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_sort_residues(self):
m = RNAChain('file', MINI_TEMPLATE) #residues_mixed.ent')
m.sort_residues()
residues = []
for resi in m:
residues.append(resi.id[1])
residues_copy = residues[:]
residues_copy.sort()
self.assertEqual(residues, residues_copy)
def test_PDB_file_with_negative_numbering(self):
"""Checks whether the order of residues with negative NRs is correct"""
# ...because this was the major problem with negative numbering...
# ...that ModeRNA read residues in a wrong order!
s = RNAChain('file', NEG_NUM_PDB, 'E')
self.assertEqual(s.get_sequence().seq_with_modifications, \
'GGCUGCCUGGGUCCGCCUUGAGUGCCCGGGUGAGAAGCAUGAUCCCGGGUAAUUAUGGCGGACCCACA')
self.assertEqual(s.get_sequence().seq_without_modifications, \
'GGCUGCCUGGGUCCGCCUUGAGUGCCCGGGUGAGAAGCAUGAUCCCGGGUAAUUAUGGCGGACCCACA')
def test_get_region(self):
"""Checks whether a region can be extracted from structure"""
s = RNAChain('file', MINI_TEMPLATE)
s2 = s.get_region('3', '6')
self.assertTrue(isinstance(s2, RNAChain))
self.assertEqual(len(s2.moderna_residues), 4)
self.assertEqual(s2.get_sequence(), Sequence('GGAU'))
s3 = s.get_region('3')
self.assertEqual(s3.get_sequence(), Sequence('GGAUUUALCUCAG'))
s4 = s.get_region(stop_id='6')
self.assertEqual(s4.get_sequence(), Sequence('GCGGAU'))
def test_load_iter(self):
"""Should load PDB files and iterate over all residues."""
s = RNAChain('file', MINI_TEMPLATE)
i = 0
for resi in s:
i += 1
self.assertEqual(i, 15)
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_getitem_slice(self):
"""Residues should be accessible by slice."""
s = RNAChain('file', MINI_TEMPLATE)
struc_slice = s['2':'5']
self.assertEqual(len(struc_slice), 4)
self.assertEqual(struc_slice[0].identifier, '2')
self.assertEqual(struc_slice[3].identifier, '5')
def test_iterate(self):
"""Iteration over RNAResidues with correct numbers."""
s = RNAChain('file', MINI_TEMPLATE)
i = 1
for resi in s:
self.assertTrue(isinstance(resi, RNAResidue))
self.assertEqual(resi.id[1], i)
i += 1
def test_getitem(self):
"""Residues should be accessible by their number as string."""
s = RNAChain('file', MINI_TEMPLATE)
self.assertEqual(s['1'].long_abbrev, 'G')
self.assertEqual(s['8'].long_abbrev, 'U')
self.assertEqual(s['9'].long_abbrev, 'A')
self.assertEqual(s['12'].long_abbrev, 'U')
self.assertEqual(s['15'].long_abbrev, 'G')
self.assertRaises(RNAChainError, s.__getitem__, '17')
def add_op12(self):
"""Adds OP1 OP2 atoms"""
self.remove_op1_op2()
phos = RNAChain('file', DATA_PATH + 'phosphate_group.pdb')['1']
#TODO: replace by Bio.PDB --> faster
mobile = [phos['OP3'], phos['P'], phos["O5'"]]
fixed = [self.r1["O3'"], self.r2['P'], self.r2["O5'"]]
s = ModernaSuperimposer(fixed, mobile, phos.child_list)
self.r2.add(phos['OP1'])
self.r2.add(phos['OP2'])
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')
def test_init_with_sequence(self):
"""Allows to skip sequence recognition"""
s = RNAChain('file', MINI_TEMPLATE, seq=Sequence("GCGGAUUUALCUCAG"))
self.assertEqual(s.get_sequence(), Sequence("GCGGAUUUALCUCAG"))
# wrong sequence should also be applied
#TODO: check whether this is OK
s = RNAChain('file', MINI_TEMPLATE, seq=Sequence("UUULLYYDDAAGAGA"))
self.assertEqual(s.get_sequence(), Sequence("UUULLYYDDAAGAGA"))
def test_getitem_slice_with_letters(self):
"""Residues should be accessible by slice."""
s = RNAChain('file', BAD_LOOP_INSERTION)
struc_slice = s['944':'961']
self.assertEqual(len(struc_slice), 9)
self.assertRaises(RNAChainError, s.__getitem__, slice('0', '961'))
def test_len(self):
"""should return correct number of residues."""
s = RNAChain('file', MINI_TEMPLATE)
self.assertEqual(len(s), 15)
def test_get_sequence(self):
s = RNAChain('file', MINI_TEMPLATE)
seq = s.get_sequence()
self.assertEqual(seq, Sequence("GCGGAUUUALCUCAG"))
def test_get_sequence_with_hydromods(self):
"""Modifications with hydrogens should be recognized."""
s = RNAChain('file', MOD_WITH_HYDROGENS, 'B')
seq = s.get_sequence()
self.assertEqual(seq, Sequence("UPA"))
def test_true(self):
"""Should always be true."""
s = RNAChain()
self.assertTrue(s)
def test_init_residues(self):
struc = PDBParser().get_structure('test', MINI_TEMPLATE)
s = RNAChain('residues',
struc[0]['A'].child_list,
seq=Sequence("GCGGAUUUALCUCAG"))
self.assertEqual(s.get_sequence(), Sequence("GCGGAUUUALCUCAG"))
def test_init_chain(self):
struc = PDBParser().get_structure('test', MINI_TEMPLATE)
s = RNAChain('chain', struc[0]['A'], seq=Sequence("GCGGAUUUALCUCAG"))
self.assertEqual(s.get_sequence(), Sequence("GCGGAUUUALCUCAG"))
def test_init_empty(self):
"""Empty chain can be initialized."""
s = RNAChain()
def test_fast(self):
for i in range(10):
s = Sequence(
'GCGGAUUUALCUCAGDDGGGAGAGCRCCAGABU#AAYAP?UGGAG7UC?UGUGTPCG"UCCACAGAAUUCGCACCA'
)
m = RNAChain('file', RNA_1EHZ, seq=s)
def test_slow(self):
for i in range(10):
m = RNAChain('file', RNA_1EHZ)
def test_getitem_number(self):
"""Calling getitem with a number gives an error."""
s = RNAChain('file', MINI_TEMPLATE)
self.assertRaises(RNAChainError, s.__getitem__, 1)
def test_last_resi(self):
"""Should return firs residue"""
s = RNAChain('file', MINI_TEMPLATE)
self.assertEqual(s.last_resi.identifier, '15')
def test_ignore_empty_residues(self):
"""Check whether residues with only one H are read and written."""
s = RNAChain('file', H_ONLY, ' ')
self.assertEqual(len(s), 0)