def test_find_fragment(self):
"""Should return a ModernaFragment instance with the right sequence"""
lf = FragmentFinder(self.struc['2'], self.struc['6'], Sequence('AGCU'),
self.struc, 10)
frag = lf.find_fragment()
frag.fix_backbone()
self.assertTrue(isinstance(frag, ModernaFragment))
self.assertEqual(
frag.struc.get_sequence().seq_with_modifications[1:-1], 'AGCU')
def test_find_secstruc(self):
"""Secstruc can be used as an optional search criterion"""
hairpin = ModernaStructure('file', RNA_HAIRPIN, 'D')
lf = FragmentFinder(hairpin['30'],
hairpin['40'],
Sequence('CGGGCG'),
self.struc,
10,
secstruc="(....)")
frag = lf.find_fragment()
self.assertEqual(frag.struc.get_secstruc(), "((....))")
def insert_best_fragment(self,
start,
stop,
sequence,
candidates_number=NUMBER_OF_FRAGMENT_CANDIDATES):
"""
Makes a LIR search to fill a gap at a given position.
looks for possible candidates, checks the first ~20 for clashes,
takes the best, removes anchor residue and inserts it in the model.
Arguments:
- start position as a string (residue identifier)e.g. '3' - this is an identifier of the preceding anchor residue
- stop position as above - this is an identifier of the fallowing anchor residue
- fragment sequence as a Sequence object
- number of fragment candidates.
"""
log.write_message(
'\nSearching fragment between residue %s and residue %s.' %
(str(start), str(stop)))
fragment_finder = FragmentFinder(self[start], self[stop], sequence,
self, candidates_number)
best_fragment = fragment_finder.find_fragment()
log.write_message('\nBest fragment:\n%s' % str(best_fragment))
self.insert_fragment(best_fragment)
def test_find_zero_length_fragment(self):
lf = FragmentFinder(self.struc['2'], self.struc['4'], Sequence(''),
self.struc, 10)
frag = lf.find_fragment()
self.assertEqual(frag.struc.get_sequence(), Sequence('C_G'))