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_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_chains(self):
"""compares contacts diff chains"""
self.input_file = os.path.join('data', '1A1X.pdb') # one chain
self.input_structure = PDBParser(open(self.input_file))
res = contact.contacts_xtra(self.input_structure)
self.assertTrue(res == {})
self.input_file = os.path.join('data', '2E12.pdb') # one chain
self.input_structure = PDBParser(open(self.input_file))
res = contact.contacts_xtra(self.input_structure)
self.assertTrue(res)
self.assertFloatEqual(\
res[('2E12', 0, 'B', ('THR', 17, ' '), ('OG1', ' '))]['CONTACTS']\
[('2E12', 0, 'A', ('ALA', 16, ' '), ('CB', ' '))][0], 5.7914192561064004)
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_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_PDBParser(self):
"""tests the UI parsing function.
"""
fh = open('data/2E12.pdb')
structure = PDBParser(fh, 'JUNK')
assert type(structure) is Structure
assert len(structure) == 1
assert (0,) in structure
assert structure.header['space_group'] == 'P 21 21 21'
assert structure.header['experiment_type'] == 'X-RAY DIFFRACTION'
assert structure.header['r_free'] == '0.280'
assert structure.header['dbref_acc'] == 'Q8P4R5'
assert structure.header['cryst1'] == '49.942 51.699 82.120 90.00 90.00 90.00'
assert structure.header['matthews'] == '2.29'
model = structure[(0,)]
assert len(model) == 2
assert structure.raw_header
assert structure.raw_trailer
assert structure.header
assert structure.trailer == {}
assert structure.getId() == ('JUNK', )
def test_symmetry(self):
"""compares contacts diff symmetry mates"""
self.input_file = os.path.join('data', '2E12.pdb') # one chain
self.input_structure = PDBParser(open(self.input_file))
res = contact.contacts_xtra(self.input_structure, \
symmetry_mode='uc',
contact_mode='diff_sym')
self.assertTrue(res)
self.assertFloatEqual(\
res[('2E12', 0, 'B', ('GLU', 77, ' '), ('OE2', ' '))]['CONTACTS']\
[('2E12', 0, 'B', ('GLU', 57, ' '), ('OE2', ' '))][0], \
5.2156557833123873)
def test_PDBParser(self):
"""tests the UI parsing function.
"""
fh = open('data/2E12.pdb')
structure = PDBParser(fh, 'JUNK')
assert type(structure) is Structure
assert len(structure) == 1
assert (0,) in structure
assert structure.header['space_group'] == 'P 21 21 21'
assert structure.header['experiment_type'] == 'X-RAY DIFFRACTION'
assert structure.header['r_free'] == '0.280'
assert structure.header['dbref_acc'] == 'Q8P4R5'
assert structure.header['cryst1'] == '49.942 51.699 82.120 90.00 90.00 90.00'
assert structure.header['matthews'] == '2.29'
model = structure[(0,)]
assert len(model) == 2
assert structure.raw_header
assert structure.raw_trailer
assert structure.header
assert structure.trailer == {}
assert structure.getId() == ('JUNK', )
def test_PDBParser(self):
"""tests the UI parsing function.
"""
fh = open("data/2E12.pdb")
structure = PDBParser(fh, "JUNK")
assert type(structure) is Structure
assert len(structure) == 1
assert (0,) in structure
assert structure.header["space_group"] == "P 21 21 21"
assert structure.header["experiment_type"] == "X-RAY DIFFRACTION"
assert structure.header["r_free"] == "0.280"
assert structure.header["dbref_acc"] == "Q8P4R5"
assert structure.header["cryst1"] == "49.942 51.699 82.120 90.00 90.00 90.00"
assert structure.header["matthews"] == "2.29"
model = structure[(0,)]
assert len(model) == 2
assert structure.raw_header
assert structure.raw_trailer
assert structure.header
assert structure.trailer == {}
assert structure.getId() == ("JUNK",)
def test_1expand_crystal(self):
"""tests the expansion of a unit-cell to a crystal"""
fh = open(fn, 'r')
input_structure = PDBParser(fh)
self.assertTrue(input_structure.values(), 4) # 4 models
sh = expand_crystal(input_structure)
self.assertTrue(len(sh) == 27)
fd, fn2 = tempfile.mkstemp('.pdb')
os.close(fd)
fh = open(fn2, 'w')
a1 = einput(input_structure, 'A')
a2 = einput(sh.values()[3], 'A')
k = a1.values()[99].getFull_id()
name = sh.values()[3].name
a1c = a1[k].coords
a2c = a2[(name,) + k[1:]].coords
self.assertTrue(len(a1), len(a2))
self.assertRaises(AssertionError, self.assertFloatEqual, a1c, a2c)
PDBWriter(fh, sh)
fh.close()
os.unlink(fn)
os.unlink(fn2)
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.)
