def test_has_clashes(self):
f1 = ModernaFragment(self.s1)
clashes = f1.has_clashes(list(self.s2))
self.assertEqual(len(clashes), 8)
struc = ModernaStructure('file', FRAGMENT1)
clashes = f1.has_clashes(list(struc))
self.assertEqual(len(clashes), 0)
def test_attributes(self):
"""object attributes should have been set up correctly."""
f1 = ModernaFragment(self.s1)
f2 = ModernaFragment(self.s2, new_sequence=Sequence('GCLG'))
modfrag = ModernaFragment(self.s3, new_sequence=Sequence('GL7L7L7ULL7L7AG'))
self.assertEqual(len(modfrag.struc), 15)
self.assertEqual(f1.struc.get_sequence(),Sequence("GCGG"))
self.assertEqual(f2.struc.get_sequence(),Sequence("GCGG"))
self.assertTrue(str(f1))
def test_apply_sequence_modified(self):
"""Applying a sequence with modifications should work."""
f2 = ModernaFragment(self.s2, new_sequence=Sequence('GCLG'))
f2.apply_seq()
self.assertEqual(self.s2.get_sequence(),Sequence("GCLG"))
modfrag = ModernaFragment(self.s3, new_sequence=Sequence('GL7L7L7ULL7L7AG'))
modfrag.apply_seq()
self.assertEqual(self.s3.get_sequence(), Sequence('GL7L7L7ULL7L7AG'))
def test_apply_sequence(self):
"""Should change the sequence of the entire fragment."""
frag = ModernaFragment(self.s1, new_sequence=Sequence('AAAA'))
frag.apply_seq()
self.assertEqual(self.s1.get_sequence(), Sequence('AAAA'))
# test lengths that do not fit
frag = ModernaFragment(self.s2, new_sequence=Sequence('AAA'))
self.assertRaises(ModernaFragmentError, frag.apply_seq)
frag = ModernaFragment(self.s2, new_sequence=Sequence('AAAAA'))
self.assertRaises(ModernaFragmentError, frag.apply_seq)
def test_init(self):
"""Should have ModernaStructure as an attribute."""
f1 = ModernaFragment(self.s1)
self.assertEqual(f1.struc.get_sequence(), Sequence('GCGG'))
def test_abstract_methods(self):
"""Some placeholder methods should be there."""
f1 = ModernaFragment(self.s1)
f1.get_resi_to_remove(self.s2)
f1.fix_backbone()
def test_renumber(self):
"""Should exist as an abstract method."""
f1 = ModernaFragment(self.s1)
f1.renumber()
self.assertEqual([r.identifier for r in self.s1],
['1A', '1B', '1C', '1D'])
def test_prepare_anchor_residues(self):
"""Should exist as an abstract method."""
f1 = ModernaFragment(self.s1)
self.assertRaises(ModernaSuperimposerError, f1.prepare_anchor_residues)
def test_superimpose(self):
"""Should just exist as an abstract method."""
f1 = ModernaFragment(self.s1)
self.assertRaises(ModernaSuperimposerError, f1.superimpose)
def test_nonanchor_residues(self):
"""Stems defined in subclasses, thus should return all residues."""
f1 = ModernaFragment(self.s1)
self.assertEqual(len(f1.nonanchor_residues), 4)
def test_anchor_residues(self):
"""Abstract superclass should have no anchors yet."""
f1 = ModernaFragment(self.s1)
self.assertEqual(f1.anchor_residues, [])