import utils import os import unittest TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..')) utils.set_search_paths(TOPDIR) import ihm.flr class Tests(unittest.TestCase): def test_probe_init(self): """Test initialization of probe_list_entry and probe_descriptor.""" p = ihm.flr.Probe(probe_list_entry='foo', probe_descriptor='bar') self.assertEqual(p.probe_list_entry, 'foo') self.assertEqual(p.probe_descriptor, 'bar') def test_probe_eq(self): """Test equality and inequality of Probe objects""" p_ref = ihm.flr.Probe(probe_list_entry='foo', probe_descriptor='bar') p_equal = ihm.flr.Probe(probe_list_entry='foo', probe_descriptor='bar') p_unequal = ihm.flr.Probe( probe_list_entry='foo2', probe_descriptor='bar') self.assertTrue(p_ref == p_equal) self.assertFalse(p_ref == p_unequal) self.assertTrue(p_ref != p_unequal) def test_probe_descriptor_init(self): """ Test initialization of ProbeDescriptor """ p = ihm.flr.ProbeDescriptor(reactive_probe_chem_descriptor='foo', chromophore_chem_descriptor='bar', chromophore_center_atom='foo2') self.assertEqual(p.reactive_probe_chem_descriptor, 'foo') self.assertEqual(p.chromophore_chem_descriptor, 'bar') self.assertEqual(p.chromophore_center_atom, 'foo2') def test_probe_descriptor_eq(self): """Test equality and inequality of ProbeDescriptor objects.""" p_ref = ihm.flr.ProbeDescriptor(reactive_probe_chem_descriptor='foo', chromophore_chem_descriptor='bar', chromophore_center_atom='foo2') p_equal = ihm.flr.ProbeDescriptor(reactive_probe_chem_descriptor='foo', chromophore_chem_descriptor='bar', chromophore_center_atom='foo2') p_unequal = ihm.flr.ProbeDescriptor( reactive_probe_chem_descriptor='foo', chromophore_chem_descriptor='bar2', chromophore_center_atom='foo2') self.assertTrue(p_ref == p_equal) self.assertFalse(p_ref == p_unequal) self.assertTrue(p_ref != p_unequal) def test_probe_list_init(self): """ Test initialization of ProbeList. """ p = ihm.flr.ProbeList(chromophore_name='foo', reactive_probe_flag=False, reactive_probe_name='bar', probe_origin='foo2', probe_link_type='bar2') self.assertEqual(p.chromophore_name, 'foo') self.assertEqual(p.reactive_probe_flag, False) self.assertEqual(p.reactive_probe_name, 'bar') self.assertEqual(p.probe_origin, 'foo2') self.assertEqual(p.probe_link_type, 'bar2') def test_probe_list_eq(self): """Test equality and inequality of ProbeList objects.""" p_ref = ihm.flr.ProbeList(chromophore_name='foo', reactive_probe_flag=False, reactive_probe_name='bar', probe_origin='foo2', probe_link_type='bar2') p_equal = ihm.flr.ProbeList(chromophore_name='foo', reactive_probe_flag=False, reactive_probe_name='bar', probe_origin='foo2', probe_link_type='bar2') p_unequal = ihm.flr.ProbeList(chromophore_name='foo2', reactive_probe_flag=True, reactive_probe_name='bar', probe_origin='foo2', probe_link_type='bar2') self.assertTrue(p_ref == p_equal) self.assertFalse(p_ref == p_unequal) self.assertTrue(p_ref != p_unequal) def test_sample_probe_details_init(self): """ Test initialization of SampleProbeDetails. """ s = ihm.flr.SampleProbeDetails(sample='foo', probe='bar', description='foo2', poly_probe_position='bar2') self.assertEqual(s.sample, 'foo') self.assertEqual(s.probe, 'bar') self.assertEqual(s.fluorophore_type, 'unspecified') self.assertEqual(s.description, 'foo2') self.assertEqual(s.poly_probe_position, 'bar2') def test_sample_probe_details_eq(self): """Test equality and inequality of SampleProbeDetails objects.""" s_ref = ihm.flr.SampleProbeDetails( sample='foo', probe='bar', description='foo2', poly_probe_position='bar2') s_equal = ihm.flr.SampleProbeDetails( sample='foo', probe='bar', description='foo2', poly_probe_position='bar2') s_unequal = ihm.flr.SampleProbeDetails( sample='foo', probe='bar3', description='foo2', poly_probe_position='bar2') self.assertTrue(s_ref == s_equal) self.assertFalse(s_ref == s_unequal) self.assertTrue(s_ref != s_unequal) def test_poly_probe_conjugate_init(self): """ Test initialization of PolyProbeConjugate. """ p = ihm.flr.PolyProbeConjugate(sample_probe='foo', chem_descriptor='bar', ambiguous_stoichiometry=True, probe_stoichiometry=0.5) self.assertEqual(p.sample_probe, 'foo') self.assertEqual(p.chem_descriptor, 'bar') self.assertEqual(p.ambiguous_stoichiometry, True) self.assertEqual(p.probe_stoichiometry, 0.5) def test_poly_probe_conjugate_eq(self): """ Test equality and inequality of PolyProbeConjugate objects. """ p_ref = ihm.flr.PolyProbeConjugate(sample_probe='foo', chem_descriptor='bar', ambiguous_stoichiometry=True, probe_stoichiometry=0.5) p_equal = ihm.flr.PolyProbeConjugate(sample_probe='foo', chem_descriptor='bar', ambiguous_stoichiometry=True, probe_stoichiometry=0.5) p_unequal = ihm.flr.PolyProbeConjugate( sample_probe='foo2', chem_descriptor='bar', ambiguous_stoichiometry=True, probe_stoichiometry=0.5) self.assertTrue(p_ref == p_equal) self.assertFalse(p_ref == p_unequal) self.assertTrue(p_ref != p_unequal) def test_poly_probe_position_init(self): """ Test initialization of PolyProbePosition. """ p = ihm.flr.PolyProbePosition(resatom='foo', mutation_flag=True, modification_flag=True, auth_name='foo3', mutated_chem_comp_id='foobar', modified_chem_descriptor='foobar2') self.assertEqual(p.resatom, 'foo') self.assertEqual(p.mutation_flag, True) self.assertEqual(p.modification_flag, True) self.assertEqual(p.auth_name, 'foo3') self.assertEqual(p.mutated_chem_comp_id, 'foobar') self.assertEqual(p.modified_chem_descriptor, 'foobar2') def test_poly_probe_position_eq(self): """Test equality and inequality of PolyProbePosition objects.""" p_ref = ihm.flr.PolyProbePosition( resatom='foo', mutation_flag=True, modification_flag=True, auth_name='foo3', mutated_chem_comp_id='foobar', modified_chem_descriptor='foobar2') p_equal = ihm.flr.PolyProbePosition( resatom='foo', mutation_flag=True, modification_flag=True, auth_name='foo3', mutated_chem_comp_id='foobar', modified_chem_descriptor='foobar2') p_unequal = ihm.flr.PolyProbePosition( resatom='bar', mutation_flag=True, modification_flag=True, auth_name='foo3', mutated_chem_comp_id='foobar', modified_chem_descriptor='foobar2') self.assertTrue(p_ref == p_equal) self.assertFalse(p_ref == p_unequal) self.assertTrue(p_ref != p_unequal) def test_sample_init(self): """Test initialization of Sample.""" s = ihm.flr.Sample(entity_assembly='foo', num_of_probes='bar', condition='foo2', description='foo3', details='foo4', solvent_phase='foobar') self.assertEqual(s.entity_assembly, 'foo') self.assertEqual(s.num_of_probes, 'bar') self.assertEqual(s.condition, 'foo2') self.assertEqual(s.description, 'foo3') self.assertEqual(s.details, 'foo4') self.assertEqual(s.solvent_phase, 'foobar') def test_sample_eq(self): """Test equality and inequality of Sample objects.""" s_ref = ihm.flr.Sample(entity_assembly='foo', num_of_probes='foo2', condition='foo3', description='foo4', details='foo5', solvent_phase='foo6') s_equal = ihm.flr.Sample(entity_assembly='foo', num_of_probes='foo2', condition='foo3', description='foo4', details='foo5', solvent_phase='foo6') s_unequal = ihm.flr.Sample(entity_assembly='bar', num_of_probes='bar2', condition='bar3', description='bar4', details='bar5', solvent_phase='bar6') self.assertTrue(s_ref == s_equal) self.assertFalse(s_ref == s_unequal) self.assertTrue(s_ref != s_unequal) def test_entity_assembly_init(self): """ Test initialization of EntityAssembly. """ e = ihm.flr.EntityAssembly(entity='foo', num_copies=1) self.assertEqual(len(e.entity_list), 1) self.assertEqual(e.entity_list[0], 'foo') self.assertEqual(e.num_copies_list[0], 1) def test_entity_assembly_add_entity(self): """Test addition of entities to the assembly.""" e = ihm.flr.EntityAssembly(entity='foo', num_copies=1) e.add_entity(entity='foo2', num_copies=2) self.assertRaises(ValueError, e.add_entity, entity='foo2', num_copies=-1) self.assertEqual(len(e.entity_list), 2) self.assertEqual(e.entity_list, ['foo', 'foo2']) self.assertEqual(e.num_copies_list, [1, 2]) def test_entity_assembly_eq(self): """ Test equality and inequality of EntityAssembly objects. """ e_ref = ihm.flr.EntityAssembly(entity='foo', num_copies=1) e_equal = ihm.flr.EntityAssembly(entity='foo', num_copies=1) e_unequal = ihm.flr.EntityAssembly(entity='foo2', num_copies=1) self.assertTrue(e_ref == e_equal) self.assertFalse(e_ref == e_unequal) self.assertTrue(e_ref != e_unequal) def test_sample_condition_init(self): """ Test initialization of SampleCondition. """ s = ihm.flr.SampleCondition(details='foo') self.assertEqual(s.details, 'foo') def test_sample_condition_eq(self): """ Test equality and inequality of SampleCondition objects. """ s_ref = ihm.flr.SampleCondition(details='foo') s_equal = ihm.flr.SampleCondition(details='foo') s_unequal = ihm.flr.SampleCondition(details='bar') self.assertTrue(s_ref == s_equal) self.assertFalse(s_ref == s_unequal) self.assertTrue(s_ref != s_unequal) def test_experiment_init(self): """Test initialization of Experiment.""" # Initialization with only one parameter given should not add an entry e1 = ihm.flr.Experiment(instrument='foo') self.assertEqual(len(e1.instrument_list), 0) self.assertEqual(len(e1.inst_setting_list), 0) self.assertEqual(len(e1.exp_condition_list), 0) self.assertEqual(len(e1.sample_list), 0) # Correct initialization should fill the lists e2 = ihm.flr.Experiment(instrument='foo', inst_setting='bar', exp_condition='foo2', sample='foo3', details='bar2') self.assertEqual(len(e2.instrument_list), 1) self.assertEqual(e2.instrument_list[0], 'foo') self.assertEqual(e2.inst_setting_list[0], 'bar') self.assertEqual(e2.exp_condition_list[0], 'foo2') self.assertEqual(e2.sample_list[0], 'foo3') self.assertEqual(e2.details_list[0], 'bar2') # Initialization without details given should still have an entry # in the list e3 = ihm.flr.Experiment(instrument='foo', inst_setting='bar', exp_condition='bar2', sample='foo2') self.assertEqual(len(e3.details_list), 1) self.assertIsNone(e3.details_list[0]) def test_experiment_add_entry(self): """ Test addition of an entry to the experiment. """ # Adding to an empty Experiment e1 = ihm.flr.Experiment() e1.add_entry(instrument='foo', inst_setting='bar', exp_condition='foo2', sample='foo3', details='bar2') self.assertEqual(e1.instrument_list[0], 'foo') self.assertEqual(e1.inst_setting_list[0], 'bar') self.assertEqual(e1.exp_condition_list[0], 'foo2') self.assertEqual(e1.sample_list[0], 'foo3') self.assertEqual(e1.details_list[0], 'bar2') # adding to an existing Experiment e2 = ihm.flr.Experiment(instrument='foo', inst_setting='foo2', exp_condition='foo3', sample='foo4', details='foo5') e2.add_entry(instrument='bar', inst_setting='bar2', exp_condition='bar3', sample='bar4', details='bar5') self.assertEqual(e2.instrument_list, ['foo', 'bar']) self.assertEqual(e2.inst_setting_list, ['foo2', 'bar2']) self.assertEqual(e2.exp_condition_list, ['foo3', 'bar3']) self.assertEqual(e2.sample_list, ['foo4', 'bar4']) self.assertEqual(e2.details_list, ['foo5', 'bar5']) def test_experiment_get_entry_by_index(self): """ Test access to entries by index. """ e = ihm.flr.Experiment() e.add_entry(instrument='foo', inst_setting='foo2', exp_condition='foo3', sample='foo4', details='foo5') e.add_entry(instrument='bar', inst_setting='bar2', exp_condition='bar3', sample='bar4', details='bar5') e.add_entry(instrument='foobar', inst_setting='foobar2', exp_condition='foobar3', sample='foobar4', details='foobar5') return_value_index0 = e.get_entry_by_index(0) return_value_index1 = e.get_entry_by_index(1) return_value_index2 = e.get_entry_by_index(2) self.assertEqual(return_value_index0, ('foo', 'foo2', 'foo3', 'foo4', 'foo5')) self.assertEqual(return_value_index1, ('bar', 'bar2', 'bar3', 'bar4', 'bar5')) self.assertEqual(return_value_index2, ('foobar', 'foobar2', 'foobar3', 'foobar4', 'foobar5')) def test_experiment_contains(self): """Test whether experiment contains a combination of instrument, exp_setting, and sample.""" # An empty experiment should not contain anything e1 = ihm.flr.Experiment() self.assertFalse(e1.contains('foo', 'foo2', 'foo3', 'foo4')) # After addition, the entry should be contained e1.add_entry(instrument='foo', inst_setting='foo2', exp_condition='foo3', sample='foo4') e1.add_entry(instrument='bar', inst_setting='bar2', exp_condition='bar3', sample='bar4') self.assertTrue(e1.contains('foo', 'foo2', 'foo3', 'foo4')) # If one of the entries is not contained, then False self.assertFalse(e1.contains('foo2', 'foo2', 'foo4', 'foo5')) self.assertFalse(e1.contains('foobar', 'foobar2', 'foobar3', 'foobar4')) def test_experiment_eq(self): """ Test equality and inequality of Experiment objects. """ e_ref = ihm.flr.Experiment() e_ref.add_entry(instrument='foo', inst_setting='foo2', exp_condition='foo3', sample='foo4') e_equal = ihm.flr.Experiment() e_equal.add_entry(instrument='foo', inst_setting='foo2', exp_condition='foo3', sample='foo4') e_unequal = ihm.flr.Experiment() e_unequal.add_entry(instrument='bar', inst_setting='bar2', exp_condition='bar3', sample='bar4') self.assertTrue(e_ref == e_equal) self.assertFalse(e_ref == e_unequal) self.assertTrue(e_ref != e_unequal) def test_instrument_init(self): """ Test initialization of Instrument. """ i = ihm.flr.Instrument(details='foo') self.assertEqual(i.details, 'foo') def test_instrument_eq(self): """Test equality and inequality of Instrument objects.""" i_ref = ihm.flr.Instrument(details='foo') i_equal = ihm.flr.Instrument(details='foo') i_unequal = ihm.flr.Instrument(details='bar') self.assertTrue(i_ref == i_equal) self.assertFalse(i_ref == i_unequal) self.assertTrue(i_ref != i_unequal) def test_inst_setting_init(self): """Test initialization of InstSetting.""" e = ihm.flr.InstSetting(details='foo') self.assertEqual(e.details, 'foo') def test_inst_setting_eq(self): """Test equality and