def test_read_lgt_not_defined(self):
pdb = readwrite.Files('test.pdb')
with self.assertRaises(ValueError) as context:
pdb.read_lgt()
self.assertTrue(
"No lgtfile has been defined" in str(context.exception))
return
def test_read_pdb_flip(self):
self.path = os.path.dirname(os.path.abspath(__file__))
pdb = readwrite.Files(os.path.join(self.path, 'test.pdb'), flip=True)
pdb.read_pdb()
assert_equal(pdb.number_of_timesteps, 6)
assert_equal(pdb.times, [0., 10000., 20000., 30000., 40000., 50000.])
assert_equal(len(pdb.atoms), 6)
for i in range(0, len(pdb.atoms)):
assert_equal(len(pdb.atoms[i]), 3)
assert_equal(pdb.atoms[i][0].atom, 'C1')
assert_equal(pdb.atoms[i][1].atom, 'C2')
assert_equal(pdb.atoms[i][2].atom, 'C3')
for i in range(0, 2):
assert_equal(pdb.atoms[i * 3][0].zpos, 02.500)
assert_equal(pdb.atoms[i * 3][1].zpos, 01.500)
assert_equal(pdb.atoms[i * 3][2].zpos, 00.500)
assert_equal(pdb.atoms[i * 3 + 1][0].zpos, 00.500)
assert_equal(pdb.atoms[i * 3 + 1][1].zpos, 02.500)
assert_equal(pdb.atoms[i * 3 + 1][2].zpos, 01.500)
assert_equal(pdb.atoms[i * 3 + 2][0].zpos, 01.500)
assert_equal(pdb.atoms[i * 3 + 2][1].zpos, 00.500)
assert_equal(pdb.atoms[i * 3 + 2][2].zpos, 02.500)
assert_equal(pdb.cell, [[1.000, 1.000, 4.000], [2.000, 1.000, 4.000],
[3.000, 1.000, 4.000], [4.000, 1.000, 4.000],
[5.000, 1.000, 4.000], [6.000, 1.000, 4.000]])
return
def test_average_sld_profile(self):
self.path = os.path.dirname(os.path.abspath(__file__))
a = readwrite.Files(os.path.join(self.path, 'test.pdb'),
lgtfile=os.path.join(self.path, 'test.lgt'),
datfile=os.path.join(self.path, 'test3.dat'))
a.read_pdb()
a.read_lgt()
a.read_dat()
b = job.Job(a, 1., 0.)
b.set_times(times=[0., 20000., 10000.])
b.set_lgts()
c = sld.SLD(b)
c.get_sld_profile()
c.average_sld_profile()
assert_equal(len(c.av_sld_profile), 4)
assert_almost_equal(c.av_sld_profile[0].real, 0.)
assert_almost_equal(c.av_sld_profile[0].imag, 0.)
assert_almost_equal(c.av_sld_profile[1].real,
(1e-5 + (2e-5 / 2.) + (3e-5 / 3.)) / 3.)
assert_almost_equal(c.av_sld_profile[1].imag,
(0 + (1e-5 / 2.) + (2e-5 / 3.)) / 3.)
assert_almost_equal(c.av_sld_profile[2].real,
(2e-5 + (3e-5 / 2.) + (1e-5 / 3.)) / 3.)
assert_almost_equal(c.av_sld_profile[2].imag,
((1e-5) + (2e-5 / 2.) + (0 / 3.)) / 3.)
assert_almost_equal(c.av_sld_profile[3].real,
(3e-5 + (1e-5 / 2.) + (2e-5 / 3.)) / 3.)
assert_almost_equal(c.av_sld_profile[3].imag,
((2e-5) + (0 / 2.) + (1e-5 / 3.)) / 3.)
return
def test_set_lgts(self):
self.path = os.path.dirname(os.path.abspath(__file__))
a = readwrite.Files(os.path.join(self.path, 'test.pdb'),
lgtfile=os.path.join(self.path, 'test.lgt'))
a.read_pdb()
a.read_lgt()
b = job.Job(a, 1., 5.)
