import os import unittest import utils TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..')) utils.set_search_paths(TOPDIR) import modelcif import modelcif.protocol import modelcif.descriptor import modelcif.associated import ihm class Tests(unittest.TestCase): def test_all_data(self): """Test _all_data() method""" s = modelcif.System() e1 = modelcif.Entity("D") e2 = modelcif.Entity("M") s.entities.extend((e1, e2)) e3 = modelcif.Entity("A") s.data.extend((e1, e3)) s.data_groups.append('something not a group') e4 = modelcif.Entity("M") s.data_groups.append(modelcif.data.DataGroup([e1, e4])) e5 = modelcif.Entity("M") f = modelcif.associated.File(path='foo', details='bar', data=e5) s.repositories.append(modelcif.associated.Repository('/', [f])) d = s._all_data() # List may contain duplicates self.assertEqual(list(d), [e1, e3, e1, e2, e1, e4, e5]) def test_all_asym_units(self): """Test _all_asym_units() method""" s = modelcif.System() e1 = modelcif.Entity("DDDD") e2 = modelcif.Entity("MMMM") a1 = modelcif.AsymUnit(e1) a2 = modelcif.AsymUnit(e2) s.asym_units.append(a1) asmb = modelcif.Assembly((a1, a2(1, 2))) s.assemblies.append(asmb) asyms = s._all_asym_units() # List may contain duplicates and should be all AsymUnit, # not AsymUnitRange self.assertEqual(list(asyms), [a1, a1, a2]) def test_all_entities(self): """Test _all_entities() method""" s = modelcif.System() e1 = modelcif.Entity("DDDD") e2 = modelcif.Entity("MMMM") s.entities.append(e1) a1 = modelcif.AsymUnit(e1) s.asym_units.append(a1) t2 = modelcif.Template(e2, asym_id='A', model_num=1, transformation=None) s.templates.append(t2) es = s._all_entities() # List may contain duplicates, but does not contain template entity e2 self.assertEqual(list(es), [e1, e1]) def test_all_data_groups(self): """Test _all_data_groups() method""" s = modelcif.System() e1 = modelcif.Entity("A") s.data_groups.append(e1) e2 = modelcif.Entity("C") p = modelcif.protocol.Protocol() p.steps.append(modelcif.protocol.ModelingStep( input_data=e1, output_data=e2)) p.steps.append(modelcif.protocol.ModelingStep( input_data=None, output_data=None)) s.protocols.append(p) d = s._all_data_groups() self.assertEqual(list(d), [e1, e1, e2]) def test_all_template_transformations(self): """Test _all_template_transformations() method""" s = modelcif.System() tr1 = 'tr1' tr2 = 'tr2' s.template_transformations.extend((tr1, tr2)) template = modelcif.Template('mockentity', asym_id="A", model_num=1, name="test template", transformation=tr1) s.templates.append(template) tt = s._all_template_transformations() # List may contain duplicates self.assertEqual(list(tt), [tr1, tr2, tr1]) def test_transformation(self): """Test Transformation class""" _ = modelcif.Transformation([[1, 0, 0], [0, 1, 0], [0, 0, 1]], [1, 2, 3]) def test_identity_transformation(self): """Test identity transformation""" t = modelcif.Transformation.identity() for i in range(3): self.assertAlmostEqual(t.tr_vector[i], 0., delta=0.1) for j in range(3): self.assertAlmostEqual(t.rot_matrix[i][j], 1. if i == j else 0., delta=0.1) # Should always get the same object t2 = modelcif.Transformation.identity() self.assertIs(t, t2) def test_all_software_groups(self): """Test _all_software_groups() method""" s = modelcif.System() sg1 = 'sg1' sg2 = 'sg2' s.software_groups.extend((sg1, sg2)) p = modelcif.protocol.Protocol() p.steps.append(modelcif.protocol.ModelingStep( input_data=None, output_data=None, software=sg1)) s.protocols.append(p) allsg = s._all_software_groups() # List may contain duplicates self.assertEqual(list(allsg), [sg1, sg2, sg1]) def test_all_ref_software(self): """Test _all_ref_software() method""" s1 = modelcif.Software( name='foo', version='1.0', classification='1', description='2', location='3') s2 = modelcif.Software( name='foo', version='2.0', classification='4', description='5', location='6') p = modelcif.SoftwareParameter(name='foo', value='bar') s2param = modelcif.SoftwareWithParameters(s2, [p]) s = modelcif.System() s.software_groups.append(modelcif.SoftwareGroup((s1, s2param))) s.software_groups.append(s1) e1 = modelcif.Entity("DDDD") t1 = modelcif.Template(e1, asym_id='A', model_num=1, transformation=None) s.templates.append(t1) # Old-style ChemComp without descriptors c1 = ihm.NonPolymerChemComp('C1', name='C1') if hasattr(c1, 'descriptors'): del c1.descriptors # ChemComp with descriptor without software c2 = ihm.NonPolymerChemComp('C2', name='C2') c2.descriptors = [modelcif.descriptor.IUPACName('foo')] # ChemComp with descriptor with software c3 = ihm.NonPolymerChemComp('C3', name='C3') s3 = modelcif.Software( name='foo', version='2.0', classification='4', description='5', location='6') c3.descriptors = [modelcif.descriptor.IUPACName('foo', software=s3)] e2 = modelcif.Entity([c1, c2, c3]) s.entities.append(e2) alls = s._all_ref_software() # List may contain duplicates self.assertEqual(list(alls), [s1, s2, s1, s3]) def test_software_parameter(self): """Test SoftwareParameter class""" p = modelcif.SoftwareParameter(name='foo', value=42) self.assertEqual(p.name, 'foo') self.assertEqual(p.value, 42) self.assertIsNone(p.description) _ = repr(p) def test_software_with_parameters(self): """Test SoftwareWithParameters class""" s = modelcif.Software( name='foo', version='1.0', classification='1', description='2', location='3') p = modelcif.SoftwareParameter(name='foo', value=42) swp = modelcif.SoftwareWithParameters(software=s, parameters=[p]) self.assertEqual(swp.software.name, 'foo') self.assertEqual(swp.parameters, [p]) self.assertEqual(swp.name, 'foo') self.assertEqual(swp.classification, '1') self.assertEqual(swp.description, '2') self.assertEqual(swp.location, '3') self.assertEqual(swp.type, 'program') self.assertEqual(swp.version, '1.0') self.assertIsNone(swp.citation) def test_template(self): """Test Template class""" e1 = modelcif.Entity("DDDD") t1 = modelcif.Template(e1, asym_id='A', model_num=1, transformation=None) self.assertEqual(t1.seq_id_range, (1, 4)) self.assertEqual(t1.template, t1) def test_software_group_parameters(self): """Test old-style SoftwareGroup construction with parameters""" s = modelcif.Software( name='foo', version='1.0', classification='1', description='2', location='3') p = modelcif.SoftwareParameter(name='foo', value=42) self.assertWarns(UserWarning, modelcif.SoftwareGroup, [s], parameters=[p]) def test_feature(self): """Test Feature base class""" f = modelcif.Feature() self.assertIs(f._get_entity_type(), ihm.unknown) if __name__ == '__main__': unittest.main()