def test_find_fragment_candidates(self):
"""Should return a FragmentCandidates instance"""
lf = FragmentFinder(self.struc['2'], self.struc['6'], Sequence('AGCU'),
self.struc, 10)
cand = lf.find_fragment_candidates()
self.assertTrue(isinstance(cand, FragmentCandidates))
self.assertTrue(1 <= len(cand) <= 10)
def test_insert_in_itself(self):
"""Best fragment for LIR structures should come from itself."""
for length, struc, chain, stem5, stem3, seq in FRAGMENTS_TO_INSERT:
m = load_model(PATH_TO_LIR_STRUCTURES + struc, chain)
lf = FragmentFinder(m[stem5], m[stem3], Sequence(seq), m, 2)
candidates = lf.find_fragment_candidates()
if len(candidates) > 0:
best = candidates[0]
self.assertEqual(best.structure, struc)
self.assertEqual(best.chain, chain)
self.assertEqual(best.preceding_residue, stem5)
self.assertEqual(best.following_residue, stem3)
self.assertAlmostEqual(best.rmsd, 0.000, 3)
def find_fragment_candidates(
self,
res5,
res3,
sequence,
candidates_number=NUMBER_OF_FRAGMENT_CANDIDATES,
lir_path=PATH_TO_LIR_STRUCTURES,
secstruc=None):
# en: candidate_number
"""
Looks for fragment candidates for missing fragment in a structure.
Returns list of fragment candidates.
Arguments:
- anchor residue on 5' end as a ModernaResidue instance (residue preceding missing fragment)
- anchor residue on 3' end as a ModernaResidue instance (residue fallowing missing fragment)
- missing sequence
"""
fragment_finder = FragmentFinder(res5, res3, sequence, self,
candidates_number, lir_path, secstruc)
return fragment_finder.find_fragment_candidates(
) # FragmentCandidates instance