def write(structures, filename=None, wrap=False, **kwargs):
"""
Write a structure or list of structures to a cif file.
Arguments:
structures:
A :mod:`~qmpy.Structure` object or list of objects. If supplied
with several Structures, they will all be written to the same cif.
Keyword Arguments:
filename:
If supplied with a file name, will write to the file. If no
filename is given, will return a string.
wrap:
If True, will include atoms at fractional coordinates 0 and 1.
Useful only for visualizing structures.
Examples::
>>> io.cif.write(structure, "test.cif")
>>> io.cif.write([structure1, structure2], "test.cif")
"""
cif = CifFile()
if not isinstance(structures, list):
structures = [structures]
for i, structure in enumerate(structures):
cif['structure_%d' % i] = _make_cif_block(structure, wrap=wrap)
if filename:
open(filename, 'w').write(str(cif))
else:
return str(cif)
def main():
#read filename
f = 'CHA.cif' #input("Filename: ")
# open and parse our cif
cf = CifFile(f)
F = f[:3]
cb = cf[F]
Crystal = Crysdata(F, cb)
Crystal.printout()
def read(self, stream, default_type='A'):
"""Read text stream and return a trajectory instance.
:param stream: The stream, which contains the ciffile.
:type stream: A file-like textstream.
:param default_type: The default particle type for
ciffile dialects without type definition.
:type default_type: str
"""
parsed_file = CifFile(stream)
keys = list(sorted(parsed_file.keys()))
# Index the stream
frames = list(self._scan(parsed_file, keys, default_type))
if len(frames) == 0:
raise ParserError("Did not read a single complete frame.")
logger.info("Read {} frames.".format(len(frames)))
return Trajectory(frames)
def drawCrystal(file):
# Check if file is file:
S = time.time()
global user_feedback
ext = file[len(file)-4:]
if(ext.lower() != ".cif"):
print("Only cif files can be visualised")
user_feedback = "Not a cif file"
return
# Check OpenBabel installation
try:
# Convert the cif file to its P1 symmetry notation as a temporary cif file
print('Converting %s to P1' %file)
obabel_fill_unit_cell(file, "temp.CIF")
cf = CifFile("temp.CIF")
except:
print("No OpenBabel installation found, install it from http://openbabel.org/wiki/Category:Installation")
user_feedback = "OpenBabel not installed"
#cf = CifFile(file) CifFile apparently can't read in long filepaths
return
# Open and parse our cif
f = file.rsplit(dir_sep, 1)[-1]
F = f[:3]
print(f)
cb = cf.first_block()
Crystal = Crysdata(F,cb)
# Print crystal data in terminal if checked
if(print_data):
Crystal.printout()
print("Crystal data read after "+ str(time.time() - S) + " seconds")
# Draw crystal if in Blender environment
if(Blender_env):
clearWS()
Crystal.drawCrystal()
bpy.ops.object.select_all(action='DESELECT')
if(add_camera):
addCamera(Crystal.cell.alen,Crystal.cell.blen,Crystal.cell.clen)
def _parseCifDataSource(self, datasource):
"""\
Open and process CIF data from the specified `datasource`.
Parameters
----------
datasource : str or a file-like object
This is used as an argument to the CifFile class. The CifFile
instance is stored in `ciffile` attribute of this Parser.
Returns
-------
Structure
The Structure object loaded from the specified data source.
Raises
------
StructureFormatError
When the data do not constitute a valid CIF format.
"""
from CifFile import CifFile, StarError
self.stru = None
try:
with _suppressCifParserOutput():
# Use `grammar` option to digest values with curly-brackets.
# Ref: https://bitbucket.org/jamesrhester/pycifrw/issues/19
self.ciffile = CifFile(datasource, grammar='auto')
for blockname in self.ciffile.keys():
self._parseCifBlock(blockname)
# stop after reading the first structure
if self.stru is not None:
break
except (StarError, ValueError, IndexError) as err:
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = str(err).strip()
e = StructureFormatError(emsg)
six.reraise(StructureFormatError, e, exc_traceback)
return self.stru
def _parseCifDataSource(self, datasource):
"""\
Open and process CIF data from the specified `datasource`.
Parameters
----------
datasource : str or a file-like object
This is used as an argument to the CifFile class. The CifFile
instance is stored in `ciffile` attribute of this Parser.
Returns
-------
Structure
The Structure object loaded from the specified data source.
Raises
------
StructureFormatError
When the data do not constitute a valid CIF format.
