def test_TiO2_rutile_cif(self):
'''Check loading of TiO2_rutile.cif and its ADP data
'''
c = loadcifdata('TiO2_rutile.cif')
self.assertTrue(c is not None)
s = c.GetScatt(0)
name = s.GetName()
sp = c.GetScatteringPower(name)
self.assertEqual(name, "Ti")
self.assertTrue(sp.IsIsotropic())
utob = 8 * pi**2
self.assertAlmostEqual(utob * 0.00532, sp.Biso, 5)
return
def test_TiO2_rutile_cif(self):
'''Check loading of TiO2_rutile.cif and its ADP data
'''
c = loadcifdata('TiO2_rutile.cif')
self.assertTrue(c is not None)
s = c.GetScatt(0)
name = s.GetName()
sp = c.GetScatteringPower(name)
self.assertEqual(name, "Ti")
self.assertTrue(sp.IsIsotropic())
utob = 8 * pi**2
self.assertAlmostEqual(utob * 0.00532, sp.Biso, 5)
return
def test_caffeine_cif(self):
'''Check loading of caffeine.cif and the data inside.
'''
c = loadcifdata('caffeine.cif')
self.assertTrue(c is not None)
self.assertEqual(24, c.GetNbScatterer())
self.assertAlmostEqual(14.9372, c.a, 6)
self.assertAlmostEqual(14.9372, c.b, 6)
self.assertAlmostEqual(6.8980, c.c, 6)
self.assertAlmostEqual(pi/2, c.alpha, 6)
self.assertAlmostEqual(pi/2, c.beta, 6)
self.assertAlmostEqual(2*pi/3, c.gamma, 6)
cifdata = """
C5 -0.06613 -0.06314 0.09562 0.00000 Uiso 1.00000 C
C4 0.02779 -0.05534 0.10000 0.00000 Uiso 1.00000 C
N3 0.11676 0.04116 0.08226 0.00000 Uiso 1.00000 N
C2 0.10866 0.12960 0.06000 0.00000 Uiso 1.00000 C
O11 0.18634 0.21385 0.04451 0.00000 Uiso 1.00000 O
N1 0.01159 0.12154 0.05547 0.00000 Uiso 1.00000 N
C6 -0.07738 0.02504 0.07321 0.00000 Uiso 1.00000 C
O13 -0.16212 0.01800 0.06926 0.00000 Uiso 1.00000 O
N7 -0.13793 -0.16353 0.11547 0.00000 Uiso 1.00000 N
N9 0.01389 -0.15092 0.12255 0.00000 Uiso 1.00000 N
C8 -0.08863 -0.21778 0.13210 0.00000 Uiso 1.00000 C
C14 -0.25110 -0.20663 0.11847 0.00000 Uiso 1.00000 C
C12 0.21968 0.04971 0.08706 0.00000 Uiso 1.00000 C
C10 0.00300 0.21530 0.03186 0.00000 Uiso 1.00000 C
H8 -0.12146 -0.29285 0.14834 0.00000 Uiso 1.00000 H
H14a -0.27317 -0.19028 -0.00382 0.00000 Uiso 1.00000 H
H14b -0.28567 -0.28182 0.13462 0.00000 Uiso 1.00000 H
H14c -0.26951 -0.17639 0.22660 0.00000 Uiso 1.00000 H
H12a 0.22513 0.00926 -0.01943 0.00000 Uiso 1.00000 H
H12b 0.27338 0.12237 0.07281 0.00000 Uiso 1.00000 H
H12c 0.22878 0.02315 0.21098 0.00000 Uiso 1.00000 H
H10a 0.03488 0.24909 -0.09109 0.00000 Uiso 1.00000 H
H10b -0.07008 0.19602 0.03170 0.00000 Uiso 1.00000 H
H10c 0.03791 0.26293 0.13930 0.00000 Uiso 1.00000 H
"""
lines = filter(None,
(line.strip() for line in cifdata.split('\n')))
for i, line in enumerate(lines):
name, x, y, z, U, junk, occ, element = line.split()
s = c.GetScatt(i)
self.assertEqual(name, s.GetName())
self.assertAlmostEqual(float(x), s.X, 6)
self.assertAlmostEqual(float(y), s.Y, 6)
self.assertAlmostEqual(float(z), s.Z, 6)
self.assertAlmostEqual(float(occ), s.Occupancy, 6)
return
def test_caffeine_cif(self):
'''Check loading of caffeine.cif and the data inside.
