def test_non_polymer_chem_comp(self):
"""Test NonPolymerChemComp class"""
cc1 = ihm.NonPolymerChemComp('HEM')
self.assertEqual(cc1.type, 'non-polymer')
self.assertEqual(cc1.code_canonical, 'X')
cc2 = ihm.NonPolymerChemComp('HEM', code_canonical='G')
self.assertEqual(cc2.code_canonical, 'G')
def test_entity_weight(self):
"""Test Entity.formula_weight"""
e1 = ihm.Entity('AHCD')
self.assertAlmostEqual(e1.formula_weight, 499.516, places=1)
# Entity containing a component with unknown weight
heme = ihm.Entity([ihm.NonPolymerChemComp('HEM')])
self.assertIsNone(heme.formula_weight)
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_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_entity(self):
"""Test Entity class"""
e1 = ihm.Entity('AHCD', description='foo')
# Should compare identical if sequences are the same
e2 = ihm.Entity('AHCD', description='bar')
e3 = ihm.Entity('AHCDE', description='foo')
heme = ihm.Entity([ihm.NonPolymerChemComp('HEM')])
self.assertEqual(e1, e2)
self.assertNotEqual(e1, e3)
self.assertEqual(e1.seq_id_range, (1, 4))
self.assertEqual(e3.seq_id_range, (1, 5))
# seq_id does not exist for nonpolymers
self.assertEqual(heme.seq_id_range, (None, None))
def test_entity_range(self):
"""Test EntityRange class"""
e = ihm.Entity('AHCDAH')
heme = ihm.Entity([ihm.NonPolymerChemComp('HEM')])
e._id = 42
self.assertEqual(e.seq_id_range, (1, 6))
r = e(3, 4)
self.assertEqual(r.seq_id_range, (3, 4))
self.assertEqual(r._id, 42)
# Cannot create ranges for nonpolymeric entities
self.assertRaises(TypeError, heme.__call__, 1, 1)
samer = e(3, 4)
otherr = e(2, 4)
self.assertEqual(r, samer)
self.assertEqual(hash(r), hash(samer))
self.assertNotEqual(r, otherr)
self.assertNotEqual(r, e) # entity_range != entity
def test_asym_range(self):
"""Test AsymUnitRange class"""
e = ihm.Entity('AHCDAH')
heme = ihm.Entity([ihm.NonPolymerChemComp('HEM')])
a = ihm.AsymUnit(e)
aheme = ihm.AsymUnit(heme)
a._id = 42
self.assertEqual(a.seq_id_range, (1, 6))
# seq_id is not defined for nonpolymers
self.assertEqual(aheme.seq_id_range, (None, None))
r = a(3, 4)
self.assertEqual(r.seq_id_range, (3, 4))
self.assertEqual(r._id, 42)
self.assertEqual(r.entity, e)
# Cannot create ranges for nonpolymeric entities
self.assertRaises(TypeError, aheme.__call__, 1, 1)
samer = a(3, 4)
otherr = a(2, 4)
self.assertEqual(r, samer)
self.assertEqual(hash(r), hash(samer))
self.assertNotEqual(r, otherr)
self.assertNotEqual(r, a) # asym_range != asym
self.assertNotEqual(r, e(3, 4)) # asym_range != entity_range
self.assertNotEqual(r, e) # asym_range != entity
def test_non_polymer_chem_comp(self):
"""Test NonPolymerChemComp class"""
cc1 = ihm.NonPolymerChemComp('HEM')
self.assertEqual(cc1.type, 'non-polymer')
# An entity corresponding to an RNA sequence
entity_rna = ihm.Entity('ACG',
alphabet=ihm.RNAAlphabet,
description='RNA chain')
# 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')
system = ihm.System()
# An entity corresponding to an amino acid (polyalanine) sequence
entity_protein = ihm.Entity('AAA', description='Subunit A')
# An entity corresponding to an RNA sequence
entity_rna = ihm.Entity('ACG', alphabet=ihm.RNAAlphabet,
description='RNA chain')
# An entity corresponding to a DNA sequence
entity_dna = ihm.Entity(['DA', 'DC', 'DG'], alphabet=ihm.DNAAlphabet,
description='DNA chain')
# A ligand entity (in this case, heme)
entity_heme = ihm.Entity([ihm.NonPolymerChemComp("HEM")], 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')
