def open_cif(param, phase):
"""
Open a cif file a build a structure for phase number "phase"
filename: param['structure_phase_%i' %phase]
returns
- a structure with cif information
sets
- param['sgno_phase_%i' %phase] : space group number
- param['sgname_phase_%i' %phase] : space group name
- param['cell_choice_phase_%i' %phase] : not 100% sure
- param['unit_cell_phase_%i' %phase] : unit cell parameters as [a,b,c,alpha,beta,gamma']
Adapted from polyxsim.structure
Created: 12/2019, S. Merkel, Univ. Lille, France
"""
file = param['structure_phase_%i' % phase]
cf = ReadCif(
file
) # Generate an error if reading cif fails which is not always true below
struct = structure.build_atomlist()
struct.CIFread(ciffile=file)
param['sgno_phase_%i' % phase] = sg.sg(sgname=struct.atomlist.sgname).no
param['sgname_phase_%i' % phase] = struct.atomlist.sgname
param['cell_choice_phase_%i' %
phase] = sg.sg(sgname=struct.atomlist.sgname).cell_choice
param['unit_cell_phase_%i' % phase] = struct.atomlist.cell
return struct
def open_structure(param, phase):
file = param['structure_phase_%i' % phase]
if file[-3:] == 'cif':
if ('structure_datablock_phase_%i' % phase) in param:
datablock = param['structure_datablock_phase_%i' % phase]
else:
datablock = None
struct = structure.build_atomlist()
struct.CIFread(ciffile=file, cifblkname=datablock)
elif file[-3:] == 'pdb':
struct = structure.build_atomlist()
struct.PDBread(pdbfile=file)
else:
raise IOError('Unknown structure file format')
param['sgno_phase_%i' % phase] = sg.sg(sgname=struct.atomlist.sgname).no
param['sgname_phase_%i' % phase] = struct.atomlist.sgname
param['cell_choice_phase_%i' %
phase] = sg.sg(sgname=struct.atomlist.sgname).cell_choice
param['unit_cell_phase_%i' % phase] = struct.atomlist.cell
return struct
def test_sfcalc(self): ## test method names begin 'test*'
# Read the cif
mylist = structure.build_atomlist()
mylist.CIFread('PPA.cif','oPPA')
# Read the fcf
fcf = ReadCif('oPPA.fcf')['oPPA']
for i in range(500):# Consider only the first 500 reflections
hkl =[eval(fcf['_refln_index_h'][i]),
eval(fcf['_refln_index_k'][i]),
eval(fcf['_refln_index_l'][i])]
(Fr, Fi) = structure.StructureFactor(hkl, mylist.atomlist.cell,
mylist.atomlist.sgname,
mylist.atomlist.atom,
mylist.atomlist.dispersion)
F2 = Fr**2 + Fi**2
reldif = F2/eval(fcf['_refln_F_squared_calc'][i])-1
print(i, reldif, F2)
if F2 > 10: # Only compare those with an F^2 larger than ten
# to avoid that the very weak reflections which
# have a relative difference that are slightly larger
self.assertAlmostEqual(reldif,0,2)
def test_cifread(self):
mylist = structure.build_atomlist()
mylist.CIFread('PPA.cif','oPPA')
self.assertEqual([8.5312,4.8321,10.125,90.00,92.031,90.00],
mylist.atomlist.cell)
def test_cifopen(self): ## test method names begin 'test*'
mylist = structure.build_atomlist()
mylist.CIFopen('PPA.cif','oPPA')