.MDAnalysisTests.topology.test_guessers.test_guess_charge ... ok testsuite.MDAnalysisTests.topology.test_guessers.test_guess_bonds_Error ... ok testsuite.MDAnalysisTests.topology.test_guessers.test_guess_impropers ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_hoomdxml.TestHoomdXMLParser.test_attr_size ... ok testsuite.MDAnalysisTests.topology.test_hoomdxml.TestHoomdXMLParser.test_angles ... ok test_single_frame_CRD (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCWriterSingleFrame) ... ok test_single_frame_GRO (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCWriterSingleFrame) ... ok test_single_frame_PDB (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCWriterSingleFrame) ... ok testsuite.MDAnalysisTests.topology.test_hoomdxml.TestHoomdXMLParser.test_dihedrals ... ok testsuite.MDAnalysisTests.topology.test_hoomdxml.TestHoomdXMLParser.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_hoomdxml.TestHoomdXMLParser.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_hoomdxml.TestHoomdXMLParser.test_mandatory_attributes ... ok Testing the call signature ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_hoomdxml.TestHoomdXMLParser.test_bonds ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT.test_angle_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT.test_bond_member ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT.test_dihedral_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT.test_improper_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT.test_creates_universe ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT.test_n_angles ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT.test_n_atom_types ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT.test_n_bonds ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT.test_n_dihedrals ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT.test_n_impropers ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT2.test_angle_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT2.test_bond_member ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT2.test_dihedral_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT2.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT2.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT2.test_improper_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT2.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT2.test_creates_universe ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT2.test_n_angles ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT2.test_n_atom_types ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT2.test_n_bonds ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT2.test_n_dihedrals ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSDeletedAtoms.test_angle_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSDeletedAtoms.test_atom_ids ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSDeletedAtoms.test_bond_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSDeletedAtoms.test_creates_universe ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSDeletedAtoms.test_dihedral_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSCNT2.test_n_impropers ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSDeletedAtoms.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSDeletedAtoms.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSDeletedAtoms.test_improper_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSDeletedAtoms.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSDeletedAtoms.test_n_angles ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSDeletedAtoms.test_n_atom_types ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSDeletedAtoms.test_n_bonds ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSDeletedAtoms.test_n_dihedrals ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSDeletedAtoms.test_n_impropers ... ok Testing the call signature ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD.test_angle_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD.test_bond_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSDeletedAtoms.test_traj ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD.test_dihedral_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD.test_creates_universe ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD.test_improper_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD.test_n_angles ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD.test_n_atom_types ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD.test_n_bonds ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD.test_n_dihedrals ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD.test_n_impropers ... ok Testing the call signature ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD2.test_angle_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD2.test_bond_member ... ok Check that the Topology is correctly sized ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD2.test_dihedral_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD2.test_creates_universe ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD2.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD2.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD2.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD2.test_improper_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD2.test_n_angles ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD2.test_n_atom_types ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD2.test_n_dihedrals ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD2.test_n_bonds ... ok Check that the Topology is correctly sized ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLAMMPSHYD2.test_n_impropers ... ok Check that the transtable is appropriately sized ... ok Testing the call signature ... ok Testing the call signature ... ok test_coordinates (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReaderBig) ... ok test_distances (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReaderBig) ... ok testing that accessing universe.trajectory.dt returns the default ... ok test_first_residue (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReaderBig) ... ok test_frame (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReaderBig) ... ok test_load_pdb (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReaderBig) ... ok test_n_atoms (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReaderBig) ... ok test_n_frames (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReaderBig) ... ok test_n_residues (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReaderBig) ... ok test_selection (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReaderBig) ... ok test_time (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReaderBig) ... ok test_unitcell (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReaderBig) ... ok test_volume (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBReaderBig) ... ok Test that illegal PDB coordinates (x > 9999.9995 A) are caught ... ok Test that illegal PDB coordinates (x <= -999.9995 A) are caught ... ok Check whether HEADER and TITLE are written just once in a multi- ... ok Test writing a single frame from a DCD trajectory to a PDB using ... ok Test writing a single frame from a DCD trajectory to a PDB using ... ok Test writing from a single frame PDB file to a PDB file. ... ok test_writer_no_altlocs (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBWriter) ... ok test_writer_no_atom_names (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBWriter) ... ok test_writer_no_icodes (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBWriter) ... ok test_writer_no_occupancies (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBWriter) ... ok test_writer_no_resids (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBWriter) ... ok test_writer_no_resnames (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBWriter) ... ok test_writer_no_segids (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBWriter) ... ok test_writer_no_tempfactors (testsuite.MDAnalysisTests.coordinates.test_pdb.TestPDBWriter) ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLammpsData.test_angle_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLammpsData.test_bond_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLammpsData.test_dihedral_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLammpsData.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLammpsData.test_guessed_attributes ... ok test_EOFraisesStopIteration (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader) ... ok test_Writer (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader) ... ok test_coordinates (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader) ... ok test_dt (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader) ... ok test_flag_convert_lengths (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader) ... ok test_frame (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader) ... ok test_get_Writer (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader) ... ok test_jump_lastframe_xdrtrj (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader) ... ok test_jump_xdrtrj (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader) ... ok test_next_xdrtrj (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader) ... ok test_reverse_xdrtrj (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader) ... ok test_rewind_xdrtrj (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader) ... ok test_slice_xdrtrj (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader) ... ok test_time (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader) ... ok test_totaltime (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader) ... ok Test that xtc/trr unitcell is read correctly (Issue 34) ... ok test_volume (testsuite.MDAnalysisTests.coordinates.test_xdr.TestXTCReader) ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLammpsData.test_improper_member ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLammpsData.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLammpsData.test_n_angles ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLammpsData.test_n_atom_types ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFFetch.test_altlocs ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFFetch.test_bfactors ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLammpsData.test_n_bonds ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFFetch.test_icodes ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFFetch.test_bonds ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFFetch.test_ids ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFFetch.test_models ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFFetch.test_names ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFFetch.test_occupancies ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFFetch.test_resids ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFFetch.test_resnames ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFFetch.test_segids ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFFetch.test_types ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFParser.test_expected_attributes ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFParser.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFParser.test_mandatory_attributes ... ok Check that the Topology is correctly sized ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFParser_gz.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFParser_gz.test_guessed_attributes ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFParser_gz.test_mandatory_attributes ... ok Check that the Topology is correctly sized ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverse.test_altlocs ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverse.test_bfactors ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverse.test_icodes ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverse.test_bonds ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverse.test_ids ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverse.test_models ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverse.test_names ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverse.test_occupancies ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverse.test_resids ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverse.test_resnames ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverse.test_segids ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverse.test_types ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverseFromDecoder.test_altlocs ... ok test_EOFraisesStopIteration (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader) ... ok test_Writer (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader) ... ok test_coordinates (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader) ... ok test_dt (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader) ... ok test_flag_convert_lengths (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader) ... ok test_frame (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader) ... ok test_get_Writer (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader) ... ok test_jump_lastframe_xdrtrj (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader) ... ok test_jump_xdrtrj (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader) ... ok test_next_xdrtrj (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader) ... ok test_reverse_xdrtrj (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader) ... ok test_rewind_xdrtrj (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader) ... ok test_slice_xdrtrj (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader) ... ok test_time (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader) ... ok test_totaltime (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader) ... ok Test that xtc/trr unitcell is read correctly (Issue 34) ... ok test_velocities (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader) ... ok test_volume (testsuite.MDAnalysisTests.coordinates.test_xdr.TestTRRReader) ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverseFromDecoder.test_bfactors ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverseFromDecoder.test_ids ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverseFromDecoder.test_bonds ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverseFromDecoder.test_icodes ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverseFromDecoder.test_models ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverseFromDecoder.test_resids ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverseFromDecoder.test_names ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLammpsData.test_creates_universe ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverseFromDecoder.test_resnames ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverseFromDecoder.test_segids ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverseFromDecoder.test_types ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFgzUniverse.test_models ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFgzUniverseFromDecoder.test_models ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFgzUniverseFromDecoder.test_universe_models ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFgzUniverse.test_universe_models ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestMMTFUniverseFromDecoder.test_occupancies ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestSelectModels.test_model_multiple_2 ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestSelectModels.test_model_multiple ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestSelectModels.test_model_multiple_3 ... ok testsuite.MDAnalysisTests.topology.test_mol2.TestMOL2Parser.test_attr_size ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestSelectModels.test_model_multiple_4 ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestSelectModels.test_model_multiple_5 ... ok testsuite.MDAnalysisTests.topology.test_mmtf.TestSelectModels.test_model_selection ... ok testsuite.MDAnalysisTests.topology.test_mol2.TestMOL2Parser.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_mol2.TestMOL2Parser.test_bonds ... ok testsuite.MDAnalysisTests.topology.test_mol2.TestMOL2Parser.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_mol2.TestMOL2Parser.test_guessed_attributes ... ok Check that Universe works with this Parser ... ok Check that the Topology is correctly sized ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_mol2.TestMOL2Parser2.test_attr_size ... ok testsuite.MDAnalysisTests.topology.test_mol2.TestMOL2Parser2.test_bonds ... ok testsuite.MDAnalysisTests.topology.test_mol2.TestMOL2Parser2.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_mol2.TestMOL2Parser2.test_guessed_attributes ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_mol2.TestMOL2Parser2.test_mandatory_attributes ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_pdb.TestPDBConect.test_conect_parser_runtime ... ok testsuite.MDAnalysisTests.topology.test_pdb.TestPDBConect.test_conect_parser ... ok Check that Universe works with this Parser ... ok Check that the parser works as intended, ... ok testsuite.MDAnalysisTests.topology.test_mol2.test_bond_orders ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLammpsData.test_n_dihedrals ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_lammpsdata.TestLammpsData.test_n_impropers ... ok Check that the Topology is correctly sized ... ok testsuite.MDAnalysisTests.topology.test_pdb.TestPDBParser.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_pdb.TestPDBParser.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_pdb.TestPDBParser.test_expected_attributes ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_pdb.TestPDBParserSegids.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_pdb.TestPDBParserSegids.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_pdb.TestPDBParserSegids.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_pdb.test_conect2ter ... ok testsuite.MDAnalysisTests.topology.test_pdb.test_single_conect ... ok testsuite.MDAnalysisTests.topology.test_pdb.test_new_chainid_new_res ... ok testsuite.MDAnalysisTests.topology.test_pdb.test_sameresid_diffresname ... ok Testing the call signature ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_pdbqt.TestPDBQT.test_expected_attributes ... ok Check that the Topology is correctly sized ... ok testsuite.MDAnalysisTests.topology.test_pdbqt.TestPDBQT.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_pdbqt.TestPDBQT.test_mandatory_attributes ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_pqr.TestPQRParser.test_attr_size ... ok testsuite.MDAnalysisTests.topology.test_pqr.TestPQRParser.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_pqr.TestPQRParser.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_pqr.TestPQRParser.test_mandatory_attributes ... ok Check that Universe works with this Parser ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_pqr.TestPQRParser2.test_attr_size ... ok testsuite.MDAnalysisTests.topology.test_pqr.TestPQRParser2.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_pqr.TestPQRParser2.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_pqr.TestPQRParser2.test_mandatory_attributes ... ok Check that Universe works with this Parser ... ok Check that the Topology is correctly sized ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_psf.TestNAMDPSFParser.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_psf.TestNAMDPSFParser.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_psf.TestNAMDPSFParser.test_mandatory_attributes ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok Check that the Topology is correctly sized ... ok testsuite.MDAnalysisTests.topology.test_psf.TestPSFParser.test_angles_identity ... ok testsuite.MDAnalysisTests.topology.test_psf.TestPSFParser.test_angles_total_counts ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_psf.TestPSFParser.test_bonds_identity ... ok testsuite.MDAnalysisTests.topology.test_psf.TestPSFParser.test_bonds_total_counts ... ok testsuite.MDAnalysisTests.topology.test_psf.TestPSFParser.test_angles_atom_counts ... ok testsuite.MDAnalysisTests.topology.test_psf.TestPSFParser.test_bonds_atom_counts ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_psf.TestPSFParser.test_dihedrals_identity ... ok testsuite.MDAnalysisTests.topology.test_psf.TestPSFParser.test_dihedrals_total_counts ... ok testsuite.MDAnalysisTests.topology.test_psf.TestPSFParser.test_expected_attributes ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_psf.TestPSFParser.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_psf.TestPSFParser.test_dihedrals_atom_counts ... ok testsuite.MDAnalysisTests.topology.test_psf.TestPSFParser2.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_psf.TestPSFParser.test_mandatory_attributes ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_psf.TestPSFParser2.test_guessed_attributes ... ok Check that Universe works with this Parser ... ok Issue #121 ... ok testsuite.MDAnalysisTests.topology.test_psf.TestPSFParser2.test_as_universe_resids ... ok Check that the Topology is correctly sized ... ok testsuite.MDAnalysisTests.topology.test_psf.TestPSFParser2.test_mandatory_attributes ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok Check that the transtable is appropriately sized ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_top.TestPRM12Parser.test_attr_size ... ok testsuite.MDAnalysisTests.topology.test_top.TestPRM12Parser.