def test_rwStr_pdb_CdSe(self):
"""check conversion to PDB file format"""
stru = self.stru
stru.read(datafile('CdSe_bulk.stru'), 'pdffit')
#print stru.description
s = stru.writeStr(self.format)
# all lines should be 80 characters long
linelens = [len(l) for l in s.split('\n') if l != ""]
self.assertEqual(linelens, len(linelens) * [80])
# now clean and re-read structure
stru = Structure()
stru.readStr(s, self.format)
#print stru.description
s_els = [a.symbol for a in stru]
f_els = ['Cd', 'Cd', 'Se', 'Se']
self.assertEqual(s_els, f_els)
s_lat = [
stru.lattice.a, stru.lattice.b, stru.lattice.c, stru.lattice.alpha,
stru.lattice.beta, stru.lattice.gamma
]
f_lat = [4.235204, 4.235204, 6.906027, 90.0, 90.0, 120.0]
self.assertListAlmostEqual(s_lat, f_lat)
a0 = stru[0]
s_Uii = [a0.U[i, i] for i in range(3)]
f_Uii = [0.01303035, 0.01303035, 0.01401959]
self.assertListAlmostEqual(s_Uii, f_Uii)
s_sigUii = [a0.sigU[i, i] for i in range(3)]
f_sigUii = [0.00011127, 0.00011127, 0.00019575]
self.assertListAlmostEqual(s_sigUii, f_sigUii)
s_title = stru.description
f_title = "Cell structure file of CdSe #186"
self.assertEqual(s_title, f_title)
def test_rwStr_pdb_CdSe(self):
"""check conversion to PDB file format"""
stru = self.stru
stru.read(datafile('CdSe_bulk.stru'), 'pdffit')
#print stru.description
s = stru.writeStr(self.format)
# all lines should be 80 characters long
linelens = [ len(l) for l in s.split('\n') if l != "" ]
self.assertEqual(linelens, len(linelens)*[80])
# now clean and re-read structure
stru = Structure()
stru.readStr(s, self.format)
#print stru.description
s_els = [a.symbol for a in stru]
f_els = ['Cd', 'Cd', 'Se', 'Se']
self.assertEqual(s_els, f_els)
s_lat = [ stru.lattice.a, stru.lattice.b, stru.lattice.c,
stru.lattice.alpha, stru.lattice.beta, stru.lattice.gamma ]
f_lat = [ 4.235204, 4.235204, 6.906027, 90.0, 90.0, 120.0 ]
self.assertListAlmostEqual(s_lat, f_lat)
a0 = stru[0]
s_Uii = [ a0.U[i,i] for i in range(3) ]
f_Uii = [ 0.01303035, 0.01303035, 0.01401959 ]
self.assertListAlmostEqual(s_Uii, f_Uii)
s_sigUii = [ a0.sigU[i,i] for i in range(3) ]
f_sigUii = [ 0.00011127, 0.00011127, 0.00019575 ]
self.assertListAlmostEqual(s_sigUii, f_sigUii)
s_title = stru.description
f_title = "Cell structure file of CdSe #186"
self.assertEqual(s_title, f_title)
def test_rwStr_xcfg_CdSe(self):
"""check conversion to XCFG file format"""
stru = self.stru
stru.read(datafile('CdSe_bulk.stru'), 'pdffit')
s = stru.writeStr(self.format)
stru = Structure()
stru.readStr(s, self.format)
s_els = [a.symbol for a in stru]
f_els = ['Cd', 'Cd', 'Se', 'Se']
self.assertEqual(s_els, f_els)
s_lat = [ stru.lattice.a, stru.lattice.b, stru.lattice.c,
stru.lattice.alpha, stru.lattice.beta, stru.lattice.gamma ]
f_lat = [ 4.235204, 4.235204, 6.906027, 90.0, 90.0, 120.0 ]
self.assertListAlmostEqual(s_lat, f_lat)
a0 = stru[0]
s_Uii = [ a0.U[i,i] for i in range(3) ]
f_Uii = [ 0.01303035, 0.01303035, 0.01401959 ]
self.assertListAlmostEqual(s_Uii, f_Uii)
def test_rwStr_xcfg_CdSe(self):
"""check conversion to XCFG file format"""
stru = self.stru
stru.read(datafile('CdSe_bulk.stru'), 'pdffit')
s = stru.writeStr(self.format)
stru = Structure()
stru.readStr(s, self.format)
s_els = [a.symbol for a in stru]
f_els = ['Cd', 'Cd', 'Se', 'Se']
self.assertEqual(s_els, f_els)
s_lat = [ stru.lattice.a, stru.lattice.b, stru.lattice.c,
stru.lattice.alpha, stru.lattice.beta, stru.lattice.gamma ]
f_lat = [ 4.235204, 4.235204, 6.906027, 90.0, 90.0, 120.0 ]
self.assertListAlmostEqual(s_lat, f_lat)
a0 = stru[0]
s_Uii = [ a0.U[i,i] for i in range(3) ]
f_Uii = [ 0.01303035, 0.01303035, 0.01401959 ]
self.assertListAlmostEqual(s_Uii, f_Uii)
def readStr(self, s, format='auto'):
"""Same as Structure.readStr, but update spcgr value in
self.pdffit when parser can get spacegroup.
Return instance of StructureParser used to load the data.
See Structure.readStr() for more info.
"""
p = Structure.readStr(self, s, format)
sg = getattr(p, 'spacegroup', None)
if sg: self.pdffit['spcgr'] = sg.short_name
return p
def readStr(self, s, format='auto'):
"""Same as Structure.readStr, but update spcgr value in
self.pdffit when parser can get spacegroup.
Return instance of StructureParser used to load the data.
See Structure.readStr() for more info.
"""
p = Structure.readStr(self, s, format)
sg = getattr(p, 'spacegroup', None)
if sg: self.pdffit['spcgr'] = sg.short_name
return p
