def test_is_backbone_intact(self):
"""Check all kinds of backbone discontinuities in one residue."""
chain=PDBParser().get_structure('test_struc',BROKEN_BACKBONE)[0].child_list[0]
residues = [r for r in chain]
for resi in residues[:5]:
mr = RNAResidue(resi)
self.assertFalse(is_backbone_intact(mr))
mr = RNAResidue(chain[6])
self.assertTrue(is_backbone_intact(mr))
def is_intact(self):
"""Checks whether the backbone is complete."""
if not is_backbone_intact(self.resi1, mode="3'") or \
not is_backbone_intact(self.resi2, mode="5'") or \
not are_residues_connected(self.resi1, self.resi2) or \
not is_phosphate_intact(self.resi2) or \
is_backbone_congested(self.resi1, mode="3'") or \
is_backbone_congested(self.resi2, mode="5'"):
return False
return True
def test_is_backbone_intact_5p3p(self):
"""Check all kinds of backbone discontinuities in one residue."""
chain=PDBParser().get_structure('test_struc',BROKEN_BACKBONE)[0].child_list[0]
residues = [r for r in chain]
result_5p = []
result_3p = []
for resi in residues[:6]:
mr = RNAResidue(resi)
result_5p.append(is_backbone_intact(mr, mode="5'"))
result_3p.append(is_backbone_intact(mr, mode="3'"))
self.assertEqual(result_5p, [False, False, False, False, True, True])
self.assertEqual(result_3p, [True, True, True, False, False, True])
def write_resi_status(self, resi):
log.write_message('Status of residue: %s' % resi.identifier)
if is_backbone_intact(resi):
log.write_message('\tbackbone OK')
else:
log.write_message('\tbackbone INTERRUPTED')
if is_phosphate_intact(resi):
log.write_message('\tphosphate OK')
else:
log.write_message('\tphosphate BROKEN')
if is_backbone_congested(resi):
log.write_message('\tclashes OCCUR')
else:
log.write_message('\clashes OK')
def test_validation(self):
"""Makes sure test data is set up properly."""
self.assertFalse(is_backbone_intact(self.resi2))
self.assertFalse(are_residues_connected(self.resi1, self.resi2))