def test_is_phosphate_intact(self):
"""Check whether OP1 and OP2 are in place"""
chain=PDBParser().get_structure('test_struc',BB_MESSED_UP)[0].child_list[0]
resi1 = RNAResidue(chain[('H_c ', 32, ' ')])
resi2 = RNAResidue(chain[(' ', 33, ' ')])
self.assertTrue(is_phosphate_intact(resi1))
self.assertFalse(is_phosphate_intact(resi2))
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 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')