'''
c = loadcifdata('caffeine.cif')
self.assertTrue(c is not None)
self.assertEqual(24, c.GetNbScatterer())
self.assertAlmostEqual(14.9372, c.a, 6)
self.assertAlmostEqual(14.9372, c.b, 6)
self.assertAlmostEqual(6.8980, c.c, 6)
self.assertAlmostEqual(pi / 2, c.alpha, 6)
self.assertAlmostEqual(pi / 2, c.beta, 6)
self.assertAlmostEqual(2 * pi / 3, c.gamma, 6)
cifdata = """
C5 -0.06613 -0.06314 0.09562 0.00000 Uiso 1.00000 C
C4 0.02779 -0.05534 0.10000 0.00000 Uiso 1.00000 C
N3 0.11676 0.04116 0.08226 0.00000 Uiso 1.00000 N
C2 0.10866 0.12960 0.06000 0.00000 Uiso 1.00000 C
O11 0.18634 0.21385 0.04451 0.00000 Uiso 1.00000 O
N1 0.01159 0.12154 0.05547 0.00000 Uiso 1.00000 N
C6 -0.07738 0.02504 0.07321 0.00000 Uiso 1.00000 C
O13 -0.16212 0.01800 0.06926 0.00000 Uiso 1.00000 O
N7 -0.13793 -0.16353 0.11547 0.00000 Uiso 1.00000 N
N9 0.01389 -0.15092 0.12255 0.00000 Uiso 1.00000 N
C8 -0.08863 -0.21778 0.13210 0.00000 Uiso 1.00000 C
C14 -0.25110 -0.20663 0.11847 0.00000 Uiso 1.00000 C
C12 0.21968 0.04971 0.08706 0.00000 Uiso 1.00000 C
C10 0.00300 0.21530 0.03186 0.00000 Uiso 1.00000 C
H8 -0.12146 -0.29285 0.14834 0.00000 Uiso 1.00000 H
H14a -0.27317 -0.19028 -0.00382 0.00000 Uiso 1.00000 H
H14b -0.28567 -0.28182 0.13462 0.00000 Uiso 1.00000 H
H14c -0.26951 -0.17639 0.22660 0.00000 Uiso 1.00000 H
H12a 0.22513 0.00926 -0.01943 0.00000 Uiso 1.00000 H
H12b 0.27338 0.12237 0.07281 0.00000 Uiso 1.00000 H
H12c 0.22878 0.02315 0.21098 0.00000 Uiso 1.00000 H
H10a 0.03488 0.24909 -0.09109 0.00000 Uiso 1.00000 H
H10b -0.07008 0.19602 0.03170 0.00000 Uiso 1.00000 H
H10c 0.03791 0.26293 0.13930 0.00000 Uiso 1.00000 H
"""
lines = filter(None, (line.strip() for line in cifdata.split('\n')))
for i, line in enumerate(lines):
name, x, y, z, U, junk, occ, element = line.split()
s = c.GetScatt(i)
self.assertEqual(name, s.GetName())
self.assertAlmostEqual(float(x), s.X, 6)
self.assertAlmostEqual(float(y), s.Y, 6)
self.assertAlmostEqual(float(z), s.Z, 6)
self.assertAlmostEqual(float(occ), s.Occupancy, 6)
return
def test_caffeine(self):
"""Check molecule conversion for caffeine.
"""
c = loadcifdata('caffeine.cif')
xyz0 = [(sc.X, sc.Y, sc.Z) for sc in c.GetScatteringComponentList()]
self.assertEqual(24, c.GetNbScatterer())
putAtomsInMolecule(c, name='espresso')
self.assertEqual(1, c.GetNbScatterer())
mol = c.GetScatterer(0)
self.assertEqual('espresso', mol.GetName())
self.assertEqual(24, mol.GetNbAtoms())
xyz1 = [(sc.X, sc.Y, sc.Z) for sc in c.GetScatteringComponentList()]
uc0 = numpy.array(xyz0) - numpy.floor(xyz0)
uc1 = numpy.array(xyz1) - numpy.floor(xyz1)
self.assertTrue(numpy.allclose(uc0, uc1))
return
def test_caffeine(self):
"""Check molecule conversion for caffeine.
