def test_write_pdb(self):
"""write_pdb should create a file."""
s = RNAChain('file', MINI_TEMPLATE)
if os.access(OUTPUT, os.F_OK):
os.remove(OUTPUT)
s.write_pdb_file(OUTPUT)
self.assertTrue(os.access, os.F_OK)
def test_write_load_sanity(self):
"""After re-reading written file, there should be the same residues."""
s = RNAChain('file', MINI_TEMPLATE)
if os.access(OUTPUT, os.F_OK):
os.remove(OUTPUT)
s.write_pdb_file(OUTPUT)
t = RNAChain('file', OUTPUT)
i = 0
while i < 15:
i += 1
self.assertEqual(s[str(i)].id[1], t[str(i)].id[1])
self.assertEqual(s[str(i)].long_abbrev, t[str(i)].long_abbrev)
s_atoms = sum([len(r) for r in s])
t_atoms = sum([len(r) for r in t])
self.assertEqual(s_atoms, t_atoms)
def test_1ehz(self):
"""Everything should work for a more complicated structure."""
m = RNAChain('file', RNA_1EHZ)
# atom count
self.assertEqual(len(m), 76)
# write
if os.access(OUTPUT, os.F_OK): os.remove(OUTPUT)
m.write_pdb_file(OUTPUT)
self.assertTrue(os.access(OUTPUT, os.F_OK))
# reload
n = RNAChain('file', OUTPUT)
self.assertEqual(len(n), 76)
# check iter
res = [r for r in n]
self.assertEqual(len(res), 76)
# check residues
self.assertEqual(n['1'].long_abbrev, 'G')
self.assertEqual(n['8'].long_abbrev, 'U')
self.assertEqual(n['10'].long_abbrev, 'm2G')
self.assertEqual(n['76'].long_abbrev, 'A')
self.assertEqual(n['16'].long_abbrev, 'D')
self.assertRaises(RNAChainError, n.__getitem__, '77')