inequality of InstSetting objects.""" e_ref = ihm.flr.InstSetting(details='foo') e_equal = ihm.flr.InstSetting(details='foo') e_unequal = ihm.flr.InstSetting(details='bar') self.assertTrue(e_ref == e_equal) self.assertFalse(e_ref == e_unequal) self.assertTrue(e_ref != e_unequal) def test_exp_condition_init(self): """Test initialization of ExpCondition.""" e = ihm.flr.ExpCondition(details='foo') self.assertEqual(e.details, 'foo') def test_exp_condition_eq(self): """Test equality and inequality of ExpCondition objects.""" e_ref = ihm.flr.ExpCondition(details='foo') e_equal = ihm.flr.ExpCondition(details='foo') e_unequal = ihm.flr.ExpCondition(details='bar') self.assertTrue(e_ref == e_equal) self.assertFalse(e_ref == e_unequal) self.assertTrue(e_ref != e_unequal) def test_fret_analysis_init(self): """Test initialization of FRETAnalysis.""" f = ihm.flr.FRETAnalysis( experiment='this_experiment', sample_probe_1='this_sample_probe_1', sample_probe_2='this_sample_probe_2', forster_radius='this_forster_radius', type='intensity-based', calibration_parameters='this_calibration_parameters', lifetime_fit_model='this_lifetime_fit_model', ref_measurement_group='this_ref_measurement_group', method_name='this_method_name', chi_square_reduced='this_chi_square_reduced', donor_only_fraction='this_donly_fraction', dataset='this_dataset_list_id', file='this_external_file', software='this_software') self.assertEqual(f.experiment, 'this_experiment') self.assertEqual(f.sample_probe_1, 'this_sample_probe_1') self.assertEqual(f.sample_probe_2, 'this_sample_probe_2') self.assertEqual(f.forster_radius, 'this_forster_radius') self.assertEqual(f.type, 'intensity-based') self.assertEqual(f.calibration_parameters, 'this_calibration_parameters') self.assertEqual(f.lifetime_fit_model, 'this_lifetime_fit_model') self.assertEqual(f.ref_measurement_group, 'this_ref_measurement_group') self.assertEqual(f.method_name, 'this_method_name') self.assertEqual(f.chi_square_reduced, 'this_chi_square_reduced') self.assertEqual(f.donor_only_fraction, 'this_donly_fraction') self.assertEqual(f.dataset, 'this_dataset_list_id') self.assertEqual(f.external_file, 'this_external_file') self.assertEqual(f.software, 'this_software') self.assertRaises( ValueError, ihm.flr.FRETAnalysis, experiment='this_experiment', sample_probe_1='this_sample_probe_1', sample_probe_2='this_sample_probe_2', forster_radius='this_forster_radius', type='garbage') def test_fret_analysis_eq(self): """Test equality and inequality of FRETAnalysis objects.""" f_ref = ihm.flr.FRETAnalysis( experiment='this_experiment', sample_probe_1='this_sample_probe_1', sample_probe_2='this_sample_probe_2', forster_radius='this_forster_radius', type='intensity-based', calibration_parameters='this_calibration_parameters', method_name='this_method_name', chi_square_reduced='this_chi_square_reduced', donor_only_fraction='this_donly_fraction', dataset='this_dataset_list_id', file='this_external_file', software='this_software') f_equal = ihm.flr.FRETAnalysis( experiment='this_experiment', sample_probe_1='this_sample_probe_1', sample_probe_2='this_sample_probe_2', forster_radius='this_forster_radius', type='intensity-based', calibration_parameters='this_calibration_parameters', method_name='this_method_name', chi_square_reduced='this_chi_square_reduced', donor_only_fraction='this_donly_fraction', dataset='this_dataset_list_id', file='this_external_file', software='this_software') f_unequal = ihm.flr.FRETAnalysis( experiment='this_experiment', sample_probe_1='foo', sample_probe_2='this_sample_probe_2', forster_radius='this_forster_radius', type='intensity-based', calibration_parameters='this_calibration_parameters', method_name='this_method_name', chi_square_reduced='this_chi_square_reduced', donor_only_fraction='this_donly_fraction', dataset='this_dataset_list_id', file='this_external_file', software='this_software') f_unequal_type = ihm.flr.FRETAnalysis( experiment='this_experiment', sample_probe_1='this_sample_probe_1', sample_probe_2='this_sample_probe_2', forster_radius='this_forster_radius', type='lifetime-based', calibration_parameters='this_calibration_parameters', method_name='this_method_name', chi_square_reduced='this_chi_square_reduced', donor_only_fraction='this_donly', dataset='this_dataset_list_id', file='this_external_file', software='this_software') self.assertTrue(f_ref == f_equal) self.assertFalse(f_ref == f_unequal) self.assertTrue(f_ref != f_unequal) self.assertFalse(f_ref == f_unequal_type) self.assertTrue(f_ref != f_unequal_type) def test_lifetime_fit_model_init(self): """ Test initialization of LifetimeFitModel.""" f = ihm.flr.LifetimeFitModel(name='this_name', description='this_description', file='this_ext_file', citation='this_citation') self.assertEqual(f.name, 'this_name') self.assertEqual(f.description, 'this_description') self.assertEqual(f.external_file, 'this_ext_file') self.assertEqual(f.citation, 'this_citation') def test_lifetime_fit_model_eq(self): """ Test equality and inequality of LifeTimeFitModel objects.""" f_ref = ihm.flr.LifetimeFitModel( name='this_name', description='this_desc') f_equal = ihm.flr.LifetimeFitModel( name='this_name', description='this_desc') f_unequal = ihm.flr.LifetimeFitModel( name='other_name', description='this_desc') self.assertTrue(f_ref == f_equal) self.assertFalse(f_ref == f_unequal) self.assertTrue(f_ref != f_unequal) def test_ref_measurement_group_init(self): """ Test initialization of RefMeasurementGroup.""" r = ihm.flr.RefMeasurementGroup() self.assertEqual(r.ref_measurement_list, []) def test_ref_measurement_group_add_ref_measurement(self): """ Test the addition of a RefMeasurement to the group.""" r = ihm.flr.RefMeasurementGroup() r.add_ref_measurement('foo') r.add_ref_measurement('bar') self.assertEqual(r.ref_measurement_list, ['foo', 'bar']) def test_ref_measurement_group_get_info(self): """ Test the retrieval of the ref_measurement_list.""" r = ihm.flr.RefMeasurementGroup() r.add_ref_measurement('foo') r.add_ref_measurement('bar') return_value = r.get_info() self.assertEqual(return_value, ['foo', 'bar']) def test_ref_measurement_group_eq(self): """ Test equality and inequality of RefMeasurementGroup objects.""" r_ref = ihm.flr.RefMeasurementGroup() r_ref.add_ref_measurement('foo') r_equal = ihm.flr.RefMeasurementGroup() r_equal.add_ref_measurement('foo') r_unequal = ihm.flr.RefMeasurementGroup() r_unequal.add_ref_measurement('foo2') self.assertTrue(r_ref == r_equal) self.assertFalse(r_ref == r_unequal) self.assertTrue(r_ref != r_unequal) def test_ref_measurement_init(self): """Test initialization of RefMeasurement.""" r1 = ihm.flr.RefMeasurement(ref_sample_probe='this_ref_sample_probe', details='this_details') self.assertEqual(r1.ref_sample_probe, 'this_ref_sample_probe') self.assertEqual(r1.details, 'this_details') self.assertEqual(r1.list_of_lifetimes, []) r2 = ihm.flr.RefMeasurement(ref_sample_probe='this_ref_sample_probe_2', details='this_details_2', list_of_lifetimes=['foo', 'bar']) self.assertEqual(r2.ref_sample_probe, 'this_ref_sample_probe_2') self.assertEqual(r2.details, 'this_details_2') self.assertEqual(r2.list_of_lifetimes, ['foo', 'bar']) def test_ref_measurement_add_lifetime(self): """ Test addition of to the list_of_lifetimes.""" r = ihm.flr.RefMeasurement(ref_sample_probe='this_ref_sample_probe', details='this_details') r.add_lifetime('foo') r.add_lifetime('bar') self.assertEqual(r.list_of_lifetimes, ['foo', 'bar']) def test_ref_measurement_eq(self): """ Test equality and inequality of RefMeasurement objects.""" r_ref = ihm.flr.RefMeasurement( ref_sample_probe='this_ref_sample_probe_1', details='this_details_1') r_equal = ihm.flr.RefMeasurement( ref_sample_probe='this_ref_sample_probe_1', details='this_details_1') r_unequal = ihm.flr.RefMeasurement( ref_sample_probe='this_ref_sample_probe_2', details='this_details_2') r_unequal_list = ihm.flr.RefMeasurement( ref_sample_probe='this_ref_sample_probe_1', details='this_details_1', list_of_lifetimes=['foo']) self.assertTrue(r_ref == r_equal) self.assertTrue(r_ref != r_unequal) self.assertTrue(r_ref != r_unequal_list) self.assertFalse(r_ref == r_unequal) self.assertFalse(r_ref == r_unequal_list) def test_ref_measurement_lifetime_init(self): """ Test initialization of RefMeasuremenLifetime objects.""" f = ihm.flr.RefMeasurementLifetime(species_fraction='this_frac', lifetime='this_lifetime', species_name='foo') self.assertEqual(f.species_fraction, 'this_frac') self.assertEqual(f.lifetime, 'this_lifetime') self.assertEqual(f.species_name, 'foo') def test_ref_measurement_lifetime_eq(self): """ Test equality and inequality of RefMeasurementLifetime objects.""" f_ref = ihm.flr.RefMeasurementLifetime(species_fraction='this_frac_1', lifetime='this_lifetime_1') f_equal = ihm.flr.RefMeasurementLifetime( species_fraction='this_frac_1', lifetime='this_lifetime_1') f_unequal = ihm.flr.RefMeasurementLifetime( species_fraction='this_frac_2', lifetime='this_lifetime_1') self.assertTrue(f_ref == f_equal) self.assertFalse(f_ref == f_unequal) self.assertTrue(f_ref != f_unequal) def test_fret_distance_restraint_group_init(self): """ Test initialization of FRETDistanceRestraintGroup. """ f = ihm.flr.FRETDistanceRestraintGroup() self.assertEqual(f.distance_restraint_list, []) def test_fret_distance_restraint_group_add_distance_restraint(self): """ Test the addition of a Fret_distance restraint to the group. """ f = ihm.flr.FRETDistanceRestraintGroup() f.add_distance_restraint('foo') f.add_distance_restraint('bar') self.assertEqual(f.distance_restraint_list, ['foo', 'bar']) def test_fret_distance_restraint_group_get_info(self): """ Test the retrieval of the distance_restraint_list. """ f = ihm.flr.FRETDistanceRestraintGroup() f.add_distance_restraint('foo') f.add_distance_restraint('bar') return_value = f.get_info() self.assertEqual(return_value, ['foo', 'bar']) def test_fret_distance_restraint_group_eq(self): """Test equality and inequality of FRETDistanceRestraintGroup objects.""" f_ref = ihm.flr.FRETDistanceRestraintGroup() f_ref.add_distance_restraint('foo') f_equal = ihm.flr.FRETDistanceRestraintGroup() f_equal.add_distance_restraint('foo') f_unequal = ihm.flr.FRETDistanceRestraintGroup() f_unequal.add_distance_restraint('bar') self.assertTrue(f_ref == f_equal) self.assertFalse(f_ref == f_unequal) self.assertTrue(f_ref != f_unequal) def test_fret_distance_restraint_init(self): """Test initialization of FRETDistanceRestraint.""" f = ihm.flr.FRETDistanceRestraint( sample_probe_1='this_sample_probe_1', sample_probe_2='this_sample_probe_2', state='this_state', analysis='this_analysis', distance='this_distance', distance_error_plus='this_distance_error_plus', distance_error_minus='this_distance_error_minus', distance_type='this_distance_type', population_fraction='this_population_fraction', peak_assignment='this_peak_assignment') self.assertEqual(f.sample_probe_1, 'this_sample_probe_1') self.assertEqual(f.sample_probe_2, 'this_sample_probe_2') self.assertEqual(f.state, 'this_state') self.assertEqual(f.analysis, 'this_analysis') self.assertEqual(f.distance, 'this_distance') self.assertEqual(f.distance_error_plus, 'this_distance_error_plus') self.assertEqual(f.distance_error_minus, 'this_distance_error_minus') self.assertEqual(f.distance_type, 'this_distance_type') self.assertEqual(f.population_fraction, 'this_population_fraction') self.assertEqual(f.peak_assignment, 'this_peak_assignment') def test_fret_distance_restraint_eq(self): """Test equality and inequality of FRETDistanceRestraint objects.""" f_ref = ihm.flr.FRETDistanceRestraint( sample_probe_1='this_sample_probe_1', sample_probe_2='this_sample_probe_2', state='this_state', analysis='this_analysis', distance='this_distance', distance_error_plus='this_distance_error_plus', distance_error_minus='this_distance_error_minus', distance_type='this_distance_type', population_fraction='this_population_fraction', peak_assignment='this_peak_assignment') f_equal = ihm.flr.FRETDistanceRestraint( sample_probe_1='this_sample_probe_1', sample_probe_2='this_sample_probe_2', state='this_state', analysis='this_analysis', distance='this_distance', distance_error_plus='this_distance_error_plus', distance_error_minus='this_distance_error_minus', distance_type='this_distance_type', population_fraction='this_population_fraction', peak_assignment='this_peak_assignment') f_unequal = ihm.flr.FRETDistanceRestraint( sample_probe_1='this_sample_probe_1', sample_probe_2='this_sample_probe_2', state='foo', analysis='this_analysis', distance='this_distance', distance_error_plus='this_distance_error_plus', distance_error_minus='this_distance_error_minus', distance_type='this_distance_type', population_fraction='this_population_fraction', peak_assignment='this_peak_assignment') self.assertTrue(f_ref == f_equal) self.assertFalse(f_ref == f_unequal) self.assertTrue(f_ref != f_unequal) def test_fret_forster_radius_init(self): """ Test initialization of FRETForsterRadius. """ f = ihm.flr.FRETForsterRadius( donor_probe='foo', acceptor_probe='bar', forster_radius='foo2', reduced_forster_radius='bar2') self.assertEqual(f.donor_probe, 'foo') self.assertEqual(f.acceptor_probe, 'bar') self.assertEqual(f.forster_radius, 'foo2') self.assertEqual(f.reduced_forster_radius, 'bar2') def test_fret_forster_radius_eq(self): """ Test equality and inequality of FRETForsterRadius objects. """ f_ref = ihm.flr.FRETForsterRadius( donor_probe='foo', acceptor_probe='bar', forster_radius='foo2', reduced_forster_radius='bar2') f_equal = ihm.flr.FRETForsterRadius( donor_probe='foo', acceptor_probe='bar', forster_radius='foo2', reduced_forster_radius='bar2') f_unequal = ihm.flr.FRETForsterRadius( donor_probe='foobar', acceptor_probe='bar', forster_radius='foo2', reduced_forster_radius='bar2') self.assertTrue(f_ref == f_equal) self.assertFalse(f_ref == f_unequal) self.assertTrue(f_ref != f_unequal) def test_fret_calibration_parameters_init(self): """Test initialization of FRETCalibrationParameters.""" f = ihm.flr.FRETCalibrationParameters(phi_acceptor='this_phi_acceptor', alpha='this_alpha', alpha_sd='this_alpha_sd', gg_gr_ratio='this_gG_gR_ratio', beta='this_beta', gamma='this_gamma', delta='this_delta', a_b='this_a_b') self.assertEqual(f.phi_acceptor, 'this_phi_acceptor') self.assertEqual(f.alpha, 'this_alpha') self.assertEqual(f.alpha_sd, 'this_alpha_sd') self.assertEqual(f.gg_gr_ratio, 'this_gG_gR_ratio') self.assertEqual(f.beta, 'this_beta') self.assertEqual(f.gamma, 'this_gamma') self.assertEqual(f.delta, 'this_delta') self.assertEqual(f.a_b, 'this_a_b') def test_fret_calibration_parameters_eq(self): """Test equality and inequality of FRETCalibrationParameters objects.""" f_ref = ihm.flr.FRETCalibrationParameters( phi_acceptor='this_phi_acceptor', alpha='this_alpha', alpha_sd='this_alpha_sd', gg_gr_ratio='this_gG_gR_ratio', beta='this_beta', gamma='this_gamma', delta='this_delta', a_b='this_a_b') f_equal = ihm.flr.FRETCalibrationParameters( phi_acceptor='this_phi_acceptor', alpha='this_alpha', alpha_sd='this_alpha_sd', gg_gr_ratio='this_gG_gR_ratio', beta='this_beta', gamma='this_gamma', delta='this_delta', a_b='this_a_b') f_unequal = ihm.flr.FRETCalibrationParameters( phi_acceptor='foo', alpha='this_alpha', alpha_sd='this_alpha_sd', gg_gr_ratio='this_gG_gR_ratio', beta='this_beta', gamma='this_gamma', delta='this_delta', a_b='this_a_b') self.assertTrue(f_ref == f_equal) self.assertFalse(f_ref == f_unequal) self.assertTrue(f_ref != f_unequal) def test_peak_assignment_init(self): """ Test initialization of PeakAssignment. """ p = ihm.flr.PeakAssignment(method_name='foo', details='bar') self.assertEqual(p.method_name, 'foo') self.assertEqual(p.details, 'bar') def test_peak_assignment_eq(self): """ Test equality and inequality of PeakAssignment objects. """ p_ref = ihm.flr.PeakAssignment(method_name='foo', details='bar') p_equal = ihm.flr.PeakAssignment(method_name='foo', details='bar') p_unequal = ihm.flr.PeakAssignment(method_name='foobar', details='bar') self.assertTrue(p_ref == p_equal) self.assertFalse(p_ref == p_unequal) self.assertTrue(p_ref != p_unequal) def test_fret_model_quality_init(self): """ Test initialization of FRETModelQuality. """ f = ihm.flr.FRETModelQuality( model='this_model_id', chi_square_reduced='this_chi_square_reduced', dataset_group='this_dataset_group_id', method='this_method', details='this_details') self.assertEqual(f.model, 'this_model_id') self.assertEqual(f.chi_square_reduced, 'this_chi_square_reduced') self.assertEqual(f.dataset_group, 'this_dataset_group_id') self.assertEqual(f.method, 'this_method') self.assertEqual(f.details, 'this_details') def test_fret_model_quality_eq(self): """ Test equality and inequality of FRETModelQuality objects. """ f_ref = ihm.flr.FRETModelQuality( model='this_model_id', chi_square_reduced='this_chi_square_reduced', dataset_group='this_dataset_group_id', method='this_method', details='this_details') f_equal = ihm.flr.FRETModelQuality( model='this_model_id', chi_square_reduced='this_chi_square_reduced', dataset_group='this_dataset_group_id', method='this_method', details='this_details') f_unequal = ihm.flr.FRETModelQuality( model='foo', chi_square_reduced='this_chi_square_reduced', dataset_group='this_dataset_group_id', method='this_method', details='this_details') self.assertTrue(f_ref == f_equal) self.assertFalse(f_ref == f_unequal) self.assertTrue(f_ref != f_unequal) def test_fret_model_distance_init(self): """Test initialization of FRETModelDistance. Also test the implicit calculation of the distance deviation""" # Initialization with explicit setting of distance deviation f1 = ihm.flr.FRETModelDistance(restraint='foo', model='bar', distance=50, distance_deviation=4.0) self.assertEqual(f1.restraint, 'foo') self.assertEqual(f1.model, 'bar') self.assertEqual(f1.distance, 50) self.assertEqual(f1.distance_deviation, 4.0) # Initialization with calculation of distance deviation class DummyRestraint(): def __init__(self, distance): self.distance = distance f2 = ihm.flr.FRETModelDistance(restraint=DummyRestraint(40), model='bar2', distance=30) self.assertEqual(f2.model, 'bar2') self.assertEqual(f2.distance, 30) self.assertEqual(f2.distance_deviation, 10.0) def test_fret_model_distance_calculate_deviation(self): """Test FRETModelDistance.calculate_deviation()""" class DummyRestraint(): def __init__(self, distance): self.distance = distance f1 = ihm.flr.FRETModelDistance(restraint=DummyRestraint(40), model='foo', distance=30) self.assertEqual(f1.distance_deviation, 10.0) # Directly changing the distance should not change the deviation f1.distance = 25 self.assertEqual(f1.distance_deviation, 10.0) # Calculation of the distance deviation should update the deviation f1.update_deviation() self.assertEqual(f1.distance_deviation, 15.0) # update_deviation() is a noop if restraint is None f2 = ihm.flr.FRETModelDistance(restraint=None, model='foo', distance=30) f2.update_deviation() self.assertIsNone(f2.distance_deviation) def test_fret_model_distance_eq(self): """ Test equality and inequality of FRETModelDistance objects. """ f_ref = ihm.flr.FRETModelDistance(restraint='foo', model='bar', distance=50, distance_deviation=4.0) f_equal = ihm.flr.FRETModelDistance(restraint='foo', model='bar', distance=50, distance_deviation=4.0) f_unequal = ihm.flr.FRETModelDistance(restraint='foo2', model='bar', distance=50, distance_deviation=4.0) self.assertTrue(f_ref == f_equal) self.assertFalse(f_ref == f_unequal) self.assertTrue(f_ref != f_unequal) def test_fps_modeling_init(self): """ Test initialization of FPSModeling. """ f = ihm.flr.FPSModeling(protocol='foo', restraint_group='bar', global_parameter='foo2', probe_modeling_method='foo3', details='bar2') self.assertEqual(f.protocol, 'foo') self.assertEqual(f.restraint_group, 'bar') self.assertEqual(f.global_parameter, 'foo2') self.assertEqual(f.probe_modeling_method, 'foo3') self.assertEqual(f.details, 'bar2') def test_fps_modeling_eq(self): """Test equality and inequality of FPSModeling objects.""" f_ref = ihm.flr.FPSModeling(protocol='foo', restraint_group='bar', global_parameter='foo2', probe_modeling_method='foo3', details='bar2') f_equal = ihm.flr.FPSModeling(protocol='foo', restraint_group='bar', global_parameter='foo2', probe_modeling_method='foo3', details='bar2') f_unequal = ihm.flr.FPSModeling(protocol='foo', restraint_group='foobar', global_parameter='foo2', probe_modeling_method='foo3', details='bar2') self.assertTrue(f_ref == f_equal) self.assertFalse(f_ref == f_unequal) self.assertTrue(f_ref != f_unequal) def test_fps_global_parameters_init(self): """Test initialization of FPSGlobalParameters.""" f = ihm.flr.FPSGlobalParameters( forster_radius='this_forster_radius', conversion_function_polynom_order='this_cfpo', repetition='this_repetition', av_grid_rel='this_AV_grid_rel', av_min_grid_a='this_AV_min_grid_A', av_allowed_sphere='this_AV_allowed_sphere', av_search_nodes='this_AV_search_nodes', av_e_samples_k='this_AV_E_samples_k', sim_viscosity_adjustment='this_sim_viscosity_adjustment', sim_dt_adjustment='this_sim_dt_adjustment', sim_max_iter_k='this_sim_max_iter_k', sim_max_force='this_sim_max_force', sim_clash_tolerance_a='this_sim_clash_tolerance_A', sim_reciprocal_kt='this_sim_reciprocal_kT', sim_clash_potential='this_sim_clash_potential', convergence_e='this_convergence_E', convergence_k='this_convergence_K', convergence_f='this_convergence_F', convergence_t='this_convergence_T', optimized_distances='this_optimized_distances') self.assertEqual(f.forster_radius, 'this_forster_radius') self.assertEqual(f.conversion_function_polynom_order, 'this_cfpo') self.assertEqual(f.repetition, 'this_repetition') self.assertEqual(f.av_grid_rel, 'this_AV_grid_rel') self.assertEqual(f.av_min_grid_a, 'this_AV_min_grid_A') self.assertEqual(f.av_allowed_sphere, 'this_AV_allowed_sphere') self.assertEqual(f.av_search_nodes, 'this_AV_search_nodes') self.assertEqual(f.av_e_samples_k, 'this_AV_E_samples_k') self.assertEqual(f.sim_viscosity_adjustment, 'this_sim_viscosity_adjustment') self.assertEqual(f.sim_dt_adjustment, 'this_sim_dt_adjustment') self.assertEqual(f.sim_max_iter_k, 'this_sim_max_iter_k') self.assertEqual(f.sim_max_force, 'this_sim_max_force') self.assertEqual(f.sim_clash_tolerance_a, 'this_sim_clash_tolerance_A') self.assertEqual(f.sim_reciprocal_kt, 'this_sim_reciprocal_kT') self.assertEqual(f.sim_clash_potential, 'this_sim_clash_potential') self.assertEqual(f.convergence_e, 'this_convergence_E') self.assertEqual(f.convergence_k, 'this_convergence_K') self.assertEqual(f.convergence_f, 'this_convergence_F') self.assertEqual(f.convergence_t, 'this_convergence_T') self.assertEqual(f.optimized_distances, 'this_optimized_distances') def test_fps_global_parameters_eq(self): """Test equality and inequality of FPSGlobalParameters objects.""" f_ref = ihm.flr.FPSGlobalParameters( forster_radius='this_forster_radius', conversion_function_polynom_order='this_cfpo', repetition='this_repetition', av_grid_rel='this_AV_grid_rel', av_min_grid_a='this_AV_min_grid_A', av_allowed_sphere='this_AV_allowed_sphere', av_search_nodes='this_AV_search_nodes', av_e_samples_k='this_AV_E_samples_k', sim_viscosity_adjustment='this_sim_viscosity_adjustment', sim_dt_adjustment='this_sim_dt_adjustment', sim_max_iter_k='this_sim_max_iter_k', sim_max_force='this_sim_max_force', sim_clash_tolerance_a='this_sim_clash_tolerance_A', sim_reciprocal_kt='this_sim_reciprocal_kT', sim_clash_potential='this_sim_clash_potential', convergence_e='this_convergence_E', convergence_k='this_convergence_K', convergence_f='this_convergence_F', convergence_t='this_convergence_T', optimized_distances='this_optimized_distances') f_equal = ihm.flr.FPSGlobalParameters( forster_radius='this_forster_radius', conversion_function_polynom_order='this_cfpo', repetition='this_repetition', av_grid_rel='this_AV_grid_rel', av_min_grid_a='this_AV_min_grid_A', av_allowed_sphere='this_AV_allowed_sphere', av_search_nodes='this_AV_search_nodes', av_e_samples_k='this_AV_E_samples_k', sim_viscosity_adjustment='this_sim_viscosity_adjustment', sim_dt_adjustment='this_sim_dt_adjustment', sim_max_iter_k='this_sim_max_iter_k', sim_max_force='this_sim_max_force', sim_clash_tolerance_a='this_sim_clash_tolerance_A', sim_reciprocal_kt='this_sim_reciprocal_kT', sim_clash_potential='this_sim_clash_potential', convergence_e='this_convergence_E', convergence_k='this_convergence_K', convergence_f='this_convergence_F', convergence_t='this_convergence_T', optimized_distances='this_optimized_distances') f_unequal = ihm.flr.FPSGlobalParameters( forster_radius='foo', conversion_function_polynom_order='this_cfpo', repetition='this_repetition', av_grid_rel='this_AV_grid_rel', av_min_grid_a='this_AV_min_grid_A', av_allowed_sphere='this_AV_allowed_sphere', av_search_nodes='this_AV_search_nodes', av_e_samples_k='this_AV_E_samples_k', sim_viscosity_adjustment='this_sim_viscosity_adjustment', sim_dt_adjustment='this_sim_dt_adjustment', sim_max_iter_k='this_sim_max_iter_k', sim_max_force='this_sim_max_force', sim_clash_tolerance_a='this_sim_clash_tolerance_A', sim_reciprocal_kt='this_sim_reciprocal_kT', sim_clash_potential='this_sim_clash_potential', convergence_e='this_convergence_E', convergence_k='this_convergence_K', convergence_f='this_convergence_F', convergence_t='this_convergence_T', optimized_distances='this_optimized_distances') self.assertTrue(f_ref == f_equal) self.assertFalse(f_ref == f_unequal) self.assertTrue(f_ref != f_unequal) def test_fps_av_modeling_init(self): """ Test initialization of FPSAVModeling. """ f = ihm.flr.FPSAVModeling(fps_modeling='foo', sample_probe='bar', parameter='foobar') self.assertEqual(f.fps_modeling, 'foo') self.assertEqual(f.sample_probe, 'bar') self.assertEqual(f.parameter, 'foobar') def test_fps_av_modeling_eq(self): """Test equality and inequality of FPSAVModeling objects.""" f_ref = ihm.flr.FPSAVModeling(fps_modeling='foo', sample_probe='bar', parameter='foobar') f_equal = ihm.flr.FPSAVModeling(fps_modeling='foo', sample_probe='bar', parameter='foobar') f_unequal = ihm.flr.FPSAVModeling(fps_modeling='foo', sample_probe='bar2', parameter='foobar') self.assertTrue(f_ref == f_equal) self.assertFalse(f_ref == f_unequal) self.assertTrue(f_ref != f_unequal) def test_fps_av_parameter_init(self): """Test initialization of FPSAVParameter.""" # Initialization with AV1 f1 = ihm.flr.FPSAVParameter(num_linker_atoms='this_num_linker_atoms_1', linker_length='this_linker_length_1', linker_width='this_linker_width_1', probe_radius_1='this_probe_radius_1_1') self.assertEqual(f1.num_linker_atoms, 'this_num_linker_atoms_1') self.assertEqual(f1.linker_length, 'this_linker_length_1') self.assertEqual(f1.linker_width, 'this_linker_width_1') self.assertEqual(f1.probe_radius_1, 'this_probe_radius_1_1') self.assertIsNone(f1.probe_radius_2) self.assertIsNone(f1.probe_radius_3) # Initialization with AV3 f2 = ihm.flr.FPSAVParameter(num_linker_atoms='this_num_linker_atoms_2', linker_length='this_linker_length_2', linker_width='this_linker_width_2', probe_radius_1='this_probe_radius_1_2', probe_radius_2='this_probe_radius_2_2', probe_radius_3='this_probe_radius_3_2') self.assertEqual(f2.num_linker_atoms, 'this_num_linker_atoms_2') self.assertEqual(f2.linker_length, 'this_linker_length_2') self.assertEqual(f2.linker_width, 'this_linker_width_2') self.assertEqual(f2.probe_radius_1, 'this_probe_radius_1_2') self.assertEqual(f2.probe_radius_2, 'this_probe_radius_2_2') self.assertEqual(f2.probe_radius_3, 'this_probe_radius_3_2') def