def test_fill_doublegap(self):
"""Should insert fragments into correct sites."""
# prepare model
t = Template(DOUBLEGAP, 'file', 'A')
m = RnaModel()
for r in t:
m.copy_residue(r)
# insert first fragment
struc = ModernaStructure('file', FRAGMENT1)
f1 = ModernaFragment53(struc, anchor5=m['20'], anchor3=m['24'], \
new_sequence=Sequence('AUA'), keep=keep_first_last)
m.insert_fragment(f1)
resids = [r.identifier for r in m]
expected_resids1 = [
'18', '19', '20', '21', '21A', '23', '24', '27', '28', '29', '30',
'31', '32', '33', '34', '35'
]
self.assertEqual(resids, expected_resids1)
# insert second fragment
struc = ModernaStructure('file', FRAGMENT2)
f2 = ModernaFragment53(struc, anchor5=m['23'], anchor3=m['28'], \
new_sequence=Sequence('AUUA'), keep=keep_first_last)
m.insert_fragment(f2)
resids = [r.identifier for r in m]
expected_resids2 = [
'18', '19', '20', '21', '21A', '23', '24', '24A', '24B', '27',
'28', '29', '30', '31', '32', '33', '34', '35'
]
self.assertEqual(resids, expected_resids2)
def test_fill_gap_numbering(self):
"""Should insert fragment with correct numbering."""
t = Template(DOUBLEGAP, 'file', 'A')
m = RnaModel()
for r in t:
m.copy_residue(r)
struc = ModernaStructure('file', FRAGMENT1)
f1 = ModernaFragment53(struc,
anchor5=m['20'],
anchor3=m['24'],
new_sequence=Sequence('AUA'))
m.insert_fragment(f1)
resids = [r.identifier for r in m]
expected_resids1 = [
'18', '19', '20', '20A', '20B', '20C', '24', '27', '28', '29',
'30', '31', '32', '33', '34', '35'
]
self.assertEqual(resids, expected_resids1)