def get_chemical_formula(atoms):
"""
Compatibility function, return mode=metal, when
available, mode=hill, when not (ASE <= 3.13)
"""
try:
return atoms.get_chemical_formula(mode='metal')
except ValueError:
return atoms.get_chemical_formula(mode='hill')
def convert_atoms(request=None):
import ase.io
import ase.io.formats
request = flask.request if request is None else request
cif = request.args.get('cif',
request.get_json().get('params', {}).get('cif', ''))
out_format = request.args.get(
'format',
request.get_json().get('params', {}).get('format', ''))
if not out_format:
out_format = 'cif'
if out_format not in VALID_OUT_FORMATS:
return {
"error":
"outFormat {outformat} is invalid. Should be on of {VALID_OUT_FORMATS}"
.format(**locals()),
}
with StringIO.StringIO() as in_file:
in_file.write(cif)
in_file.seek(0)
atoms = ase.io.read(
filename=in_file,
index=None,
format='cif',
)
composition = atoms.get_chemical_formula(mode='metal')
with StringIO.StringIO() as out_file:
# Castep file writer needs name
out_file.name = 'CatApp Browser Export'
ase.io.write(out_file, atoms, out_format)
out_content = out_file.getvalue()
format2extension = {
value: key
for key, value in ase.io.formats.extension2format.items()
}
extension = format2extension.get(out_format, out_format)
return flask.jsonify({
'version':
VERSION,
'image':
str(out_content),
'input_filetype':
'cif',
'output_filetype':
out_format,
'filename':
'structure_{composition}.{extension}'.format(**locals()),
'filename_trunk':
'structure_{composition}'.format(**locals()),
'extension':
extension,
})