def parse(self):
self.names = []
self.adp_frac = {}
self.adp_error_frac = {}
self.adp_cart = {}
self.adp_error_cart = {}
self.frac = {}
self.cart = {}
self.element = {}
self.cif = CIF(self.filename)
self.cell = self.cif.cell
self.T = value(self.cif['_diffrn_ambient_temperature'])
for atomname, values in self.cif.positions.items():
self.names.append(atomname)
self.frac[atomname] = values['frac']
self.cart[atomname] = frac2cart(values['frac'], self.cell)
self.element[atomname] = values['element']
if atomname in self.cif.atoms.keys():
self.adp_frac[atomname] = self.cif.atoms[atomname]['adp']
self.adp_error_frac[atomname] = self.cif.atoms[atomname]['adp_error']
self.adp_cart[atomname] = frac2cart_ADP(self.cif.atoms[atomname]['adp'], self.cell)
try:
self.adp_error_cart[atomname] = frac2cart_ADP(self.cif.atoms[atomname]['adp_error'], self.cell)
except TypeError:
self.adp_error_cart[atomname] = None
else:
self.adp_error_frac[atomname] = None
self.adp_frac[atomname] = None
self.adp_error_cart[atomname] = None
self.adp_cart[atomname] = None
def check_cell(cif, p4p_values):
"""
The values of the parameters are compared to those
in the primary CIF. If the values do not match a
Warning is printed.
"""
cif_values = []
cif_values.append('{:.4f}'.format(value(cif['_cell_length_a'])))
cif_values.append('{:.4f}'.format(value(cif['_cell_length_b'])))
cif_values.append('{:.4f}'.format(value(cif['_cell_length_c'])))
cif_values.append('{:.4f}'.format(value(cif['_cell_angle_alpha'])))
cif_values.append('{:.4f}'.format(value(cif['_cell_angle_beta'])))
cif_values.append('{:.4f}'.format(value(cif['_cell_angle_gamma'])))
for i, par in enumerate(p4p_values[:-1]):
if not par == cif_values[i]:
global cell_error
cell_error = True
printer.highlight(' Warning: Cell parameters from CIF and P4P-file do not match.', char='//\\\\')