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))
