def test_helix(self):
struc = ModernaStructure('file', BROKEN_HELIX_EXAMPLE)
resi1 = struc['0Z']
resi2 = struc['1']
bb = BackboneBuilder(resi1, resi2, struc)
struc.write_pdb_file('out.pdb')
self.assertTrue(bb.is_intact())
def test_fccd(self):
struc = ModernaStructure('file',FCCD_EXAMPLE)
resi1 = struc['5']
resi2 = struc['6']
struc.remove_residue('5A')
bb = BackboneBuilder(resi1, resi2, struc)
self.assertTrue(bb.is_intact())
def test_build(self):
struc = ModernaStructure('file',FIXABLE_BACKBONE)
resi1 = struc['4']
resi2 = struc['5']
bb = BackboneBuilder(resi1, resi2, struc)
#struc.write_pdb_file('out.pdb')
self.assertTrue(bb.is_intact())
def _test_repair_congested(self):
"""Should avoid clashes between atoms."""
#TODO: reactivate test
struc = ModernaStructure('file',BB_MESSED_UP)
self.assertFalse(struc['33'].is_phosphate_intact())
bb = BackboneBuilder(struc['32'], struc['33'], struc)
struc.write_pdb_file('out.pdb')
self.assertTrue(bb.is_intact())
#TODO: criteria are now more strict, therefore test fails.
self.assertTrue(struc['32'].is_backbone_intact())
self.assertTrue(struc['33'].is_backbone_intact())
self.assertTrue(struc['33'].is_phosphate_intact())
self.assertFalse(struc['33'].is_backbone_congested())
self.assertFalse(struc['32'].is_backbone_congested())
def test_disconnected(self):
"""Structure example should not be OK"""
# trna Leu by Marcin Skorupskiego
struc = ModernaStructure('file',DISCONNECTED)
self.assertFalse(is_chain_continuous(struc))
bb = BackboneBuilder(struc['16'], struc['17'], struc)
self.assertTrue(is_chain_continuous(struc))
def test_build_backbone_atomnames(self):
"""Checks whether the P+O5' atoms are constructed."""
bb = BackboneBuilder(self.resi1,self.resi2, self.struc)
self.assertTrue(self.resi2['P'])
self.assertTrue(self.resi2["O5'"])
self.assertEqual(self.resi2["P"].fullname, ' P')
self.assertEqual(self.resi2["O5'"].fullname, " O5'")
self.assertEqual(self.resi2["P"].element, 'P')
self.assertEqual(self.resi2["O5'"].element, "O")
def test_bad_insertion(self):
"""Should fix at least some breaks in a disastrous case"""
struc = ModernaStructure('file', BAD_LOOP_INSERTION)
breaks_before = str(struc.get_sequence()).count('_')
self.assertEqual(breaks_before, 3)
prev = None
for resi in struc:
if prev:
bb = BackboneBuilder(prev, resi, struc)
prev = resi
breaks_after = str(struc.get_sequence()).count('_')
self.assertTrue(breaks_after < breaks_before)
def test_build_conserve_c2c3(self):
"""downstream C2' and C3' positions should not change"""
struc = ModernaStructure('file',FIXABLE_BACKBONE)
resi1 = struc['4']
resi2 = struc['5']
c3_before = resi2["C3'"].get_vector()
c2_before = resi2["C2'"].get_vector()
bb = BackboneBuilder(resi1, resi2, struc)
resi1 = struc['4']
resi2 = struc['5']
c3_after = resi2["C3'"].get_vector()
c2_after = resi2["C2'"].get_vector()
c2dist = c2_before-c2_after
c3dist = c3_before-c3_after
self.assertAlmostEqual(c2dist.norm(), 0.0, 3)
self.assertAlmostEqual(c3dist.norm(), 0.0, 3)
def fix_backbone_between_resis(self, resi1, resi2):
"""Attempts to fix the backbone between the two given residues."""
BackboneBuilder(resi1, resi2, self)
def test_build_po3_distance(self):
"""Checks whether the P-O3' distance is OK."""
bb = BackboneBuilder(self.resi1,self.resi2, self.struc)
expected,stddev = GeometryStandards.bonds["X:O3',X+1:P"][0]
self.assertTrue((self.resi2["P"]-self.resi1["O3'"]) - expected < stddev)
def test_build_o5p_distance(self):
"""Checks whether the O5'-P distance is OK."""
bb = BackboneBuilder(self.resi1,self.resi2, self.struc)
expected,stddev = GeometryStandards.bonds["X:P,X:O5'"][0]
self.assertTrue((self.resi2["O5'"]-self.resi2["P"]) - expected < stddev)
def test_build_op1op2(self):
"""Checks whether the OP1 and OP2 atoms are constructed."""
bb = BackboneBuilder(self.resi1,self.resi2, self.struc)
self.assertTrue(self.resi2.child_dict.get('OP1'))
self.assertTrue(self.resi2.child_dict.get("OP2"))
def test_build_backbone(self):
"""Checks whether the P+O5' atoms are constructed."""
bb = BackboneBuilder(self.resi1,self.resi2, self.struc)
self.assertTrue(self.resi2.child_dict.get('P'))
self.assertTrue(self.resi2.child_dict.get("O5'"))