"""
c = loadcifdata('caffeine.cif')
xyz0 = [(sc.X, sc.Y, sc.Z) for sc in c.GetScatteringComponentList()]
self.assertEqual(24, c.GetNbScatterer())
putAtomsInMolecule(c, name='espresso')
self.assertEqual(1, c.GetNbScatterer())
mol = c.GetScatterer(0)
self.assertEqual('espresso', mol.GetName())
self.assertEqual(24, mol.GetNbAtoms())
xyz1 = [(sc.X, sc.Y, sc.Z) for sc in c.GetScatteringComponentList()]
uc0 = numpy.array(xyz0) - numpy.floor(xyz0)
uc1 = numpy.array(xyz1) - numpy.floor(xyz1)
self.assertTrue(numpy.allclose(uc0, uc1))
return
def test_CaTiO3_cif(self):
'''Check loading of CaTiO3.cif and its ADPs.
'''
c = loadcifdata('CaTiO3.cif')
self.assertTrue(c is not None)
s = c.GetScatt(3)
name = s.GetName()
self.assertEqual(name, "O2")
sp = c.GetScatteringPower(name)
self.assertFalse(sp.IsIsotropic())
utob = 8 * pi**2
self.assertAlmostEqual(utob * 0.0065, sp.B11)
self.assertAlmostEqual(utob * 0.0060, sp.B22)
self.assertAlmostEqual(utob * 0.0095, sp.B33)
self.assertAlmostEqual(utob * 0.0020, sp.B12)
self.assertAlmostEqual(utob * -0.0008, sp.B13)
self.assertAlmostEqual(utob * -0.0010, sp.B23)
self.assertAlmostEqual(0.2897, s.X, 5)
self.assertAlmostEqual(0.2888, s.Y, 5)
self.assertAlmostEqual(0.0373, s.Z, 2)
self.assertAlmostEqual(1, s.Occupancy)
return
def test_CaTiO3_cif(self):
'''Check loading of CaTiO3.cif and its ADPs.
'''
c = loadcifdata('CaTiO3.cif')
self.assertTrue(c is not None)
s = c.GetScatt(3)
name = s.GetName()
self.assertEqual(name, "O2")
sp = c.GetScatteringPower(name)
self.assertFalse(sp.IsIsotropic())
utob = 8 * pi**2
self.assertAlmostEqual(utob * 0.0065, sp.B11)
self.assertAlmostEqual(utob * 0.0060, sp.B22)
self.assertAlmostEqual(utob * 0.0095, sp.B33)
self.assertAlmostEqual(utob * 0.0020, sp.B12)
self.assertAlmostEqual(utob * -0.0008, sp.B13)
self.assertAlmostEqual(utob * -0.0010, sp.B23)
self.assertAlmostEqual(0.2897, s.X, 5)
self.assertAlmostEqual(0.2888, s.Y, 5)
self.assertAlmostEqual(0.0373, s.Z, 2)
self.assertAlmostEqual(1, s.Occupancy)
return
def test_Ni_cif(self):
'''Check loading of Ni.cif
'''
c = loadcifdata('Ni.cif')
self.assertTrue(c is not None)
return
def test_CdSe_cadmoselite_cif(self):
'''Check loading of CdSe_cadmoselite.cif
'''
c = loadcifdata('CdSe_cadmoselite.cif')
self.assertTrue(c is not None)
return
def test_PbTe_cif(self):
'''Check loading of PbTe.cif
'''
c = loadcifdata('PbTe.cif')
self.assertTrue(c is not None)
return
def test_Zn_zinc_cif(self):
'''Check loading of Zn_zinc.cif
'''
c = loadcifdata('Zn_zinc.cif')
self.assertTrue(c is not None)
return
def test_SrTiO3_tausonite_cif(self):
'''Check loading of SrTiO3_tausonite.cif
'''
c = loadcifdata('SrTiO3_tausonite.cif')
self.assertTrue(c is not None)
return
def test_Si_setting2_cif(self):
'''Check loading of Si_setting2.cif
'''
c = loadcifdata('Si_setting2.cif')
self.assertTrue(c is not None)
return
def test_TiO2_anatase_cif(self):
'''Check loading of TiO2_anatase.cif
'''
c = loadcifdata('TiO2_anatase.cif')
self.assertTrue(c is not None)
return
def test_BaTiO3_cif(self):
'''Check loading of BaTiO3.cif
'''
c = loadcifdata('BaTiO3.cif')
self.assertTrue(c is not None)
return
def test_C_graphite_hex_cif(self):