b.set_lgts()
assert_equal(b.new_file, False)
def test_files_standard(self):
pdb = readwrite.Files('test.pdb')
assert_equal(pdb.pdbfile, 'test.pdb')
assert_equal(pdb.lgtfile, None)
assert_equal(pdb.datfile, None)
assert_equal(pdb.resolution, 5.)
assert_equal(pdb.ierror, 5.)
assert_equal(pdb.flip, False)
return
def test_set_times(self):
self.path = os.path.dirname(os.path.abspath(__file__))
a = readwrite.Files(os.path.join(self.path, 'test.pdb'),
lgtfile=os.path.join(self.path, 'test.lgt'))
a.read_pdb()
a.read_lgt()
b = job.Job(a, 1., 5.)
b.set_times([0., 20000., 10000.])
assert_equal(len(b.times), 3)
assert_equal(b.times, [0., 10000., 20000.])
def test_set_run(self):
self.path = os.path.dirname(os.path.abspath(__file__))
a = readwrite.Files(os.path.join(self.path, 'test.pdb'),
lgtfile=os.path.join(self.path, 'test.lgt'),
datfile=os.path.join(self.path, 'test3.dat'))
a.read_pdb()
a.read_lgt()
a.read_dat()
b = job.Job(a, 1., 5.)
self.path = os.path.dirname(os.path.abspath(__file__))
a2 = readwrite.Files(os.path.join(self.path, 'test2.pdb'),
lgtfile=os.path.join(self.path, 'test.lgt'),
datfile=os.path.join(self.path, 'test3.dat'))
a2.read_pdb()
a2.read_lgt()
a2.read_dat()
b.set_run(files=a2, layer_thickness=2., cut_off_size=3.)
assert_equal(b.layer_thickness, 2.)
assert_equal(b.cut_off_size, 3.)
assert_equal(b.times, [0., 10000., 20000., 30000., 40000.])
def test_get_sld_profile(self):
self.path = os.path.dirname(os.path.abspath(__file__))
a = readwrite.Files(os.path.join(self.path, 'test.pdb'),
lgtfile=os.path.join(self.path, 'test.lgt'),
datfile=os.path.join(self.path, 'test3.dat'))
a.read_pdb()
a.read_lgt()
a.read_dat()
b = job.Job(a, 1., 0.)
b.set_times(times=[0., 20000., 10000.])
b.set_lgts()
c = sld.SLD(b)
c.get_sld_profile()
assert_equal(len(c.sld_profile), 3)
for i in range(0, len(c.sld_profile)):
assert_equal(len(c.sld_profile[i]), 4)
assert_almost_equal(c.sld_profile[0][0].thick, 1.)
assert_almost_equal(c.sld_profile[0][0].real, 0.)
assert_almost_equal(c.sld_profile[0][0].imag, 0.)
assert_almost_equal(c.sld_profile[0][1].thick, 1.)
assert_almost_equal(c.sld_profile[0][1].real, 1e-5)
assert_almost_equal(c.sld_profile[0][1].imag, 0.)
assert_almost_equal(c.sld_profile[0][2].thick, 1.)
assert_almost_equal(c.sld_profile[0][2].real, 2e-5)
assert_almost_equal(c.sld_profile[0][2].imag, 1e-5)
assert_almost_equal(c.sld_profile[0][3].thick, 1.)
assert_almost_equal(c.sld_profile[0][3].real, 3e-5)
assert_almost_equal(c.sld_profile[0][3].imag, 2e-5)
assert_almost_equal(c.sld_profile[1][0].thick, 1.)
assert_almost_equal(c.sld_profile[1][0].real, 0. / 2.)
assert_almost_equal(c.sld_profile[1][0].imag, 0. / 2.)
assert_almost_equal(c.sld_profile[1][1].thick, 1.)
assert_almost_equal(c.sld_profile[1][1].real, 2e-5 / 2.)
assert_almost_equal(c.sld_profile[1][1].imag, 1e-5 / 2.)
