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_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_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_job(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.)
assert_equal(b.layer_thickness, 1.)
assert_equal(b.cut_off_size, 5.)
assert_equal(b.times, [0., 10000., 20000., 30000., 40000., 50000.])
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