class asaTest(TestCase):
"""Tests for surface calculations."""
def setUp(self):
self.arr = np.random.random(3000).reshape((1000, 3))
self.point = np.random.random(3)
self.center = np.array([0.5, 0.5, 0.5])
def test_0import(self):
# sort by name
"""tests if can import _asa cython extension."""
global _asa
from cogent.struct import _asa
assert 'asa_loop' in dir(_asa)
def test_1import(self):
# sort by name
"""tests if can import asa."""
global asa
from cogent.struct import asa
def test_asa_loop(self):
"""tests if inner asa_loop (cython) performs correctly"""
self.lcoords = np.array([[-4., 0, 0], [0, 0, 0], [4, 0, 0], [10, 0, 0]])
self.qcoords = np.array([[0., 0, 0], [4., 0, 0]])
self.lradii = np.array([2., 3.])
self.qradii = np.array([3., 2.])
#spoints, np.ndarray[DTYPE_t, ndim =1] box,\
# DTYPE_t probe, unsigned int bucket_size, MAXSYM =200000)
self.spoints = np.array([[1., 0., 0.], [-1., 0., 0.], [0., 1., 0.], \
[0., -1., 0.], [0., 0., 1.], [0., 0., -1.]])
output = _asa.asa_loop(self.qcoords, self.lcoords, self.qradii, \
self.lradii, self.spoints, \
np.array([-100., -100., -100., 100., 100., 100.]), 1., 10)
self.assertFloatEqual(output, np.array([ 75.39822369, 41.88790205]))
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)
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_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_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__prepare_entities(self):
self.input_structure = PDBParser(dummy_water)
self.assertRaises(ValueError, asa._prepare_entities, self.input_structure)
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__prepare_entities(self):
self.input_structure = PDBParser(dummy_water)
self.assertRaises(ValueError, asa._prepare_entities, self.input_structure)
def setUp(self):
input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(input_file))
stride_app = Stride()
res = stride_app(self.input_structure)
self.lines = res['StdOut'].readlines()
class ManipulationTest(TestCase):
"""tests manipulationg entities"""
def setUp(self):
self.input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(self.input_file))
def test_clean_ical(self):
"""tests the clean ical function which cleans structures."""
chainB = self.input_structure.table['C'][('2E12', 0, 'B')]
leu25 = self.input_structure.table['R'][('2E12', 0, 'B', \
('LEU', 25, ' '))]
leu25icA = copy(leu25)
self.assertTrue(leu25icA.parent is None)
self.assertTrue(leu25icA is not leu25)
self.assertTrue(leu25icA[(('N', ' '),)] is not leu25[(('N', ' '),)])
leu25icA.setIc('A')
self.assertEquals(leu25icA.getId(), (('LEU', 25, 'A'),))
chainB.addChild(leu25icA)
self.assertFalse(chainB[(('LEU', 25, 'A'),)] is \
chainB[(('LEU', 25, ' '),)])
self.assertEquals(clean_ical(self.input_structure), \
([], [('2E12', 0, 'B', ('LEU', 25, 'A'))]))
clean_ical(self.input_structure, pretend=False)
self.assertTrue(chainB[(('LEU', 25, 'A'),)] is leu25icA)
self.assertFalse((('LEU', 25, 'A'),) in chainB.keys())
self.assertFalse((('LEU', 25, 'A'),) in chainB)
self.assertTrue((('LEU', 25, 'A'),) in chainB.keys(unmask=True))
self.input_structure.setUnmasked(force=True)
self.assertEquals(clean_ical(self.input_structure), \
([], [('2E12', 0, 'B', ('LEU', 25, 'A'))]))
clean_ical(self.input_structure, pretend=False, mask=False)
self.assertFalse((('LEU', 25, 'A'),) in chainB.keys())
self.assertFalse((('LEU', 25, 'A'),) in chainB)
self.assertFalse((('LEU', 25, 'A'),) in chainB.keys(unmask=True))
def test_0expand_symmetry(self):
"""tests the expansion of a asu to a unit-cell."""