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_top.TestPRM12Parser.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_top.TestPRM12Parser.test_mandatory_attributes ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_top.TestPRM2.test_attr_size ... ok Check that the Topology is correctly sized ... ok testsuite.MDAnalysisTests.topology.test_top.TestPRM2.test_expected_attributes ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_top.TestPRMParser.test_attr_size ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_top.TestPRM2.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_top.TestPRM2.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_top.TestPRMParser.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_top.TestPRMParser.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_top.TestPRMParser.test_mandatory_attributes ... ok Check that Universe works with this Parser ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok Testing the call signature ... ok Check that the Topology is correctly sized ... ok Testing the call signature ... ok Check that Universe works with this Parser ... ok Check that the transtable is appropriately sized ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_topology_base.TestChangeSquash.test_resid_squash ... ok testsuite.MDAnalysisTests.topology.test_topology_base.TestChangeSquash.test_segid_squash ... ok testsuite.MDAnalysisTests.topology.test_topology_base.TestSquash.test_squash ... ok testsuite.MDAnalysisTests.topology.test_top.TestParm7Parser.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_top.TestParm7Parser.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_top.TestParm7Parser.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_top.TestParm7Parser.test_attr_size ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok Check that Universe works with this Parser ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR400.test_expected_attributes ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR.test_mandatory_attributes ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR400.test_guessed_attributes ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR402.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR402.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR402.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR400.test_mandatory_attributes ... ok Check that the Topology is correctly sized ... ok Testing the call signature ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR403.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR403.test_guessed_attributes ... ok Check that Universe works with this Parser ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR403.test_mandatory_attributes ... ok Check that Universe works with this Parser ... ok Testing the call signature ... ok Check that the Topology is correctly sized ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR404.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR404.test_mandatory_attributes ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok Check that the Topology is correctly sized ... ok Check that Universe works with this Parser ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR404.test_guessed_attributes ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR405.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR405.test_guessed_attributes ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR405.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR406.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR406.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR406.test_expected_attributes ... ok Check that Universe works with this Parser ... ok Check that Universe works with this Parser ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok Check that the Topology is correctly sized ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR407.test_expected_attributes ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR407.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR407.test_mandatory_attributes ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR450.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR450.test_guessed_attributes ... ok Check that Universe works with this Parser ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR450.test_mandatory_attributes ... ok Check that the Topology is correctly sized ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR451.test_guessed_attributes ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR451.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR451.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR452.test_expected_attributes ... ok Check that Universe works with this Parser ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR452.test_mandatory_attributes ... ok Testing the call signature ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR452.test_guessed_attributes ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR453.test_expected_attributes ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR453.test_mandatory_attributes ... ok Check that the transtable is appropriately sized ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR453.test_guessed_attributes ... ok Check that the Topology is correctly sized ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR454.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR454.test_mandatory_attributes ... ok Testing the call signature ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR454.test_expected_attributes ... ok Check that the transtable is appropriately sized ... ok Check that the Topology is correctly sized ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR455.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR455.test_mandatory_attributes ... ok Testing the call signature ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR455.test_expected_attributes ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR455Double.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR455Double.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR455Double.test_mandatory_attributes ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok Testing the call signature ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR460.test_guessed_attributes ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR460.test_mandatory_attributes ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR460.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR461.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR461.test_mandatory_attributes ... ok Check that the Topology is correctly sized ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR461.test_expected_attributes ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR502.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR502.test_guessed_attributes ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok Check that Universe works with this Parser ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR502.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR504.test_expected_attributes ... ok Check that the Topology is correctly sized ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR504.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR504.test_mandatory_attributes ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR505.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR505.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR505.test_mandatory_attributes ... ok Check that Universe works with this Parser ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR510.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR510.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.TestTPR510.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_angles('UREY_BRADLEY', [(4, 5, 6)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_5.1.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_angles('QANGLES', [(5, 6, 7)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_5.1.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_angles('ANGLES', [(0, 1, 2)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_5.1.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_angles('G96ANGLES', [(1, 2, 3)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_5.1.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_angles('RESTRANGLES', [(6, 7, 8)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_5.1.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_angles('TABANGLES', [(7, 8, 9)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_5.1.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_angles('CROSS_BOND_BOND', [(2, 3, 4)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_5.1.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_angles('CROSS_BOND_ANGLE', [(3, 4, 5)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_5.1.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_angles('UREY_BRADLEY', [(4, 5, 6)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_2016.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_angles('QANGLES', [(5, 6, 7)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_2016.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_angles('ANGLES', [(0, 1, 2)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_2016.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_angles('G96ANGLES', [(1, 2, 3)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_2016.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_angles('RESTRANGLES', [(6, 7, 8)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_2016.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_angles('TABANGLES', [(7, 8, 9)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_2016.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_angles('CROSS_BOND_BOND', [(2, 3, 4)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_2016.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_angles('CROSS_BOND_ANGLE', [(3, 4, 5)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_2016.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_impropers('PIDIHS', [(5, 6, 7, 8)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_5.1.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_impropers('IDIHS', [(2, 3, 4, 5), (3, 4, 5, 6)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_5.1.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_impropers('PIDIHS', [(5, 6, 7, 8)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_2016.