"""
from CifFile import CifFile, StarError
self.stru = None
try:
with _suppressCifParserOutput():
self.ciffile = CifFile(datasource)
for blockname in self.ciffile.keys():
self._parseCifBlock(blockname)
# stop after reading the first structure
if self.stru is not None:
break
except (StarError, ValueError, IndexError) as err:
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = str(err).strip()
e = StructureFormatError(emsg)
six.reraise(StructureFormatError, e, exc_traceback)
return self.stru
def prepareGulpInput(cifFile,
gulpFile,
jobName,
verbose=False,
auto_fractions=False):
"""
Example file:
mgh2
cell
4.5168 4.5168 3.0205 90.0 90.0 90.0
frac
Mg 0.0 0.0 0.0
H 0.306 0.306 0.0
space
136
output xyz mgh2
"""
from CifFile import CifFile
if not os.path.exists(cifFile):
raise IOError("CIF file '%s' was not found!" % (cifFile))
cf = CifFile(cifFile)
if verbose:
print(
"------------------------------------------------------------------"
)
if len(cf) != 1:
raise StandardError(
"The cif file contains %i data blocks, while one was expected")
# A cif file can contain several "datablocks" that each start
# with "data_".
if verbose:
print("Reading data block '%s'..." % (cf.keys()[0]))
cb = cf[cf.keys()[0]] # open the first block
AA = float(re.match('([0-9.e]*)', cb['_cell_length_a']).group(0))
BB = float(re.match('([0-9.e]*)', cb['_cell_length_b']).group(0))
CC = float(re.match('([0-9.e]*)', cb['_cell_length_c']).group(0))
alpha = float(cb['_cell_angle_alpha'])
beta = float(cb['_cell_angle_beta'])
gamma = float(cb['_cell_angle_gamma'])
# Spacegroup number (1-230)
# '_symmetry_Int_Tables_number' has been superseded by '_space_group_IT_number'
if '_space_group_IT_number' in cb.keys():
SG = int(cb['_space_group_IT_number'])
elif '_symmetry_Int_Tables_number' in cb.keys():
SG = int(cb['_symmetry_Int_Tables_number'])
else:
#print "WARNING: No space group specified. Assuming P1."
SG = 1
# CCTBX:
#unit_cell = uctbx.unit_cell([AA,BB,CC,alpha,beta,gamma])
#space_group_info = sgtbx.space_group_info(symbol=cb['_symmetry_space_group_name_H-M'])
#crystal_symmetry = crystal.symmetry(unit_cell=unit_cell,space_group_info=space_group_info)
##print "CIF file read successfully:"
#crystal_symmetry.show_summary()
if verbose:
print(" Space group:", SG)
print(" a=%s, b=%s, c=%s, alpha=%s, beta=%s, gamma=%s" %
(AA, BB, CC, alpha, beta, gamma))
atomTypes = []
atoms = ''
fracOccFound = False
firstAtom = True
atoms = ""
# The coordinates of the atom (_atom_site_fract_x/y/z) may have
# a last digit in parenthesis, like "-0.6636(7)". Therefore we
# extract the part consisting of only digits and a decimal separator:
coordsMatch = re.compile('[0-9.e-]*')
for atom in cb.GetLoop('_atom_site_label'):
atomKeys = dir(atom)
if '_atom_site_type_symbol' in atomKeys:
m = re.match('[a-z]*', atom._atom_site_type_symbol, re.I)
atomType = m.group(0)
else:
m = re.match('[a-z]*', atom._atom_site_label, re.I)
atomType = m.group(0)
if '_atom_site_occupancy' in atomKeys:
occ = float(coordsMatch.match(atom._atom_site_occupancy).group())
if not occ == 1.0:
if not fracOccFound:
#print " "
#print " WARNING: Fractional occupancy (" + str(occ) +") " \
+ "found for atom of type " + atomType + "."
fracOccFound = True
else:
occ = 1.0
# Some crystal structures obtained by neutron diffraction use D for H:
if atomType == 'D':
atomType = 'H'
if '_atom_site_symmetry_multiplicity' in atomKeys and '_atom_site_Wyckoff_symbol' in atomKeys:
atomTypes.append(atomType + ' at ' +
atom._atom_site_symmetry_multiplicity +
atom._atom_site_Wyckoff_symbol)
else:
atomTypes.append(atomType)
atomX = coordsMatch.match(atom._atom_site_fract_x).group()
atomY = coordsMatch.match(atom._atom_site_fract_y).group()
atomZ = coordsMatch.match(atom._atom_site_fract_z).group()
atomPos = [atomX, atomY, atomZ]
for i in range(3):
pp = atomPos[i].split(".")