global fn
mh = expand_symmetry(self.input_structure[(0,)])
fd, fn = tempfile.mkstemp('.pdb')
os.close(fd)
fh = open(fn, 'w')
PDBWriter(fh, mh, self.input_structure.raw_header)
fh.close()
def test_1expand_crystal(self):
"""tests the expansion of a unit-cell to a crystal"""
fh = open(fn, 'r')
input_structure = PDBParser(fh)
self.assertTrue(input_structure.values(), 4) # 4 models
sh = expand_crystal(input_structure)
self.assertTrue(len(sh) == 27)
fd, fn2 = tempfile.mkstemp('.pdb')
os.close(fd)
fh = open(fn2, 'w')
a1 = einput(input_structure, 'A')
a2 = einput(sh.values()[3], 'A')
k = a1.values()[99].getFull_id()
name = sh.values()[3].name
a1c = a1[k].coords
a2c = a2[(name,) + k[1:]].coords
self.assertTrue(len(a1), len(a2))
self.assertRaises(AssertionError, self.assertFloatEqual, a1c, a2c)
PDBWriter(fh, sh)
fh.close()
os.unlink(fn)
os.unlink(fn2)
def test__prepare_entities(self):
self.input_structure = PDBParser(dummy_water)
self.assertRaises(ValueError, asa._prepare_entities,
self.input_structure)
def setUp(self):
self.input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(self.input_file))
class asaTest(TestCase):
"""Tests for surface calculations."""
def setUp(self):
self.arr = np.random.random(3000).reshape((1000, 3))
self.point = np.random.random(3)
self.center = np.array([0.5, 0.5, 0.5])
def test_0import(self):
# sort by name
"""tests if can import _asa cython extension."""
global _asa
from cogent.struct import _asa
assert 'asa_loop' in dir(_asa)
def test_1import(self):
# sort by name
"""tests if can import asa."""
global asa
from cogent.struct import asa
def test_asa_loop(self):
"""tests if inner asa_loop (cython) performs correctly"""
self.lcoords = np.array([[-4., 0, 0], [0, 0, 0], [4, 0, 0], [10, 0,
0]])
self.qcoords = np.array([[0., 0, 0], [4., 0, 0]])
self.lradii = np.array([2., 3.])
self.qradii = np.array([3., 2.])
#spoints, np.ndarray[DTYPE_t, ndim =1] box,\
# DTYPE_t probe, unsigned int bucket_size, MAXSYM =200000)
self.spoints = np.array([[1., 0., 0.], [-1., 0., 0.], [0., 1., 0.], \
[0., -1., 0.], [0., 0., 1.], [0., 0., -1.]])
output = _asa.asa_loop(self.qcoords, self.lcoords, self.qradii, \
self.lradii, self.spoints, \
np.array([-100., -100., -100., 100., 100., 100.]), 1., 10)
self.assertFloatEqual(output, np.array([75.39822369, 41.88790205]))
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)
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_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_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__prepare_entities(self):
self.input_structure = PDBParser(dummy_water)
self.assertRaises(ValueError, asa._prepare_entities,
self.input_structure)
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])
#!/usr/bin/env python
# taken from http://pycogent.sourceforge.net/
from cogent.parse.pdb import PDBParser
from cogent.format.pdb import PDBWriter
import tempfile, os
pdb_file = open('data/4TSV.pdb')
new_structure = PDBParser(pdb_file)
open_handle, file_name = tempfile.mkstemp()
os.close(open_handle)
new_pdb_file = open(file_name, 'wb')
PDBWriter(new_pdb_file, new_structure)
print structure.id
print structure.getId()
print structure.getFull_id()
print structure.header.keys()
print structure.header['id']
print structure.header['expdta']
structure.items()
structure.values()
structure.keys()
first_model = structure.values()[0]
first_model_id = first_model.getId()
structure.getChildren()
children_list = structure.getChildren([first_model_id])
some_model = structure.values()[0]
some_chain = some_model.values()[0]
for residue in some_chain.values():
residue.setName('UNK')
print sorted(structure.table.keys())
print structure.table['C']
