def test_chains(self):
"""compares contacts diff chains"""
self.input_file = os.path.join('data', '1A1X.pdb') # one chain
self.input_structure = PDBParser(open(self.input_file))
res = contact.contacts_xtra(self.input_structure)
self.assertTrue(res == {})
self.input_file = os.path.join('data', '2E12.pdb') # one chain
self.input_structure = PDBParser(open(self.input_file))
res = contact.contacts_xtra(self.input_structure)
self.assertTrue(res)
self.assertFloatEqual(\
res[('2E12', 0, 'B', ('THR', 17, ' '), ('OG1', ' '))]['CONTACTS']\
[('2E12', 0, 'A', ('ALA', 16, ' '), ('CB', ' '))][0], 5.7914192561064004)
def test_chains(self):
"""compares contacts diff chains"""
self.input_file = os.path.join('data', '1A1X.pdb') # one chain
self.input_structure = PDBParser(open(self.input_file))
res = contact.contacts_xtra(self.input_structure)
self.assertTrue(res == {})
self.input_file = os.path.join('data', '2E12.pdb') # one chain
self.input_structure = PDBParser(open(self.input_file))
res = contact.contacts_xtra(self.input_structure)
self.assertTrue(res)
self.assertFloatEqual(\
res[('2E12', 0, 'B', ('THR', 17, ' '), ('OG1', ' '))]['CONTACTS']\
[('2E12', 0, 'A', ('ALA', 16, ' '), ('CB', ' '))][0], 5.7914192561064004)
def test_symmetry(self):
"""compares contacts diff symmetry mates"""
self.input_file = os.path.join('data', '2E12.pdb') # one chain
self.input_structure = PDBParser(open(self.input_file))
res = contact.contacts_xtra(self.input_structure, \
symmetry_mode='uc',
contact_mode='diff_sym')
self.assertTrue(res)
self.assertFloatEqual(\
res[('2E12', 0, 'B', ('GLU', 77, ' '), ('OE2', ' '))]['CONTACTS']\
[('2E12', 0, 'B', ('GLU', 57, ' '), ('OE2', ' '))][0], \
5.2156557833123873)
def test_symmetry(self):
"""compares contacts diff symmetry mates"""
self.input_file = os.path.join('data', '2E12.pdb') # one chain
self.input_structure = PDBParser(open(self.input_file))
res = contact.contacts_xtra(self.input_structure, \
symmetry_mode='uc',
contact_mode='diff_sym')
self.assertTrue(res)
self.assertFloatEqual(\
res[('2E12', 0, 'B', ('GLU', 77, ' '), ('OE2', ' '))]['CONTACTS']\
[('2E12', 0, 'B', ('GLU', 57, ' '), ('OE2', ' '))][0], \
5.2156557833123873)