def test_assembly(self):
st = gemmi.read_structure(full_path('1pfe.cif.gz'),
merge_chain_parts=False)
model = st[0]
self.assertEqual([ch.name for ch in model],
['A', 'B', 'A', 'B', 'A', 'B'])
a_mass = sum(ch.calculate_mass() for ch in model if ch.name == 'A')
b_mass = sum(ch.calculate_mass() for ch in model if ch.name == 'B')
model_mass = model.calculate_mass()
self.assertAlmostEqual(model_mass, a_mass + b_mass)
self.assertEqual(len(st.assemblies), 1)
asem = st.assemblies[0]
bio = gemmi.make_assembly(asem, model,
gemmi.HowToNameCopiedChain.Short)
self.assertEqual([ch.name for ch in bio], ['A', 'B', 'C', 'D'])
self.assertAlmostEqual(bio.calculate_mass(), 2 * model_mass)
self.assertAlmostEqual(bio[0].calculate_mass(), a_mass)
self.assertAlmostEqual(bio[1].calculate_mass(), b_mass)
self.assertAlmostEqual(bio[2].calculate_mass(), a_mass)
self.assertAlmostEqual(bio[3].calculate_mass(), b_mass)
bio = gemmi.make_assembly(asem, model,
gemmi.HowToNameCopiedChain.AddNumber)
self.assertEqual([ch.name for ch in bio], ['A1', 'B1', 'A2', 'B2'])
def test_assembly_naming(self):
st = gemmi.read_structure(full_path('4oz7.pdb'))
model = st[0]
a1 = st.assemblies[1]
bio = gemmi.make_assembly(a1, model,
gemmi.HowToNameCopiedChain.AddNumber)
self.assertEqual([ch.name for ch in bio], ['B1'])
bio = gemmi.make_assembly(a1, model, gemmi.HowToNameCopiedChain.Dup)
self.assertEqual([ch.name for ch in bio], ['B'])
bio = gemmi.make_assembly(a1, model, gemmi.HowToNameCopiedChain.Short)
self.assertEqual([ch.name for ch in bio], ['B'])