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_impropers('IDIHS', [(2, 3, 4, 5), (3, 4, 5, 6)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_2016.tpr') ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_xpdb.TestXPDBParser.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_xpdb.TestXPDBParser.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_xpdb.TestXPDBParser.test_mandatory_attributes ... ok Testing the call signature ... ok Check that the Topology is correctly sized ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_dihedrals('RESTRDIHS', [(8, 9, 10, 11)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_5.1.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_dihedrals('TABDIHS', [(10, 11, 12, 13)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_5.1.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_dihedrals('PDIHS', [(0, 1, 2, 3), (1, 2, 3, 4), (7, 8, 9, 10)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_5.1.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_dihedrals('CBTDIHS', [(9, 10, 11, 12)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_5.1.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_dihedrals('RBDIHS', [(4, 5, 6, 7)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_5.1.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_dihedrals('FOURDIHS', [(6, 7, 8, 9)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_5.1.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_dihedrals('RESTRDIHS', [(8, 9, 10, 11)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_2016.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_dihedrals('TABDIHS', [(10, 11, 12, 13)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_2016.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_dihedrals('PDIHS', [(0, 1, 2, 3), (1, 2, 3, 4), (7, 8, 9, 10)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_2016.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_dihedrals('CBTDIHS', [(9, 10, 11, 12)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_2016.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_dihedrals('RBDIHS', [(4, 5, 6, 7)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_2016.tpr') ... ok testsuite.MDAnalysisTests.topology.test_tprparser.test_all_dihedrals('FOURDIHS', [(6, 7, 8, 9)], '/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/tprs/all_bonded/dummy_2016.tpr') ... ok Check that the transtable is appropriately sized ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Test that all bond types are parsed as expected ... ok Check that Universe works with this Parser ... ok testsuite.MDAnalysisTests.topology.test_xyz.TestXYZMini.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_xyz.TestXYZMini.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_xyz.TestXYZMini.test_guessed_attributes ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok Check that the Topology is correctly sized ... ok testsuite.MDAnalysisTests.topology.test_xyz.TestXYZParser.test_expected_attributes ... ok testsuite.MDAnalysisTests.topology.test_xyz.TestXYZParser.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_xyz.TestXYZParser.test_mandatory_attributes ... ok Testing the call signature ... ok Check that the transtable is appropriately sized ... ok Check that Universe works with this Parser ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.topology.test_xyz.TestXYZParserBz2.test_guessed_attributes ... ok testsuite.MDAnalysisTests.topology.test_xyz.TestXYZParserBz2.test_mandatory_attributes ... ok testsuite.MDAnalysisTests.topology.test_xyz.TestXYZParserBz2.test_expected_attributes ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.utils.test_authors.test_package_authors ... ok testsuite.MDAnalysisTests.utils.test_authors.test_testsuite_authors ... ok testsuite.MDAnalysisTests.utils.test_datafiles.TestDatafiles.test_all_exports ... ok Testing the call signature ... ok testsuite.MDAnalysisTests.utils.test_datafiles.TestDatafiles.test_export_variables ... ok testsuite.MDAnalysisTests.utils.test_datafiles.TestDatafiles.test_import ... ok testsuite.MDAnalysisTests.utils.test_deprecated.TestImports.test_KDTree ... ok testsuite.MDAnalysisTests.utils.test_deprecated.TestImports.test_core_distances ... ok testsuite.MDAnalysisTests.utils.test_deprecated.TestImports.test_analysis_x3dna ... ok testsuite.MDAnalysisTests.utils.test_deprecated.TestImports.test_core_log ... ok testsuite.MDAnalysisTests.utils.test_deprecated.TestImports.test_core_qcprot ... ok testsuite.MDAnalysisTests.utils.test_deprecated.TestImports.test_core_transformations ... ok Check that the Topology is correctly sized ... ok Check that the transtable is appropriately sized ... ok testsuite.MDAnalysisTests.utils.test_deprecated.TestImports.test_core_units ... ok testsuite.MDAnalysisTests.utils.test_deprecated.TestImports.test_core_util ... ok testsuite.MDAnalysisTests.utils.test_deprecated.test_collections_NotImplementedError ... ok test_angles (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_Serial) ... ok test_angles_bad_result (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_Serial) ... ok test_angles_wrongtype (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_Serial) ... ok test_bonds (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_Serial) ... ok test_bonds_badbox (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_Serial) ... ok test_bonds_badresult (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_Serial) ... ok test_bonds_triclinic (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_Serial) ... ok test_bonds_wrongtype (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_Serial) ... ok test_dihedrals (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_Serial) ... ok test_dihedrals_bad_result (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_Serial) ... ok test_dihedrals_wronglength (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_Serial) ... ok test_dihedrals_wrongtype (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_Serial) ... ok test_numpy_compliance (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_Serial) ... ok Check that the Topology is correctly sized ... ok Check that Universe works with this Parser ... ok test_PBC (testsuite.MDAnalysisTests.utils.test_distances.TestDistanceArray_Serial) ... ok test_PBC2 (testsuite.MDAnalysisTests.utils.test_distances.TestDistanceArray_Serial) ... ok test_noPBC (testsuite.MDAnalysisTests.utils.test_distances.TestDistanceArray_Serial) ... ok testsuite.MDAnalysisTests.utils.test_distances.TestDistanceBackendSelection.test_missing_backend_raises_ValueError ... ok test_PBC (testsuite.MDAnalysisTests.utils.test_distances.TestDistanceArray_OpenMP) ... ok test_PBC2 (testsuite.MDAnalysisTests.utils.test_distances.TestDistanceArray_OpenMP) ... ok test_noPBC (testsuite.MDAnalysisTests.utils.test_distances.TestDistanceArray_OpenMP) ... ok test_angles (testsuite.MDAnalysisTests.utils.test_distances.TestPeriodicAngles_Serial) ... ok test_dihedrals (testsuite.MDAnalysisTests.utils.test_distances.TestPeriodicAngles_Serial) ... ok testsuite.MDAnalysisTests.utils.test_distances.TestDistanceBackendSelection.test_case_insensitivity('serial',) ... ok testsuite.MDAnalysisTests.utils.test_distances.TestDistanceBackendSelection.test_case_insensitivity('Serial',) ... ok testsuite.MDAnalysisTests.utils.test_distances.TestDistanceBackendSelection.test_case_insensitivity('SeRiAL',) ... ok testsuite.MDAnalysisTests.utils.test_distances.TestDistanceBackendSelection.test_case_insensitivity('SERIAL',) ... ok testsuite.MDAnalysisTests.utils.test_distances.TestDistanceBackendSelection.test_case_insensitivity('openmp',) ... ok testsuite.MDAnalysisTests.utils.test_distances.TestDistanceBackendSelection.test_case_insensitivity('OpenMP',) ... ok testsuite.MDAnalysisTests.utils.test_distances.TestDistanceBackendSelection.test_case_insensitivity('oPENmP',) ... ok testsuite.MDAnalysisTests.utils.test_distances.TestDistanceBackendSelection.test_case_insensitivity('OPENMP',) ... ok test_angles (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_OpenMP) ... ok test_angles_bad_result (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_OpenMP) ... ok test_angles_wrongtype (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_OpenMP) ... ok test_bonds (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_OpenMP) ... ok test_bonds_badbox (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_OpenMP) ... ok test_bonds_badresult (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_OpenMP) ... ok test_bonds_triclinic (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_OpenMP) ... ok test_bonds_wrongtype (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_OpenMP) ... ok test_dihedrals (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_OpenMP) ... ok test_dihedrals_bad_result (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_OpenMP) ... ok test_dihedrals_wronglength (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_OpenMP) ... ok test_dihedrals_wrongtype (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_OpenMP) ... ok test_numpy_compliance (testsuite.MDAnalysisTests.utils.test_distances.TestCythonFunctions_OpenMP) ... ok Check that Universe works with this Parser ... ok test_angles (testsuite.MDAnalysisTests.utils.test_distances.TestPeriodicAngles_OpenMP) ... ok test_dihedrals (testsuite.MDAnalysisTests.utils.test_distances.TestPeriodicAngles_OpenMP) ... ok testsuite.MDAnalysisTests.utils.test_distances.test_used_openmpflag ... ok Fail if the MDA_FAILURE_TEST environment variable is set. ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_velocities_forces.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_altloc.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_nuclinfo.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_lammpsdata.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_distances.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_libxdrfile2.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_streamio.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_qcprot.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_tprparser.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_atomgroup.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_datafiles.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_meta.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_log.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_persistence.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_deprecated.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_util.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_modelling.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_topology.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_transformations.