if len(pp) is 2:
decimals = pp[1]
if len(decimals) > 3 and len(decimals) < 6 and decimals[
0] == decimals[1] and decimals[0] == decimals[
2] and decimals[-1] != "0":
if auto_fractions:
oldPos = atomPos[i]
atomPos[i] = "%.6f" % (float(
eval('1.*' + float2fraction(atomPos[i]))))
#print " Notice: Converted %s into %s" %(oldPos,atomPos[i])
else:
#print "\n"\
+ " ! Warning: The coordinate "+atomPos[i]+" looks similar to the fraction %s, but\n" % float2fraction(atomPos[i]) \
+ " ! has insufficient decimals to be recognized as so by GULP. If you want\n" \
+ " ! this coordinate to be recognized as a special high-symmetry position,\n" \
+ " ! you need to specify at least six digits. If you run cif2vasp with the \n" \
+ " ! -f switch, cif2vasp will try to add the necessary decimals automaticly."
atoms += "%s %s %s %s %f %f\n" % (atomType, atomPos[0], atomPos[1],
atomPos[2], 0.0, occ)
firstAtom = False
if fracOccFound:
#print " "
#print "ERROR: Fractional occupancies are not currently supported.\n"
exit()
if verbose:
print(" Atom types: " + ', '.join(atomTypes))
gulpFile = open(gulpFile, 'w') #Create and write the GULP
gulpFile.writelines([
jobName + '\n', 'cell\n',
'%s %s %s %s %s %s\n' % (AA, BB, CC, alpha, beta, gamma), 'frac\n',
atoms, 'space\n',
str(SG) + '\n', 'output xyz ' + jobName + '\n'
])
def readCifFile(cifFile):
from CifFile import CifFile
if not os.path.exists(cifFile):
raise IOError("CIF file '%s' was not found!" % (cifFile))
cf = CifFile(cifFile)
#print "------------------------------------------------------------------"
if len(cf) != 1:
print("xx")
# raise(tandardError("The cif file contains %i data blocks, while one was expected"))
# A cif file can contain several "datablocks" that each start
# with "data_".
cb = cf[cf.keys()[0]] # open the first block
AA = float(re.match('([0-9.]*)', cb['_cell_length_a']).group(0))
BB = float(re.match('([0-9.]*)', cb['_cell_length_b']).group(0))
CC = float(re.match('([0-9.]*)', cb['_cell_length_c']).group(0))
alpha = float(cb['_cell_angle_alpha'])
beta = float(cb['_cell_angle_beta'])
gamma = float(cb['_cell_angle_gamma'])
SG = int(cb['_symmetry_Int_Tables_number']) # spacegroup
atomTypes = []
atoms = ''
fracOccFound = False
firstAtom = True
atoms = []
for atom in cb.GetLoop('_atom_site_label'):
atomKeys = dir(atom)
if '_atom_site_type_symbol' in atomKeys:
m = re.match('[a-z]*', atom._atom_site_type_symbol, re.I)
atomType = m.group(0)
else:
m = re.match('[a-z]*', atom._atom_site_label, re.I)
atomType = m.group(0)
atomLabel = atom._atom_site_label
if '_atom_site_occupancy' in atomKeys:
occ = float(atom._atom_site_occupancy)
if not occ == 1.0:
if not fracOccFound:
#print " "
#print " WARNING: Fractional occupancy (" + str(occ) +") " \
+ "found for atom of type " + atomType + "."
fracOccFound = True
else:
occ = 1.0
# Some crystal structures obtained by neutron diffraction use D for H:
if atomType == 'D':
atomType = 'H'
atomLabel.replace('H', 'D')
if '_atom_site_symmetry_multiplicity' in atomKeys and '_atom_site_Wyckoff_symbol' in atomKeys:
atomTypes.append(atomType + ' at ' +
atom._atom_site_symmetry_multiplicity +
atom._atom_site_Wyckoff_symbol)
else:
atomTypes.append(atomType)
atomPos = [
atom._atom_site_fract_x, atom._atom_site_fract_y,
atom._atom_site_fract_z
]
for p in atomPos:
pp = p.split(".")
if len(pp) is 2:
decimals = p.split(".")[1]
# if len(decimals) > 3 and len(decimals) < 6 and decimals[0] == decimals[1] and decimals[-1] != "0":
#print "\n ---------------------\n"\
# + " Warning: If the fractional coordinate "+p+" is a recurring decimal, such as 1/3,\n" \
# + " then it is necessary to specify this value to six decimal places to be sure of \n" \
# + " it being recognised correctly as a spcecial position.\n ------------------"
# The coordinates of the atom (_atom_site_fract_x/y/z) may have
# a last digit in parenthesis, like "0.6636(7)". Therefore we
# extract the part consisting of only digits and a decimal separator:
p = re.compile('[0-9.]*')
atomX = float(p.match(atom._atom_site_fract_x).group())
atomY = float(p.match(atom._atom_site_fract_y).group())
atomZ = float(p.match(atom._atom_site_fract_z).group())
#atoms += "%s %f %f %f %f %f\n" % (atomType, atomX, atomY, atomZ, 0.0, occ)
atoms.append({
'label': atomLabel,
'type': atomType,
'pos': (atomX, atomY, atomZ)
})
firstAtom = False
if fracOccFound:
#print " "
#print "ERROR: Fractional occupancies are not currently supported.\n"
exit()
#print " Atom types: " + ', '.join(atomTypes)
return {
'spacegroup': SG,
'unit_cell': [AA, BB, CC, alpha, beta, gamma],
'scatterers': atoms
}
class P_cif(StructureParser):
"""Simple parser for CIF structure format.
