def import_cif_file(self):
file = self.ui.cif_file.text()
if not os.path.isfile(file):
return
try:
cf = ReadCif(file)
search_params = {
'_cell_length_a': InterplanarSpacing.PARAMETER_A,
'_cell_length_b': InterplanarSpacing.PARAMETER_B,
'_cell_length_c': InterplanarSpacing.PARAMETER_C,
'_cell_angle_alpha': InterplanarSpacing.PARAMETER_ALPHA,
'_cell_angle_beta': InterplanarSpacing.PARAMETER_BETA,
'_cell_angle_gamma': InterplanarSpacing.PARAMETER_GAMMA,
}
ui_mapping = self.get_parameter_mapping()
import re
# find the lattice parameters in the cif file
for key, entry in cf.items():
for search_key, search_mapping in search_params.items():
if entry.has_key(search_key):
try:
number = float(entry[search_key])
except:
number = re.findall(r"[-+]?\d*\.\d+|\d+",
entry[search_key])
if len(number) == 0:
continue
number = number[0]
ui_mapping[search_mapping].setText(str(number))
self.system.set_parameter(self.get_lattice_parameters())
system_class = self.system.detect_system()
# Now set the input text field for the crystal system
crystal_family = None
for key, crystal_class in self.CLASS_MAPPING.items():
if crystal_class == system_class:
crystal_family = key
self.set_crystal_family(crystal_family)
self.update_view()
except BaseException as e:
print(e)
def read_structure(path_to_file):
cwd = os.getcwd()
try:
os.chdir(os.path.dirname(path_to_file))
file_name = os.path.split(path_to_file)[-1]
cif_data = ReadCif(file_name)
os.chdir(cwd)
except:
os.chdir(cwd)
raise ValueError("The reading or parsing of the " + file_name +
" is failed!")
try:
name, data = list(cif_data.items())[0]
structure_data = StructureData(name, data)
structure = Structure().build_structure(structure_data)
structure.reamove_connectivity()
return structure
except:
print("Reading structure is failed!")
def read_structures(path_to_file):
cwd = os.getcwd()
try:
os.chdir(os.path.dirname(path_to_file))
file_name = os.path.split(path_to_file)[-1]
cif_data = ReadCif(file_name)
os.chdir(cwd)
except:
os.chdir(cwd)
raise ValueError("The reading or parsing of the " + file_name +
" is failed!")
for i, (name, data) in enumerate(cif_data.items()):
try:
structure_data = StructureData(name, data)
structure = Structure().build_structure(structure_data)
structure.reamove_connectivity()
yield structure
except:
os.chdir(cwd)
print("Reading " + str(i) + " structure is failed!")
from CifFile import ReadCif
cf = ReadCif('4_SnO2_0.0288nm.cif')
for key,value in cf.items():
#print( '{0}{1}'.format(key,value) )
print( type(value))