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_atomselections.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_imports.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_units.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/test_selections.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/util.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/authors.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/tempdir.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/__init__.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/datafiles.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/coordinates/create_data.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/formats/test_xdrlib.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/formats/__init__.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/formats/test_libmdaxdr.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_coordinates.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_timestep_api.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_netcdf_ORIG.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_lammps.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_memory.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/__init__.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_pqr.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_dms.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_dlpoly.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_dcd.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_gro.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_null.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_xdr.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_pdbqt.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_trz.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_mol2.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_gms.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_chainreader.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_trj.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_xyz.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_crd.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_netcdf.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_pdb.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_writer_registration.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_amber_inpcrd.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/base.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/reference.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_mmtf.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/coordinates/test_reader_api.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/auxiliary/test_xvg.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/auxiliary/__init__.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/auxiliary/base.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/test_atom.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/test_residuegroup.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/test_index_dtype.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/test_fragments.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/test_updating_atomgroup.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/test_groups.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/__init__.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/test_topologyattrs.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/test_atomgroup.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/test_group_traj_access.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/test_residue.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/test_requires.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/test_universe.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/test_segment.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/util.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/test_topologyobjects.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/test_topology.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/test_atomselections.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/core/test_segmentgroup.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/utils/test_altloc.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/utils/test_nuclinfo.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/utils/test_distances.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/utils/test_streamio.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/utils/test_failure.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/utils/test_qcprot.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/utils/__init__.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/utils/test_datafiles.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/utils/test_meta.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/utils/test_log.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/utils/test_persistence.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/utils/test_deprecated.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/utils/test_modelling.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/utils/test_authors.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/utils/test_transformations.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/utils/test_imports.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/utils/test_units.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/utils/test_selections.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/lib/__init__.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/lib/test_util.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_persistencelength.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_nuclinfo.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_distances.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_base.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_leaflet.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_helanal.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_gnm.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_lineardensity.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/__init__.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_hbonds.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_density.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_contacts.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_pca.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_rms.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_align.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_hole.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_diffusionmap.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_psa.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_encore.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_rdf.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/analysis/test_waterdynamics.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_xpdb.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_guessers.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_lammpsdata.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_hoomdxml.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/__init__.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_pqr.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_tprparser.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_topology_base.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_dms.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_dlpoly.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_gro.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_pdbqt.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_psf.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_mol2.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_gms.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_top.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_xyz.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_crd.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_pdb.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/base.py',) ... ok testsuite.MDAnalysisTests.utils.test_imports.TestRelativeImports.test_relative_imports('/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/topology/test_mmtf.py',) ... ok test_start_stop_logging (testsuite.MDAnalysisTests.utils.test_log.TestLogging) ... ok test_custom_ProgressMeter (testsuite.MDAnalysisTests.utils.test_log.TestProgressMeter) ... ok test_default_ProgressMeter (testsuite.MDAnalysisTests.utils.test_log.TestProgressMeter) ... ok test_legacy_ProgressMeter (testsuite.MDAnalysisTests.utils.test_log.TestProgressMeter) ... ok test_not_dynamic_ProgressMeter (testsuite.MDAnalysisTests.utils.test_log.TestProgressMeter) ... ok testsuite.MDAnalysisTests.utils.test_log.test__set_verbose ... ok testsuite.MDAnalysisTests.utils.test_meta.test_import ... ok testsuite.MDAnalysisTests.utils.test_meta.test_matching_versions ... ok testsuite.MDAnalysisTests.utils.test_meta.test_version_format ... ok testsuite.MDAnalysisTests.utils.test_meta.test_version_at_packagelevel ... ok test_distarray (testsuite.MDAnalysisTests.utils.test_distances.TestTriclinicDistances_Serial) ... ok test_pbc_dist (testsuite.MDAnalysisTests.utils.test_distances.TestTriclinicDistances_Serial) ... ok test_selfdist (testsuite.MDAnalysisTests.utils.test_distances.TestTriclinicDistances_Serial) ... ok test_transforms (testsuite.MDAnalysisTests.utils.test_distances.TestTriclinicDistances_Serial) ... ok Testing the call signature ... ok test_capping_file (testsuite.MDAnalysisTests.utils.test_modelling.TestCapping) ... ok test_capping_inmemory (testsuite.MDAnalysisTests.utils.test_modelling.TestCapping) ... ok test_distarray (testsuite.MDAnalysisTests.utils.test_distances.TestTriclinicDistances_OpenMP) ... ok test_pbc_dist (testsuite.MDAnalysisTests.utils.test_distances.TestTriclinicDistances_OpenMP) ... ok test_selfdist (testsuite.MDAnalysisTests.utils.test_distances.TestTriclinicDistances_OpenMP) ... ok test_transforms (testsuite.MDAnalysisTests.utils.test_distances.TestTriclinicDistances_OpenMP) ... ok testsuite.MDAnalysisTests.utils.test_modelling.TestMergeTopology.test_merge_with_topology ... ok testsuite.MDAnalysisTests.utils.test_modelling.TestMergeTopology.test_merge_with_topology_from_different_universes ... ok test_hydroxyl (testsuite.MDAnalysisTests.utils.test_nuclinfo.TestNuclinfo) ... ok test_major_pair (testsuite.MDAnalysisTests.utils.test_nuclinfo.TestNuclinfo) ... ok test_minor_pair (testsuite.MDAnalysisTests.utils.test_nuclinfo.TestNuclinfo) ... ok test_pseudo_dihe_baseflip (testsuite.MDAnalysisTests.utils.test_nuclinfo.TestNuclinfo) ... ok