assert_almost_equal(c.sld_profile[1][2].thick, 1.)
assert_almost_equal(c.sld_profile[1][2].real, 3e-5 / 2.)
assert_almost_equal(c.sld_profile[1][2].imag, 2e-5 / 2.)
assert_almost_equal(c.sld_profile[1][3].thick, 1.)
assert_almost_equal(c.sld_profile[1][3].real, 1e-5 / 2.)
assert_almost_equal(c.sld_profile[1][3].imag, 0 / 2.)
assert_almost_equal(c.sld_profile[2][0].thick, 1.)
assert_almost_equal(c.sld_profile[2][0].real, 0. / 3.)
assert_almost_equal(c.sld_profile[2][0].imag, 0. / 3.)
assert_almost_equal(c.sld_profile[2][1].thick, 1.)
assert_almost_equal(c.sld_profile[2][1].real, 3e-5 / 3.)
assert_almost_equal(c.sld_profile[2][1].imag, 2e-5 / 3.)
assert_almost_equal(c.sld_profile[2][2].thick, 1.)
assert_almost_equal(c.sld_profile[2][2].real, 1e-5 / 3.)
assert_almost_equal(c.sld_profile[2][2].imag, 0 / 3.)
assert_almost_equal(c.sld_profile[2][3].thick, 1.)
assert_almost_equal(c.sld_profile[2][3].real, 2e-5 / 3.)
assert_almost_equal(c.sld_profile[2][3].imag, 1e-5 / 3.)
return
def test_get_qs(self):
pdb = readwrite.Files('test.pdb')
pdb.get_qs(0.0005, 0.0020, 4)
assert_equal(len(pdb.expdata), 4)
assert_equal(pdb.expdata[0].q, 0.0005)
assert_almost_equal(pdb.expdata[0].dq, 0.0005 * 0.05)
assert_equal(pdb.expdata[1].q, 0.0010)
assert_almost_equal(pdb.expdata[1].dq, 0.0010 * 0.05)
assert_equal(pdb.expdata[2].q, 0.0015)
assert_almost_equal(pdb.expdata[2].dq, 0.0015 * 0.05)
assert_equal(pdb.expdata[3].q, 0.0020)
assert_almost_equal(pdb.expdata[3].dq, 0.0020 * 0.05)
return
def test_read_dat_not_defined(self):
pdb = readwrite.Files('test.pdb')
assert_equal(pdb.expdata, [])
captured_output = StringIO()
sys.stdout = captured_output
pdb.read_dat()
sys.stdout = sys.__stdout__
assert_equal(
captured_output.getvalue(),
'No DAT file has been given, therefore no comparison will be conducted, please use the get_qs '
'function. Alternatively the DAT file can be added using the setFile function.\n'
)
return
def test_files_variation(self):
pdb = readwrite.Files('test1.pdb',
lgtfile='test1.lgt',
datfile='test1.dat',
resolution=1.,
ierror=1.,
flip=True)
assert_equal(pdb.pdbfile, 'test1.pdb')
assert_equal(pdb.lgtfile, 'test1.lgt')
assert_equal(pdb.datfile, 'test1.dat')
assert_equal(pdb.resolution, 1.)
assert_equal(pdb.ierror, 1.)
