def test_entity_type(self): """Test Entity.type""" protein = ihm.Entity('AHCD') heme = ihm.Entity([ihm.NonPolymerChemComp('HEM')]) water = ihm.Entity([ihm.WaterChemComp()]) self.assertEqual(protein.type, 'polymer') self.assertTrue(protein.is_polymeric()) self.assertEqual(heme.type, 'non-polymer') self.assertFalse(heme.is_polymeric()) self.assertEqual(water.type, 'water') self.assertFalse(water.is_polymeric()) # A single amino acid should be classified non-polymer single_aa = ihm.Entity('A') self.assertEqual(single_aa.type, 'non-polymer') self.assertFalse(single_aa.is_polymeric()) # ... unless forced polymer single_aa._force_polymer = True self.assertEqual(single_aa.type, 'polymer') self.assertTrue(single_aa.is_polymeric()) # An entity with no sequence is a polymer empty = ihm.Entity([]) self.assertEqual(empty.type, 'polymer') self.assertTrue(empty.is_polymeric())
def test_entity_src_method_default(self): """Test default values of Entity.src_method""" protein = ihm.Entity('AHCD') water = ihm.Entity([ihm.WaterChemComp()]) self.assertEqual(protein.src_method, "man") self.assertEqual(water.src_method, "nat") # src_method is readonly def try_set(): protein.src_method = 'foo' self.assertRaises(TypeError, try_set)
def test_entity_type(self): """Test Entity.type""" protein = ihm.Entity('AHCD') heme = ihm.Entity([ihm.NonPolymerChemComp('HEM')]) water = ihm.Entity([ihm.WaterChemComp()]) self.assertEqual(protein.type, 'polymer') self.assertTrue(protein.is_polymeric()) self.assertEqual(heme.type, 'non-polymer') self.assertFalse(heme.is_polymeric()) self.assertEqual(water.type, 'water') self.assertFalse(water.is_polymeric())
def test_water_chem_comp(self): """Test WaterChemComp class""" cc1 = ihm.WaterChemComp() self.assertEqual(cc1.type, 'non-polymer')
# An entity corresponding to a DNA sequence entity_dna = ihm.Entity(['DA', 'DC', 'DG'], alphabet=ihm.DNAAlphabet, description='DNA chain') # Non-polymers such as ligands or water should each live in their own Entity: # A ligand entity (in this case, heme) heme = ihm.NonPolymerChemComp("HEM", name='PROTOPORPHYRIN IX CONTAINING FE', formula='C34 H32 Fe N4 O4') entity_heme = ihm.Entity([heme], description='Heme') # Water entity_h2o = ihm.Entity([ihm.WaterChemComp()], description='Water') system.entities.extend( (entity_protein, entity_rna, entity_dna, entity_heme, entity_h2o)) # Next, we define asymmetric units for everything we modeled. # Here, we have a single instance of each protein, RNA and DNA, two hemes, # plus crystal waters asym_protein = ihm.AsymUnit(entity_protein, details='Subunit A') asym_rna = ihm.AsymUnit(entity_rna, details='RNA chain') asym_dna = ihm.AsymUnit(entity_dna, details='DNA chain') asym_heme1 = ihm.AsymUnit(entity_heme, details='First heme') asym_heme2 = ihm.AsymUnit(entity_heme, details='Second heme') asym_h2o = ihm.AsymUnit(entity_h2o, details='Crystal waters') system.asym_units.extend( (asym_protein, asym_rna, asym_dna, asym_heme1, asym_heme2, asym_h2o))