test_torsions (testsuite.MDAnalysisTests.utils.test_nuclinfo.TestNuclinfo) ... ok test_wc_pair (testsuite.MDAnalysisTests.utils.test_nuclinfo.TestNuclinfo) ... ok test_outarray (testsuite.MDAnalysisTests.utils.test_distances.TestDistanceArrayDCD_OpenMP) ... ok test_periodic (testsuite.MDAnalysisTests.utils.test_distances.TestDistanceArrayDCD_OpenMP) ... ok test_simple (testsuite.MDAnalysisTests.utils.test_distances.TestDistanceArrayDCD_OpenMP) ... ok test_outarray (testsuite.MDAnalysisTests.utils.test_distances.TestSelfDistanceArrayDCD_OpenMP) ... ok test_periodic (testsuite.MDAnalysisTests.utils.test_distances.TestSelfDistanceArrayDCD_OpenMP) ... ok test_simple (testsuite.MDAnalysisTests.utils.test_distances.TestSelfDistanceArrayDCD_OpenMP) ... ok Test that an empty AtomGroup can be pickled/unpickled (Issue 293) ... ok testsuite.MDAnalysisTests.utils.test_modelling.TestMergeTopology.test_merge_without_topology ... ok Test that an AtomGroup can be unpickled (Issue 293) ... ok test_outarray (testsuite.MDAnalysisTests.utils.test_distances.TestSelfDistanceArrayDCD_Serial) ... ok test_periodic (testsuite.MDAnalysisTests.utils.test_distances.TestSelfDistanceArrayDCD_Serial) ... ok test_simple (testsuite.MDAnalysisTests.utils.test_distances.TestSelfDistanceArrayDCD_Serial) ... ok Test that an AtomGroup can be unpickled (Issue 293) ... ok testsuite.MDAnalysisTests.utils.test_persistence.TestAtomGroupPickle.test_unpickle_noanchor ... ok test_outarray (testsuite.MDAnalysisTests.utils.test_distances.TestDistanceArrayDCD_Serial) ... ok test_periodic (testsuite.MDAnalysisTests.utils.test_distances.TestDistanceArrayDCD_Serial) ... ok test_simple (testsuite.MDAnalysisTests.utils.test_distances.TestDistanceArrayDCD_Serial) ... ok testsuite.MDAnalysisTests.utils.test_qcprot.test_CalcRMSDRotationalMatrix ... ok testsuite.MDAnalysisTests.utils.test_qcprot.test_innerproduct ... ok testsuite.MDAnalysisTests.utils.test_qcprot.test_RMSDmatrix ... ok testsuite.MDAnalysisTests.utils.test_qcprot.test_rmsd ... ok testsuite.MDAnalysisTests.utils.test_qcprot.test_weights ... ok testsuite.MDAnalysisTests.utils.test_persistence.TestAtomGroupPickle.test_unpickle_reanchor ... ok testsuite.MDAnalysisTests.utils.test_persistence.TestPicklingUpdatingAtomGroups.test_pickling_uag ... ok testsuite.MDAnalysisTests.utils.test_persistence.TestAtomGroupPickle.test_unpickle_rename ... ok testsuite.MDAnalysisTests.utils.test_persistence.TestPicklingUpdatingAtomGroups.test_pickling_uag_of_uag ... ok testsuite.MDAnalysisTests.utils.test_persistence.TestAtomGroupPickle.test_unpickle_missing ... ok test_StringIO_read (testsuite.MDAnalysisTests.utils.test_streamio.TestIsstream) ... ok test_StringIO_write (testsuite.MDAnalysisTests.utils.test_streamio.TestIsstream) ... ok test_cStringIO_read (testsuite.MDAnalysisTests.utils.test_streamio.TestIsstream) ... ok test_cStringIO_write (testsuite.MDAnalysisTests.utils.test_streamio.TestIsstream) ... ok test_file (testsuite.MDAnalysisTests.utils.test_streamio.TestIsstream) ... ok test_hasmethod (testsuite.MDAnalysisTests.utils.test_streamio.TestIsstream) ... ok test_iterator (testsuite.MDAnalysisTests.utils.test_streamio.TestIsstream) ... ok test_list (testsuite.MDAnalysisTests.utils.test_streamio.TestIsstream) ... ok test_string (testsuite.MDAnalysisTests.utils.test_streamio.TestIsstream) ... ok test_File_read (testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream) ... ok test_File_write (testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream) ... ok test_cStringIO_read (testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream) ... ok test_cStringIO_write (testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream) ... ok test_closing (testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream) ... ok test_closing_force (testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream) ... ok testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream_filename_behavior.test_add ... ok testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream_filename_behavior.test_expanduser_noexpansion_returns_NamedStream ... SKIP: Skipping test: test_expanduser_noexpansion_returns_NamedStream: Test skipped due to test condition testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream_filename_behavior.test_expandvars ... SKIP: Skipping test: test_expandvars: Test skipped due to test condition testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream_filename_behavior.test_expandvars_noexpansion_returns_NamedStream ... SKIP: Skipping test: test_expandvars_noexpansion_returns_NamedStream: Test skipped due to test condition testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream_filename_behavior.test_ospath_funcs('abspath',) ... ok testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream_filename_behavior.test_ospath_funcs('basename',) ... ok testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream_filename_behavior.test_ospath_funcs('dirname',) ... ok testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream_filename_behavior.test_ospath_funcs('expanduser',) ... ok testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream_filename_behavior.test_ospath_funcs('normpath',) ... ok testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream_filename_behavior.test_ospath_funcs('relpath',) ... ok testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream_filename_behavior.test_ospath_funcs('split',) ... ok testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream_filename_behavior.test_ospath_funcs('splitext',) ... ok testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream_filename_behavior.test_ospath_funcs('join',) ... ok testsuite.MDAnalysisTests.utils.test_streamio.TestNamedStream_filename_behavior.test_radd ... ok testsuite.MDAnalysisTests.utils.test_persistence.TestAtomGroupPickle.test_unpickle_wrongname ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestArcBall.test_arcball_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestArcBall.test_arcball_2 ... ok test_clip_matrix_1 (testsuite.MDAnalysisTests.utils.test_transformations.TestClipMatrixCy) ... ok test_clip_matrix_2 (testsuite.MDAnalysisTests.utils.test_transformations.TestClipMatrixCy) ... ok ValueError should be raised if bottom > top. ... ok ValueError should be raised if left > right. ... ok ValueError should be raised if near > far. ... ok test_clip_matrix_1 (testsuite.MDAnalysisTests.utils.test_transformations.TestClipMatrixNP) ... ok test_clip_matrix_2 (testsuite.MDAnalysisTests.utils.test_transformations.TestClipMatrixNP) ... ok ValueError should be raised if bottom > top. ... ok ValueError should be raised if left > right. ... ok ValueError should be raised if near > far. ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestDecomposeMatrix.test_decompose_matrix_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestDecomposeMatrix.test_decompose_matrix_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestDecomposeMatrix.test_decompose_matrix_3 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestEulerFromMatrixCy.test_euler_from_matrix_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestEulerFromMatrixCy.test_euler_from_matrix_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestEulerFromMatrixNP.test_euler_from_matrix_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestEulerFromMatrixNP.test_euler_from_matrix_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestEulerMatrixCy.test_euler_matrix_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestEulerMatrixCy.test_euler_matrix_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestEulerMatrixNP.test_euler_matrix_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestEulerMatrixNP.test_euler_matrix_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestIdentityMatrixCy.test_identity_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestIdentityMatrixNP.test_identity_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestInverseMatrixCy.test_inverse_matrix(1,) ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestInverseMatrixCy.test_inverse_matrix(2,) ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestInverseMatrixCy.test_inverse_matrix(3,) ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestInverseMatrixCy.test_inverse_matrix(4,) ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestInverseMatrixCy.test_inverse_matrix(5,) ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestInverseMatrixCy.test_inverse_matrix(6,) ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestInverseMatrixNP.test_inverse_matrix(1,) ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestInverseMatrixNP.test_inverse_matrix(2,) ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestInverseMatrixNP.test_inverse_matrix(3,) ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestInverseMatrixNP.test_inverse_matrix(4,) ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestInverseMatrixNP.test_inverse_matrix(5,) ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestInverseMatrixNP.test_inverse_matrix(6,) ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestIsSameTransformCy.test_is_same_transform_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestIsSameTransformCy.test_is_same_transform_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestIsSameTransformNP.test_is_same_transform_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestIsSameTransformNP.test_is_same_transform_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestOrthogonalizationMatrixCy.test_orthogonalization_matrix_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestOrthogonalizationMatrixCy.test_orthogonalization_matrix_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestOrthogonalizationMatrixNP.test_orthogonalization_matrix_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestOrthogonalizationMatrixNP.test_orthogonalization_matrix_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestProjectionFromMatrix.test_projection_from_matrix_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestProjectionFromMatrix.test_projection_from_matrix_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestProjectionFromMatrix.test_projection_from_matrix_3 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestProjectionFromMatrix.test_projection_from_matrix_4 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestProjectionMatrixCy.test_projection_matrix_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestProjectionMatrixCy.test_projection_matrix_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestProjectionMatrixCy.test_projection_matrix_3 