assert_equal(pdb.flip, True)
return
def test_read_lgt(self):
self.path = os.path.dirname(os.path.abspath(__file__))
pdb = readwrite.Files('test.pdb',
lgtfile=os.path.join(self.path, 'test.lgt'))
pdb.read_lgt()
assert_equal(pdb.scat_lens[0].atom, 'C1')
assert_almost_equal(pdb.scat_lens[0].real, 1e-5)
assert_almost_equal(pdb.scat_lens[0].imag, 0)
assert_equal(pdb.scat_lens[1].atom, 'C2')
assert_almost_equal(pdb.scat_lens[1].real, 2e-5)
assert_almost_equal(pdb.scat_lens[1].imag, 1e-5)
assert_equal(pdb.scat_lens[2].atom, 'C3')
assert_almost_equal(pdb.scat_lens[2].real, 3e-5)
assert_almost_equal(pdb.scat_lens[2].imag, 2e-5)
return
def test_read_dat4(self):
self.path = os.path.dirname(os.path.abspath(__file__))
pdb = readwrite.Files('test.pdb',
datfile=os.path.join(self.path, 'test4.dat'))
pdb.read_dat()
assert_almost_equal(pdb.expdata[0].q, 0.051793)
assert_almost_equal(pdb.expdata[0].i, 0.00034985)
assert_almost_equal(pdb.expdata[0].di, 5.0354e-6)
assert_almost_equal(pdb.expdata[0].dq, 0.0003)
assert_almost_equal(pdb.expdata[1].q, 0.13742)
assert_almost_equal(pdb.expdata[1].i, 1.4924e-5)
assert_almost_equal(pdb.expdata[1].di, 3.7729e-7)
assert_almost_equal(pdb.expdata[1].dq, 0.0007)
assert_almost_equal(pdb.expdata[2].q, 0.38285)
assert_almost_equal(pdb.expdata[2].i, 1.215e-6)
assert_almost_equal(pdb.expdata[2].di, 3.478e-7)
assert_almost_equal(pdb.expdata[2].dq, 0.0019)
return
def test_read_dat2(self):
self.path = os.path.dirname(os.path.abspath(__file__))
pdb = readwrite.Files('test.pdb',
datfile=os.path.join(self.path, 'test2.dat'))
pdb.read_dat()
assert_almost_equal(pdb.expdata[0].q, 0.051793)
assert_almost_equal(pdb.expdata[0].i, 0.00034985)
assert_almost_equal(pdb.expdata[0].di, 0.00034985 * 0.05)
assert_almost_equal(pdb.expdata[0].dq, 0.051793 * 0.05)
assert_almost_equal(pdb.expdata[1].q, 0.13742)
assert_almost_equal(pdb.expdata[1].i, 1.4924e-5)
assert_almost_equal(pdb.expdata[1].di, 1.4924e-5 * 0.05)
assert_almost_equal(pdb.expdata[1].dq, 0.13742 * 0.05)
assert_almost_equal(pdb.expdata[2].q, 0.38285)
assert_almost_equal(pdb.expdata[2].i, 1.215e-6)
assert_almost_equal(pdb.expdata[2].di, 1.215e-6 * 0.05)
assert_almost_equal(pdb.expdata[2].dq, 0.38285 * 0.05)
return
def test_sld(self):
self.path = os.path.dirname(os.path.abspath(__file__))
a = readwrite.Files(os.path.join(self.path, 'test.pdb'),
lgtfile=os.path.join(self.path, 'test.lgt'),
datfile=os.path.join(self.path, 'test3.dat'))
a.read_pdb()
a.read_lgt()
a.read_dat()
b = job.Job(a, 1., 5.)
b.set_times(times=[0., 20000., 10000.])
b.set_lgts()
c = sld.SLD(b)
assert_equal(len(c.assigned_job.files.times), 6)
assert_equal(c.assigned_job.files.times,
[0, 10000., 20000., 30000., 40000., 50000.])
assert_equal(len(c.assigned_job.times), 3)
assert_equal(c.assigned_job.times, [0, 10000., 20000.])
assert_equal(c.assigned_job.layer_thickness, 1.)
assert_equal(c.assigned_job.cut_off_size, 5.)
return
def test_set_pdbfile(self):
pdb = readwrite.Files('test.pdb')
assert_equal(pdb.pdbfile, 'test.pdb')
pdb.set_file(pdbfile='test1.pdb')
assert_equal(pdb.pdbfile, 'test1.pdb')
return
def test_set_datfile(self):
pdb = readwrite.Files('test.pdb')
assert_equal(pdb.datfile, None)
pdb.set_file(datfile='test1.dat')
assert_equal(pdb.datfile, 'test1.dat')
return