test_fps_av_parameter_eq(self): """ Test equality and inequality of FPSAVParameter objects. """ f_ref = ihm.flr.FPSAVParameter( num_linker_atoms='this_num_linker_atoms_1', linker_length='this_linker_length_1', linker_width='this_linker_width_1', probe_radius_1='this_probe_radius_1_1') f_equal = ihm.flr.FPSAVParameter( num_linker_atoms='this_num_linker_atoms_1', linker_length='this_linker_length_1', linker_width='this_linker_width_1', probe_radius_1='this_probe_radius_1_1') f_unequal = ihm.flr.FPSAVParameter( num_linker_atoms='this_num_linker_atoms_1', linker_length='foo', linker_width='this_linker_width_1', probe_radius_1='this_probe_radius_1_1') self.assertTrue(f_ref == f_equal) self.assertFalse(f_ref == f_unequal) self.assertTrue(f_ref != f_unequal) def test_fps_mpp_modeling_init(self): """Test initialization of FPSMPPModeling.""" f = ihm.flr.FPSMPPModeling(fps_modeling='foo', mpp='bar', mpp_atom_position_group='foobar') self.assertEqual(f.fps_modeling, 'foo') self.assertEqual(f.mpp, 'bar') self.assertEqual(f.mpp_atom_position_group, 'foobar') def test_fps_mpp_modeling_eq(self): """Test equality and inequality of FPSMPPModeling objects.""" f_ref = ihm.flr.FPSMPPModeling(fps_modeling='foo', mpp='bar', mpp_atom_position_group='foobar') f_equal = ihm.flr.FPSMPPModeling(fps_modeling='foo', mpp='bar', mpp_atom_position_group='foobar') f_unequal = ihm.flr.FPSMPPModeling(fps_modeling='foo2', mpp='bar', mpp_atom_position_group='foobar') self.assertTrue(f_ref == f_equal) self.assertFalse(f_ref == f_unequal) self.assertTrue(f_ref != f_unequal) def test_fps_mean_probe_position_init(self): """Test initialization of FPSMeanProbePosition.""" f = ihm.flr.FPSMeanProbePosition(sample_probe='foo', x='bar', y='bar2', z='bar3') self.assertEqual(f.sample_probe, 'foo') self.assertEqual(f.x, 'bar') self.assertEqual(f.y, 'bar2') self.assertEqual(f.z, 'bar3') def test_fps_mean_probe_position_eq(self): """Test equality and inequality of FPSMeanProbePosition objects.""" f_ref = ihm.flr.FPSMeanProbePosition(sample_probe='foo', x='bar', y='bar2', z='bar3') f_equal = ihm.flr.FPSMeanProbePosition(sample_probe='foo', x='bar', y='bar2', z='bar3') f_unequal = ihm.flr.FPSMeanProbePosition( sample_probe='foobar', x='bar', y='bar2', z='bar3') self.assertTrue(f_ref == f_equal) self.assertFalse(f_ref == f_unequal) self.assertTrue(f_ref != f_unequal) def test_fps_mpp_atom_position_group_init(self): """ Test initialization of FPSMPPAtomPositionGroup. """ f = ihm.flr.FPSMPPAtomPositionGroup() self.assertEqual(f.mpp_atom_position_list, []) def test_fps_mpp_atom_position_group_add_atom_position(self): """ Test addition of an atom position to FPSMPPAtomPositionGroup. """ f = ihm.flr.FPSMPPAtomPositionGroup() f.add_atom_position('foo') f.add_atom_position('bar') self.assertEqual(f.mpp_atom_position_list, ['foo', 'bar']) def test_fps_mpp_atom_position_group_eq(self): """Test equality and inequality of FPSMPPAtomPositionGroup objects.""" f_ref = ihm.flr.FPSMPPAtomPositionGroup() f_ref.add_atom_position('foo') f_equal = ihm.flr.FPSMPPAtomPositionGroup() f_equal.add_atom_position('foo') f_unequal = ihm.flr.FPSMPPAtomPositionGroup() f_unequal.add_atom_position('bar') self.assertTrue(f_ref == f_equal) self.assertFalse(f_ref == f_unequal) self.assertTrue(f_ref != f_unequal) def test_fps_mpp_atom_position_init(self): """Test initialization of FPSMPPAtomPosition.""" f = ihm.flr.FPSMPPAtomPosition(atom='this_atom_id', x='this_xcoord', y='this_ycoord', z='this_zcoord') self.assertEqual(f.atom, 'this_atom_id') self.assertEqual(f.x, 'this_xcoord') self.assertEqual(f.y, 'this_ycoord') self.assertEqual(f.z, 'this_zcoord') def test_fps_mpp_atom_position_eq(self): """Test equality and inequality of FPSMPPAtomPosition objects.""" f_ref = ihm.flr.FPSMPPAtomPosition(atom='this_atom_id', x='this_xcoord', y='this_ycoord', z='this_zcoord') f_equal = ihm.flr.FPSMPPAtomPosition(atom='this_atom_id', x='this_xcoord', y='this_ycoord', z='this_zcoord') f_unequal = ihm.flr.FPSMPPAtomPosition( atom='other_atom_id', x='this_xcoord', y='this_ycoord', z='this_zcoord') self.assertTrue(f_ref == f_equal) self.assertFalse(f_ref == f_unequal) self.assertTrue(f_ref != f_unequal) def test_kinetic_rate_fret_analysis_connection_init(self): """Test initialization of KineticRateFretAnalysisConnection objects.""" c = ihm.flr.KineticRateFretAnalysisConnection(fret_analysis='f', kinetic_rate='k', details='d') self.assertEqual(c.fret_analysis, 'f') self.assertEqual(c.kinetic_rate, 'k') self.assertEqual(c.details, 'd') def test_kinetic_rate_fret_analysis_connection_eq(self): """Test equality of KineticRateFretAnalysisConnection objects.""" class MockObject: pass f1 = MockObject() f1._id = '1' f1.name = 'fret_analysis1' f2 = MockObject() f2._id = '2' f2.name = 'fret_analysis2' k1 = MockObject() k1._id = '11' k1.name = 'kinetic_rate1' k2 = MockObject() k2._id = '12' k2.name = 'kinetic_rate2' c_ref = ihm.flr.KineticRateFretAnalysisConnection( fret_analysis=f1, kinetic_rate=k1, details='details1') c_equal = ihm.flr.KineticRateFretAnalysisConnection( fret_analysis=f1, kinetic_rate=k1, details='details1') c_unequal = ihm.flr.KineticRateFretAnalysisConnection( fret_analysis=f2, kinetic_rate=k2, details='details2') self.assertTrue(c_ref == c_equal) self.assertFalse(c_ref == c_unequal) self.assertTrue(c_ref != c_unequal) def test_relaxation_time_fret_analysis_connection_init(self): """Test initialization of RelaxationTimeFretAnalysisConnection objects.""" c = ihm.flr.RelaxationTimeFretAnalysisConnection( fret_analysis='f', relaxation_time='r', details='d') self.assertEqual(c.fret_analysis, 'f') self.assertEqual(c.relaxation_time, 'r') self.assertEqual(c.details, 'd') def test_relaxation_time_fret_analysis_connection_eq(self): """Test equality of RelaxationTimeFretAnalysisConnection objects.""" class MockObject: pass f1 = MockObject() f1._id = '1' f1.name = 'fret_analysis1' f2 = MockObject() f2._id = '2' f2.name = 'fret_analysis2' r1 = MockObject() r1._id = '11' r1.name = 'relaxation_time1' r2 = MockObject() r2._id = '12' r2.name = 'relaxation_time2' c_ref = ihm.flr.RelaxationTimeFretAnalysisConnection( fret_analysis=f1, relaxation_time=r1, details='details1') c_equal = ihm.flr.RelaxationTimeFretAnalysisConnection( fret_analysis=f1, relaxation_time=r1, details='details1') c_unequal = ihm.flr.RelaxationTimeFretAnalysisConnection( fret_analysis=f2, relaxation_time=r2, details='details2') self.assertTrue(c_ref == c_equal) self.assertFalse(c_ref == c_unequal) self.assertTrue(c_ref != c_unequal) def test_flr_data_init(self): """ Test initialization of FLRData. """ f = ihm.flr.FLRData() self.assertEqual(f.distance_restraint_groups, []) self.assertEqual(f.poly_probe_conjugates, []) self.assertEqual(f.fret_model_qualities, []) self.assertEqual(f.fret_model_distances, []) self.assertEqual(f.fps_modeling, []) self.assertEqual(f.kinetic_rate_fret_analysis_connections, []) def