'''Check loading of C_graphite_hex.cif
'''
c = loadcifdata('C_graphite_hex.cif')
self.assertTrue(c is not None)
return
def test_Ag_silver_cif(self):
'''Check loading of Ag_silver.cif
'''
c = loadcifdata('Ag_silver.cif')
self.assertTrue(c is not None)
return
def test_ZnS_wurtzite_cif(self):
'''Check loading of ZnS_wurtzite.cif
'''
c = loadcifdata('ZnS_wurtzite.cif')
self.assertTrue(c is not None)
return
def test_Zn_zinc_cif(self):
'''Check loading of Zn_zinc.cif
'''
c = loadcifdata('Zn_zinc.cif')
self.assertTrue(c is not None)
return
def test_Ni_cif(self):
'''Check loading of Ni.cif
'''
c = loadcifdata('Ni.cif')
self.assertTrue(c is not None)
return
def test_TiO2_anatase_cif(self):
'''Check loading of TiO2_anatase.cif
'''
c = loadcifdata('TiO2_anatase.cif')
self.assertTrue(c is not None)
return
def test_paracetamol_cif(self):
'''Check loading of paracetamol.cif
'''
c = loadcifdata('paracetamol.cif')
self.assertTrue(c is not None)
return
def test_CaF2_fluorite_cif(self):
'''Check loading of CaF2_fluorite.cif
'''
c = loadcifdata('CaF2_fluorite.cif')
self.assertTrue(c is not None)
return
def test_PbTe_cif(self):
'''Check loading of PbTe.cif
'''
c = loadcifdata('PbTe.cif')
self.assertTrue(c is not None)
return
def test_lidocainementhol_cif(self):
'''Check loading of lidocainementhol.cif
'''
c = loadcifdata('lidocainementhol.cif')
self.assertTrue(c is not None)
return
def test_SrTiO3_tausonite_cif(self):
'''Check loading of SrTiO3_tausonite.cif
'''
c = loadcifdata('SrTiO3_tausonite.cif')
self.assertTrue(c is not None)
return
def test_Ag_silver_cif(self):
'''Check loading of Ag_silver.cif
'''
c = loadcifdata('Ag_silver.cif')
self.assertTrue(c is not None)
return
def test_CeO2_cif(self):
'''Check loading of CeO2.cif
'''
c = loadcifdata('CeO2.cif')
self.assertTrue(c is not None)
return
def test_C_graphite_hex_cif(self):
'''Check loading of C_graphite_hex.cif
'''
c = loadcifdata('C_graphite_hex.cif')
self.assertTrue(c is not None)
return
def test_ZnS_wurtzite_cif(self):
'''Check loading of ZnS_wurtzite.cif
'''
c = loadcifdata('ZnS_wurtzite.cif')
self.assertTrue(c is not None)
return
def test_Si_setting2_cif(self):
'''Check loading of Si_setting2.cif
'''
c = loadcifdata('Si_setting2.cif')
self.assertTrue(c is not None)
return
def test_BaTiO3_cif(self):
'''Check loading of BaTiO3.cif
'''
c = loadcifdata('BaTiO3.cif')
self.assertTrue(c is not None)
return
def test_CdSe_cadmoselite_cif(self):
'''Check loading of CdSe_cadmoselite.cif
'''
c = loadcifdata('CdSe_cadmoselite.cif')
self.assertTrue(c is not None)
return
def test_CaF2_fluorite_cif(self):
'''Check loading of CaF2_fluorite.cif
'''
c = loadcifdata('CaF2_fluorite.cif')
self.assertTrue(c is not None)
return
def test_CeO2_cif(self):
'''Check loading of CeO2.cif
'''
c = loadcifdata('CeO2.cif')
self.assertTrue(c is not None)
return
def test_lidocainementhol_cif(self):
'''Check loading of lidocainementhol.cif
'''
c = loadcifdata('lidocainementhol.cif')
self.assertTrue(c is not None)
return
def test_paracetamol_cif(self):
'''Check loading of paracetamol.cif
'''
c = loadcifdata('paracetamol.cif')
self.assertTrue(c is not None)
return
