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_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_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_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_get_sequence(self):
s = RNAChain('file', MINI_TEMPLATE)
seq = s.get_sequence()
self.assertEqual(seq, Sequence("GCGGAUUUALCUCAG"))