def test_uc(self):
"""compares asa within unit cell."""
self.input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(self.input_file))
asa.asa_xtra(self.input_structure, symmetry_mode='uc', xtra_key='ASA_UC')
asa.asa_xtra(self.input_structure)
self.input_structure.propagateData(sum, 'A', 'ASA', xtra=True)
self.input_structure.propagateData(sum, 'A', 'ASA_UC', xtra=True)
residues = einput(self.input_structure, 'R')
x = residues[('2E12', 0, 'B', ('GLU', 77, ' '))].xtra.values()
self.assertTrue(x[0] != x[1])
def test_uc2(self):
self.input_file = os.path.join('data', '1LJO.pdb')
self.input_structure = PDBParser(open(self.input_file))
asa.asa_xtra(self.input_structure, symmetry_mode='uc', xtra_key='ASA_XTAL')
asa.asa_xtra(self.input_structure)
self.input_structure.propagateData(sum, 'A', 'ASA', xtra=True)
self.input_structure.propagateData(sum, 'A', 'ASA_XTAL', xtra=True)
residues = einput(self.input_structure, 'R')
r1 = residues[('1LJO', 0, 'A', ('ARG', 65, ' '))]
r2 = residues[('1LJO', 0, 'A', ('ASN', 46, ' '))]
self.assertFloatEqual(r1.xtra.values(),
[128.94081270529105, 22.807700865674093])
self.assertFloatEqual(r2.xtra.values(),
[115.35738419425566, 115.35738419425566])
def _test_bio(self):
"""compares asa within a bio unit."""
self.input_file = os.path.join('data', '1A1X.pdb')
self.input_structure = PDBParser(open(self.input_file))
asa.asa_xtra(self.input_structure, symmetry_mode='bio', xtra_key='ASA_BIO')
asa.asa_xtra(self.input_structure)
self.input_structure.propagateData(sum, 'A', 'ASA', xtra=True)
self.input_structure.propagateData(sum, 'A', 'ASA_BIO', xtra=True)
residues = einput(self.input_structure, 'R')
r1 = residues[('1A1X', 0, 'A', ('GLU', 37, ' '))]
r2 = residues[('1A1X', 0, 'A', ('TRP', 15, ' '))]
self.assertFloatEqual(r1.xtra.values(), \
[20.583191467544726, 78.996394472066541])
self.assertFloatEqual(r2.xtra.values(), \
[136.41436710386989, 136.41436710386989])
def test_compare(self):
"""compares internal asa to stride."""
self.input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(self.input_file))
try:
asa.asa_xtra(self.input_structure, mode='stride')
except ApplicationNotFoundError:
return
asa.asa_xtra(self.input_structure)
self.input_structure.propagateData(sum, 'A', 'ASA', xtra=True)
residues = einput(self.input_structure, 'R')
asa1 = []
asa2 = []
for residue in residues.selectChildren('H_HOH', 'ne', 'name').values():
asa1.append(residue.xtra['ASA'])
asa2.append(residue.xtra['STRIDE_ASA'])
self.assertAlmostEqual(correlation(asa1, asa2)[1], 0.)
def test_compare(self):
"""compares internal asa to stride."""
self.input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(self.input_file))
try:
asa.asa_xtra(self.input_structure, mode='stride')
except ApplicationNotFoundError:
return
asa.asa_xtra(self.input_structure)
self.input_structure.propagateData(sum, 'A', 'ASA', xtra=True)
residues = einput(self.input_structure, 'R')
asa1 = []
asa2 = []
for residue in residues.selectChildren('H_HOH', 'ne', 'name').values():
asa1.append(residue.xtra['ASA'])
asa2.append(residue.xtra['STRIDE_ASA'])
self.assertAlmostEqual(correlation(asa1, asa2)[1], 0.)
def test_crystal(self):
"""compares asa within unit cell."""
self.input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(self.input_file))
asa.asa_xtra(self.input_structure, symmetry_mode='uc', crystal_mode=2, xtra_key='ASA_XTAL')
asa.asa_xtra(self.input_structure)
self.input_structure.propagateData(sum, 'A', 'ASA', xtra=True)
self.input_structure.propagateData(sum, 'A', 'ASA_XTAL', xtra=True)
residues = einput(self.input_structure, 'R')
r1 = residues[('2E12', 0, 'A', ('ALA', 42, ' '))]
r2 = residues[('2E12', 0, 'A', ('VAL', 8, ' '))]
r3 = residues[('2E12', 0, 'A', ('LEU', 25, ' '))]
self.assertFloatEqual(r1.xtra.values(), \
[32.041070749038823, 32.041070749038823])
self.assertFloatEqual(r3.xtra.values(), \
[0., 0.])
self.assertFloatEqual(r2.xtra.values(), \
[28.873559956056916, 0.0])
def test_asa_xtra_stride(self):
"""test asa via stride"""
self.input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(self.input_file))
try:
result = asa.asa_xtra(self.input_structure, 'stride')
except ApplicationNotFoundError:
return
self.assertAlmostEqual(self.input_structure[(0,)][('B',)]\
[(('LEU', 35, ' '),)].xtra['STRIDE_ASA'], 17.20)
def test_asa_xtra(self):
"""test internal asa"""
self.input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(self.input_file))
self.assertRaises(ValueError, asa.asa_xtra, self.input_structure, mode='a')
result = asa.asa_xtra(self.input_structure)
a = einput(self.input_structure, 'A')
for i in range(len(result)):
self.assertEquals(result.values()[i]['ASA'], a[result.keys()[i]].xtra['ASA'])
r = einput(self.input_structure, 'R')
for water in r.selectChildren('H_HOH', 'eq', 'name').values():
self.assertFalse('ASA' in water.xtra)
for residue in r.selectChildren('H_HOH', 'ne', 'name').values():
for a in residue:
self.assertTrue('ASA' in a.xtra)
result = asa.asa_xtra(self.input_structure, xtra_key='SASA')
for residue in r.selectChildren('H_HOH', 'ne', 'name').values():
for a in residue:
a.xtra['ASA'] == a.xtra['SASA']
def test_asa_xtra_stride(self):
"""test asa via stride"""
self.input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(self.input_file))
try:
result = asa.asa_xtra(self.input_structure, 'stride')
except ApplicationNotFoundError:
return
self.assertAlmostEqual(self.input_structure[(0,)][('B',)]\
[(('LEU', 35, ' '),)].xtra['STRIDE_ASA'], 17.20)