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestProjectionMatrixNP.test_projection_matrix_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestProjectionMatrixNP.test_projection_matrix_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestProjectionMatrixNP.test_projection_matrix_3 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionAboutAxisCy.test_quaternion_about_axis ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionAboutAxisNP.test_quaternion_about_axis ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionConjugateCy.test_quaternion_conjugate ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionConjugateNP.test_quaternion_conjugate ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionFromEulerCy.test_quaternion_from_euler ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionFromEulerNP.test_quaternion_from_euler ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionFromMatrixCy.test_quaternion_from_matrix_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionFromMatrixCy.test_quaternion_from_matrix_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionFromMatrixCy.test_quaternion_from_matrix_3 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionFromMatrixCy.test_quaternion_from_matrix_4 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionFromMatrixCy.test_quaternion_from_matrix_5 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionFromMatrixCy.test_quaternion_from_matrix_6 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionFromMatrixNP.test_quaternion_from_matrix_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionFromMatrixNP.test_quaternion_from_matrix_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionFromMatrixNP.test_quaternion_from_matrix_3 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionFromMatrixNP.test_quaternion_from_matrix_4 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionFromMatrixNP.test_quaternion_from_matrix_5 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionFromMatrixNP.test_quaternion_from_matrix_6 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionInverseCy.test_quaternion_inverse ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionInverseNP.test_quaternion_inverse ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionMatrixCy.test_quaternion_matrix_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionMatrixCy.test_quaternion_matrix_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionMatrixCy.test_quaternion_matrix_3 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionMatrixNP.test_quaternion_matrix_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionMatrixNP.test_quaternion_matrix_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionMatrixNP.test_quaternion_matrix_3 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionMultiplyCy.test_quaternion_multiply ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionMultiplyNP.test_quaternion_multiply ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionSlerpCy.test_quaternion_slerp ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestQuaternionSlerpNP.test_quaternion_slerp ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestRandomQuaternionCy.test_random_quaternion_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestRandomQuaternionCy.test_random_quaternion_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestRandomQuaternionNP.test_random_quaternion_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestRandomQuaternionNP.test_random_quaternion_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestRandomRotationMatrixCy.test_random_rotation_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestRandomRotationMatrixNP.test_random_rotation_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestRandomVectorCy.test_random_vector_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestRandomVectorCy.test_random_vector_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestRandomVectorNP.test_random_vector_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestRandomVectorNP.test_random_vector_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestReflectionMatrixCy.test_reflection_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestReflectionMatrixNP.test_reflection_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestRotationMatrixCy.test_rotation_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestRotationMatrixNP.test_rotation_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestScaleMatrixCy.test_scale_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestScaleMatrixNP.test_scale_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestShearMatrixCy.test_shear_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestShearMatrixNP.test_shear_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestSuperimpositionMatrixCy.test_superimposition_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestSuperimpositionMatrixNP.test_superimposition_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestTranslationMatrixCy.test_translation_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestTranslationMatrixNP.test_translation_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestUnitVectorCy.test_unit_vector_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestUnitVectorCy.test_unit_vector_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestUnitVectorCy.test_unit_vector_3 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestUnitVectorCy.test_unit_vector_4 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestUnitVectorCy.test_unit_vector_5 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestUnitVectorCy.test_unit_vector_6 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestUnitVectorNP.test_unit_vector_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestUnitVectorNP.test_unit_vector_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestUnitVectorNP.test_unit_vector_3 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestUnitVectorNP.test_unit_vector_4 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestUnitVectorNP.test_unit_vector_5 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestUnitVectorNP.test_unit_vector_6 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestVectorNormCy.test_vector_norm_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestVectorNormCy.test_vector_norm_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestVectorNormCy.test_vector_norm_3 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestVectorNormCy.test_vector_norm_4 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestVectorNormCy.test_vector_norm_5 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestVectorNormCy.test_vector_norm_6 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestVectorNormNP.test_vector_norm_1 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestVectorNormNP.test_vector_norm_2 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestVectorNormNP.test_vector_norm_3 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestVectorNormNP.test_vector_norm_4 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestVectorNormNP.test_vector_norm_5 ... ok testsuite.MDAnalysisTests.utils.test_transformations.TestVectorNormNP.test_vector_norm_6 ... ok testsuite.MDAnalysisTests.utils.test_transformations.test_translation_from_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.test_reflection_from_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.test_rotation_from_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.test_scale_from_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.test_shear_from_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.test_compose_matrix ... ok testsuite.MDAnalysisTests.utils.test_transformations.test_euler_from_quaternion ... ok testsuite.MDAnalysisTests.utils.test_transformations.test_quaternion_real ... ok testsuite.MDAnalysisTests.utils.test_transformations.test_quaternion_imag ... ok test that MDAnalysis.core.transformations is still importable ... ok testsuite.MDAnalysisTests.utils.test_transformations.test_rotaxis_equal_vectors ... ok testsuite.MDAnalysisTests.utils.test_transformations.test_rotaxis_different_vectors ... ok testsuite.MDAnalysisTests.utils.test_units.TestConstants.test_constant(u'elementary_charge', 1.602176565e-19) ... ok testsuite.MDAnalysisTests.utils.test_units.TestConstants.test_constant(u'N_Avogadro', 6.02214129e+23) ... ok testsuite.MDAnalysisTests.utils.test_units.TestConstants.test_constant(u'calorie', 4.184) ... ok testsuite.MDAnalysisTests.utils.test_units.TestConversion.test_energy(1, u'kcal/mol', u'kJ/mol', 4.184) ... ok testsuite.MDAnalysisTests.utils.test_units.TestConversion.test_energy(1, u'kcal/mol', u'eV', 0.0433641) ... ok testsuite.MDAnalysisTests.utils.test_units.TestConversion.test_force(1, u'kJ/(mol*A)', u'J/m', 1.66053892103219e-11) ... ok testsuite.MDAnalysisTests.utils.test_units.TestConversion.test_force(2.5, u'kJ/(mol*nm)', u'kJ/(mol*A)', 0.25) ... ok testsuite.MDAnalysisTests.utils.test_units.TestConversion.test_force(1, u'kcal/(mol*Angstrom)', u'kJ/(mol*Angstrom)', 4.184) ... ok testsuite.MDAnalysisTests.utils.test_units.TestConversion.test_length(12.34567, u'nm', u'A', 123.4567) ... ok testsuite.MDAnalysisTests.utils.test_units.TestConversion.test_length(123.4567, u'Angstrom', u'nm', 12.34567) ... ok testsuite.MDAnalysisTests.utils.test_units.TestConversion.test_time(1, u'ps', u'AKMA', 20.45482949774598) ... ok testsuite.MDAnalysisTests.utils.test_units.TestConversion.test_time(1, u'AKMA', u'ps', 0.04888821) ... ok testsuite.MDAnalysisTests.utils.test_units.TestConversion.test_unit_unconvertable ... ok testsuite.MDAnalysisTests.utils.test_units.TestConversion.test_unit_unknown ... ok test_convert_gromacs_trajectories (testsuite.MDAnalysisTests.utils.test_units.TestDefaultUnits) ... ok test_length (testsuite.MDAnalysisTests.utils.test_units.TestDefaultUnits) ... ok test_time (testsuite.MDAnalysisTests.utils.test_units.TestDefaultUnits) ... ok test_unicode (testsuite.MDAnalysisTests.utils.test_units.TestUnitEncoding) ... ok test_unicode_encoding_with_symbol (testsuite.MDAnalysisTests.utils.test_units.TestUnitEncoding) ... ok test_write (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_Gromacs) ... ok test_write_bad_mode (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_Gromacs) ... ok test_write_with (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_Gromacs) ... ok test_writeselection (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_Gromacs) ... ok test_write (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_PyMOL) ... ok test_write_bad_mode (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_PyMOL) ... ok test_write_with (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_PyMOL) ... ok test_writeselection (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_PyMOL) ... ok test_write (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_Charmm) ... ok test_write_bad_mode (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_Charmm) ... ok test_write_with (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_Charmm) ... ok test_writeselection (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_Charmm) ... ok test_write (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_VMD) ... ok test_write_bad_mode (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_VMD) ... ok test_write_with (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_VMD) ... ok test_writeselection (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_VMD) ... ok test_write (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_Jmol) ... ok test_write_bad_mode (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_Jmol) ... ok test_write_with (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_Jmol) ... ok test_writeselection (testsuite.MDAnalysisTests.utils.test_selections.TestSelectionWriter_Jmol) ... ok test_emptyAG_ValueError (testsuite.MDAnalysisTests.utils.test_modelling.TestMerge) ... ok test_empty_ValueError (testsuite.MDAnalysisTests.utils.test_modelling.TestMerge) ... ok test_merge (testsuite.MDAnalysisTests.utils.test_modelling.TestMerge) ... ok test_merge_same_universe (testsuite.MDAnalysisTests.utils.test_modelling.TestMerge) ... ok test_nonsense_TypeError (testsuite.MDAnalysisTests.utils.test_modelling.TestMerge) ... ok test_residue_references (testsuite.MDAnalysisTests.utils.test_modelling.TestMerge) ... ok test_segment_references (testsuite.MDAnalysisTests.utils.test_modelling.TestMerge) ... ok test_atomgroups (testsuite.MDAnalysisTests.utils.test_altloc.TestAltloc) ... ok test_bonds (testsuite.MDAnalysisTests.utils.test_altloc.TestAltloc) ... ok test_write_read (testsuite.MDAnalysisTests.utils.test_altloc.TestAltloc) ... ok test_CRDReader (testsuite.MDAnalysisTests.utils.test_streamio.TestStreamIO) ... ok test_GROReader (testsuite.MDAnalysisTests.utils.test_streamio.TestStreamIO) ... ok test_MOL2Reader (testsuite.MDAnalysisTests.utils.test_streamio.TestStreamIO) ... ok test_PDBQTReader (testsuite.MDAnalysisTests.utils.test_streamio.TestStreamIO) ... ok test_PDBReader (testsuite.MDAnalysisTests.utils.test_streamio.TestStreamIO) ... ok test_PQRReader (testsuite.MDAnalysisTests.utils.test_streamio.TestStreamIO) ... ok test_PSFParser (testsuite.MDAnalysisTests.utils.test_streamio.TestStreamIO) ... ok test_PSF_CRD (testsuite.MDAnalysisTests.utils.test_streamio.TestStreamIO) ... ok test_PrimitivePDBReader (testsuite.MDAnalysisTests.utils.test_streamio.TestStreamIO) ... ok test_XYZReader (testsuite.MDAnalysisTests.utils.test_streamio.TestStreamIO) ... ok testsuite.MDAnalysisTests.coordinates.test_lammps.TestLAMMPSDATAWriter_data.test_Writer_atoms ... ok test_conect_bonds_all (testsuite.MDAnalysisTests.coordinates.test_pdb.TestMultiPDBReader) ... ok test_conect_bonds_conect (testsuite.MDAnalysisTests.coordinates.test_pdb.TestMultiPDBReader) ... ok test_iteration (testsuite.MDAnalysisTests.coordinates.test_pdb.TestMultiPDBReader) ... ok test_n_atoms_frame (testsuite.MDAnalysisTests.coordinates.test_pdb.TestMultiPDBReader) ... ok test_n_frames (testsuite.MDAnalysisTests.coordinates.test_pdb.TestMultiPDBReader) ... ok test_numconnections (testsuite.MDAnalysisTests.coordinates.test_pdb.TestMultiPDBReader) ... ok test_rewind (testsuite.MDAnalysisTests.coordinates.test_pdb.TestMultiPDBReader) ... ok test_slice_iteration (testsuite.MDAnalysisTests.coordinates.test_pdb.TestMultiPDBReader) ... ok test_dendrogram_produced (testsuite.MDAnalysisTests.analysis.test_psa.TestPSAnalysis) ... ok Test the index of corresponding distance vector is correct if i > j ... ok Test the index of corresponding distance vector is correct if i < j ... ok Test whether inputs are supported as numpy integers rather than normal Integers ... ok Test whether inputs are supported as numpy integers rather than normal Integers ... ok test_hausdorff_bound (testsuite.MDAnalysisTests.analysis.test_psa.TestPSAnalysis) ... ok test_reversal_frechet (testsuite.MDAnalysisTests.analysis.test_psa.TestPSAnalysis) ... ok test_reversal_hausdorff (testsuite.MDAnalysisTests.analysis.test_psa.TestPSAnalysis) ... ok ====================================================================== ERROR: testsuite.MDAnalysisTests.analysis.test_diffusionmap.TestDiffusionmap.test_dist_weights ---------------------------------------------------------------------- Traceback (most recent call last): File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/nose/util.py", line 471, in try_run return func() File "/nfs/homes2/oliver/Library/python/mdanalysis/testsuite/MDAnalysisTests/analysis/test_diffusionmap.py", line 35, in setUp self.u = MDAnalysis.Universe(PDB, XTC) File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysis/core/universe.py", line 283, in __init__ self.load_new(coordinatefile, **kwargs) File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysis/core/universe.py", line 435, in load_new self.trajectory = reader(filename, **kwargs) File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysis/coordinates/XDR.py", line 144, in __init__ self._load_offsets() File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysis/coordinates/XDR.py", line 177, in _load_offsets data = read_numpy_offsets(fname) File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysis/coordinates/XDR.py", line 84, in read_numpy_offsets return {k: v for k, v in six.iteritems(np.load(filename))} File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/numpy/lib/npyio.py", line 412, in load pickle_kwargs=pickle_kwargs) File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/numpy/lib/npyio.py", line 171, in __init__ _zip = zipfile_factory(fid) File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/numpy/lib/npyio.py", line 101, in zipfile_factory return zipfile.ZipFile(file, *args, **kwargs) File "/usr/lib/python2.7/zipfile.py", line 770, in __init__ self._RealGetContents() File "/usr/lib/python2.7/zipfile.py", line 811, in _RealGetContents raise BadZipfile, "File is not a zip file" BadZipfile: File is not a zip file -------------------- >> begin captured stderr << --------------------- /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysis/topology/guessers.py:56: UserWarning: Failed to guess the mass for the following atom types: M "".format(', '.join(misses))) --------------------- >> end captured stderr << ---------------------- -------------------- >> begin captured logging << -------------------- MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: Universe.load_new(): loading /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/adk_oplsaa.xtc... --------------------- >> end captured logging << --------------------- ====================================================================== ERROR: testsuite.MDAnalysisTests.core.test_group_traj_access.TestAtom_ForceVelocity.test_atom_force_set ---------------------------------------------------------------------- Traceback (most recent call last): File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/nose/case.py", line 381, in setUp try_run(self.inst, ('setup', 'setUp')) File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/nose/util.py", line 471, in try_run return func() File "/nfs/homes2/oliver/Library/python/mdanalysis/testsuite/MDAnalysisTests/core/test_group_traj_access.py", line 279, in setUp self.u = MDAnalysis.Universe(PDB_xvf, TRR_xvf) File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysis/core/universe.py", line 283, in __init__ self.load_new(coordinatefile, **kwargs) File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysis/core/universe.py", line 435, in load_new self.trajectory = reader(filename, **kwargs) File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysis/coordinates/XDR.py", line 144, in __init__ self._load_offsets() File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysis/coordinates/XDR.py", line 177, in _load_offsets data = read_numpy_offsets(fname) File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysis/coordinates/XDR.py", line 84, in read_numpy_offsets return {k: v for k, v in six.iteritems(np.load(filename))} File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/numpy/lib/npyio.py", line 412, in load pickle_kwargs=pickle_kwargs) File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/numpy/lib/npyio.py", line 171, in __init__ _zip = zipfile_factory(fid) File "/nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/numpy/lib/npyio.py", line 101, in zipfile_factory return zipfile.ZipFile(file, *args, **kwargs) File "/usr/lib/python2.7/zipfile.py", line 770, in __init__ self._RealGetContents() File "/usr/lib/python2.7/zipfile.py", line 811, in _RealGetContents raise BadZipfile, "File is not a zip file" BadZipfile: File is not a zip file -------------------- >> begin captured stderr << --------------------- /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysis/topology/guessers.py:56: UserWarning: Failed to guess the mass for the following atom types: M "".format(', '.join(misses))) --------------------- >> end captured stderr << ---------------------- -------------------- >> begin captured logging << -------------------- MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: _process_attr: Adding to topology MDAnalysis.core.universe: DEBUG: Universe.load_new(): loading /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/cobrotoxin.trr... --------------------- >> end captured logging << --------------------- Cleanup: deleting offset files in /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data Cleanup: deleting offset file /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/.xyz_random_walk.xtc_offsets.npz Cleanup: deleting offset file /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/.cobrotoxin.trr_offsets.npz Cleanup: deleting offset file /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/.adk_oplsaa.xtc_offsets.npz Cleanup: deleting offset file /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/.adk_oplsaa.trr_offsets.npz Cleanup: deleting offset file /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/.cobrotoxin.xtc_offsets.npz Cleanup: deleting offset file /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/coordinates/.test.trr_offsets.npz Cleanup: deleting offset file /nfs/homes2/oliver/.virtualenvs/mda_sandbox/local/lib/python2.7/site-packages/MDAnalysisTests/data/coordinates/.test.xtc_offsets.npz ---------------------------------------------------------------------- Ran 5439 tests in 149.601s FAILED (KNOWNFAIL=4, SKIP=3, errors=2)