test_flr_data_add_distance_restraint_group(self): """Test addition of a distance restraint group.""" f = ihm.flr.FLRData() f.distance_restraint_groups.append('foo') f.distance_restraint_groups.append('bar') self.assertEqual(f.distance_restraint_groups, ['foo', 'bar']) def test_flr_data_add_poly_probe_conjugate(self): """Test addition of a poly_probe_conjugate.""" f = ihm.flr.FLRData() f.poly_probe_conjugates.extend(('foo', 'bar')) self.assertEqual(f.poly_probe_conjugates, ['foo', 'bar']) def test_flr_data_add_fret_model_quality(self): """Test addition of a fret_model_quality.""" f = ihm.flr.FLRData() f.fret_model_qualities.extend(('foo', 'bar')) self.assertEqual(f.fret_model_qualities, ['foo', 'bar']) def test_flr_data_add_fret_model_distance(self): """Test addition of a fret_model_distance.""" f = ihm.flr.FLRData() f.fret_model_distances.append('foo') f.fret_model_distances.append('bar') self.assertEqual(f.fret_model_distances, ['foo', 'bar']) def test_flr_data_add_flr_fps_modeling(self): """Test addition of flr_FPS_modeling.""" f = ihm.flr.FLRData() f.fps_modeling.append('foo') f.fps_modeling.append('bar') self.assertEqual(f.fps_modeling, ['foo', 'bar']) def test_flr_data_add_kinetic_rate_fret_analysis_connection(self): """Test addition of object to kinetic_rate_fret_analysis_connections.""" f = ihm.flr.FLRData() f.kinetic_rate_fret_analysis_connections.append('foo') f.kinetic_rate_fret_analysis_connections.append('bar') self.assertEqual(f.kinetic_rate_fret_analysis_connections, ['foo', 'bar']) def test_flr_data_add_relaxation_time_fret_analysis_connection(self): """Test addition of object to relaxation_time_fret_analysis_connections.""" f = ihm.flr.FLRData() f.relaxation_time_fret_analysis_connections.append('foo') f.relaxation_time_fret_analysis_connections.append('bar') self.assertEqual(f.relaxation_time_fret_analysis_connections, ['foo', 'bar']) def test_flr_data_all_chemical_descriptors(self): """Test for collection of all chemical descriptors.""" f = ihm.flr.FLRData() # Define probe descriptors this_probe_descriptor_1 = ihm.flr.ProbeDescriptor( reactive_probe_chem_descriptor='This_reactive_probe_desc_1', chromophore_chem_descriptor='This_chromophore_desc_1') this_probe_descriptor_2 = ihm.flr.ProbeDescriptor( reactive_probe_chem_descriptor='This_reactive_probe_desc_2', chromophore_chem_descriptor='This_chromophore_desc_2') this_probe_descriptor_3 = ihm.flr.ProbeDescriptor( reactive_probe_chem_descriptor='This_reactive_probe_desc_3', chromophore_chem_descriptor='This_chromophore_desc_3') this_probe_descriptor_4 = ihm.flr.ProbeDescriptor( reactive_probe_chem_descriptor='Ref_reactive_probe_desc', chromophore_chem_descriptor='Ref_chromophore_desc') # Define probes this_probe_1 = ihm.flr.Probe(probe_list_entry='foo', probe_descriptor=this_probe_descriptor_1) this_probe_2 = ihm.flr.Probe(probe_list_entry='foo', probe_descriptor=this_probe_descriptor_2) this_probe_3 = ihm.flr.Probe(probe_list_entry='foo', probe_descriptor=this_probe_descriptor_3) this_probe_4 = ihm.flr.Probe(probe_list_entry='foo', probe_descriptor=this_probe_descriptor_4) # Define poly probe positions this_poly_probe_position_1 = ihm.flr.PolyProbePosition( resatom='foo', mutation_flag=True, mutated_chem_comp_id='Mutated_Chem_comp_id_1', modification_flag=False) this_poly_probe_position_2 = ihm.flr.PolyProbePosition( resatom='foo', mutation_flag=False, modification_flag=True, modified_chem_descriptor='Modified_Chem_descriptor_1') this_poly_probe_position_3 = ihm.flr.PolyProbePosition( resatom='foo', mutation_flag=False, modification_flag=False) this_poly_probe_position_4 = ihm.flr.PolyProbePosition( resatom='foo', mutation_flag=True, mutated_chem_comp_id='Mutated_Chem_comp_id_2') this_poly_probe_position_5 = ihm.flr.PolyProbePosition( resatom='foo', modification_flag=True, modified_chem_descriptor='Modified_Chem_descriptor_2') this_sample_probe_1 = ihm.flr.SampleProbeDetails( sample='foo', probe=this_probe_1, fluorophore_type='donor', poly_probe_position=this_poly_probe_position_1) this_sample_probe_2 = ihm.flr.SampleProbeDetails( sample='foo2', probe=this_probe_2, fluorophore_type='donor', poly_probe_position=this_poly_probe_position_2) this_sample_probe_3 = ihm.flr.SampleProbeDetails( sample='foo3', probe=this_probe_3, fluorophore_type='donor', poly_probe_position=this_poly_probe_position_3) this_sample_probe_4 = ihm.flr.SampleProbeDetails( sample='foo4', probe=this_probe_4, fluorophore_type='donor', poly_probe_position=this_poly_probe_position_4) this_sample_probe_5 = ihm.flr.SampleProbeDetails( sample='foo5', probe=this_probe_4, fluorophore_type='donor', poly_probe_position=this_poly_probe_position_5) this_reference_measurement_1 = ihm.flr.RefMeasurement( ref_sample_probe=this_sample_probe_4) this_reference_measurement_2 = ihm.flr.RefMeasurement( ref_sample_probe=this_sample_probe_5) this_reference_measurement_group_1 = ihm.flr.RefMeasurementGroup() this_reference_measurement_group_1.add_ref_measurement( this_reference_measurement_1) this_reference_measurement_group_1.add_ref_measurement( this_reference_measurement_2) this_analysis_1 = ihm.flr.FRETAnalysis( experiment='foo', sample_probe_1=this_sample_probe_1, sample_probe_2=this_sample_probe_2, forster_radius='foo', type='lifetime-based', ref_measurement_group=this_reference_measurement_group_1) this_analysis_2 = ihm.flr.FRETAnalysis( experiment='bar', sample_probe_1=this_sample_probe_1, sample_probe_2=this_sample_probe_2, forster_radius='bar', type='intensity-based') this_distance_restraint_1 = ihm.flr.FRETDistanceRestraint( sample_probe_1=this_sample_probe_1, sample_probe_2=this_sample_probe_2, analysis=this_analysis_1, distance=50) this_distance_restraint_2 = ihm.flr.FRETDistanceRestraint( sample_probe_1=this_sample_probe_1, sample_probe_2=this_sample_probe_3, analysis=this_analysis_2, distance=50) this_distance_restraint_group = ihm.flr.FRETDistanceRestraintGroup() this_distance_restraint_group.add_distance_restraint( this_distance_restraint_1) this_distance_restraint_group.add_distance_restraint( this_distance_restraint_2) f.distance_restraint_groups.append(this_distance_restraint_group) conj = ihm.flr.PolyProbeConjugate( sample_probe=this_sample_probe_1, chem_descriptor='Conjugate_probe_desc', ambiguous_stoichiometry=False) f.poly_probe_conjugates.append(conj) descs = list(f._all_flr_chemical_descriptors()) self.assertEqual( descs, ['This_reactive_probe_desc_1', 'This_chromophore_desc_1', 'This_reactive_probe_desc_2', 'This_chromophore_desc_2', 'Modified_Chem_descriptor_1', 'Ref_reactive_probe_desc', 'Ref_chromophore_desc', 'Ref_reactive_probe_desc', 'Ref_chromophore_desc', 'Modified_Chem_descriptor_2', 'This_reactive_probe_desc_1', 'This_chromophore_desc_1', 'This_reactive_probe_desc_3', 'This_chromophore_desc_3', 'Conjugate_probe_desc']) if __name__ == '__main__': unittest.main()