Reads Structure from the first block containing _atom_site_label key.
Following blocks, if any are ignored.
Data members:
format -- structure format name
ciffile -- instance of CifFile from PyCifRW
stru -- Structure instance used for cif input or output
Data members used for input only:
spacegroup -- instance of SpaceGroup used for symmetry expansion
eps -- resolution in fractional coordinates for non-equal
positions. Use for expansion of asymmetric unit.
eau -- instance of ExpandAsymmetricUnit from SymmetryUtilities
asymmetric_unit -- list of atom instances for the original asymmetric
unit in the CIF file
labelindex -- dictionary mapping unique atom label to index of atom
in self.asymmetric_unit
cif_sgname -- space group name obtained by looking up the value of
_space_group_name_Hall, _symmetry_space_group_name_Hall,
_space_group_name_H-M_alt, _symmetry_space_group_name_H-M
items. None when neither is defined.
"""
# static data and methods ------------------------------------------------
# dictionary set of class methods for translating CIF values
# to Atom attributes
_atom_setters = dict.fromkeys((
'_tr_ignore',
'_tr_atom_site_label',
'_tr_atom_site_type_symbol',
'_tr_atom_site_fract_x',
'_tr_atom_site_fract_y',
'_tr_atom_site_fract_z',
'_tr_atom_site_cartn_x',
'_tr_atom_site_cartn_y',
'_tr_atom_site_cartn_z',
'_tr_atom_site_U_iso_or_equiv',
'_tr_atom_site_B_iso_or_equiv',
'_tr_atom_site_adp_type', '_tr_atom_site_thermal_displace_type',
'_tr_atom_site_occupancy',
'_tr_atom_site_aniso_U_11',
'_tr_atom_site_aniso_U_22',
'_tr_atom_site_aniso_U_33',
'_tr_atom_site_aniso_U_12',
'_tr_atom_site_aniso_U_13',
'_tr_atom_site_aniso_U_23',
'_tr_atom_site_aniso_B_11',
'_tr_atom_site_aniso_B_22',
'_tr_atom_site_aniso_B_33',
'_tr_atom_site_aniso_B_12',
'_tr_atom_site_aniso_B_13',
'_tr_atom_site_aniso_B_23',
))
# make _atom_setters case insensitive
for k in list(_atom_setters.keys()):
_atom_setters[k] = _atom_setters[k.lower()] = k
del k
BtoU = 1.0/(8 * numpy.pi**2)
def _tr_ignore(a, value):
return
_tr_ignore = staticmethod(_tr_ignore)
def _tr_atom_site_label(a, value):
a.label = str(value)
# set element when not specified by _atom_site_type_symbol
if not a.element:
P_cif._tr_atom_site_type_symbol(a, value)
_tr_atom_site_label = staticmethod(_tr_atom_site_label)
# 3 regexp groups for nucleon number, atom symbol, and oxidation state
_psymb = re.compile(r'(\d+-)?([a-zA-Z]+)(\d[+-])?')
def _tr_atom_site_type_symbol(a, value):
rx = P_cif._psymb.match(value)
smbl = rx and rx.group(0) or value
smbl = str(smbl)
a.element = smbl[:1].upper() + smbl[1:].lower()
_tr_atom_site_type_symbol = staticmethod(_tr_atom_site_type_symbol)
def _tr_atom_site_fract_x(a, value):
a.xyz[0] = leading_float(value)
_tr_atom_site_fract_x = staticmethod(_tr_atom_site_fract_x)
def _tr_atom_site_fract_y(a, value):
a.xyz[1] = leading_float(value)
_tr_atom_site_fract_y = staticmethod(_tr_atom_site_fract_y)
def _tr_atom_site_fract_z(a, value):
a.xyz[2] = leading_float(value)
_tr_atom_site_fract_z = staticmethod(_tr_atom_site_fract_z)
def _tr_atom_site_cartn_x(a, value):
a.xyz_cartn[0] = leading_float(value)
_tr_atom_site_cartn_x = staticmethod(_tr_atom_site_cartn_x)
def _tr_atom_site_cartn_y(a, value):
a.xyz_cartn[1] = leading_float(value)
_tr_atom_site_cartn_y = staticmethod(_tr_atom_site_cartn_y)
def _tr_atom_site_cartn_z(a, value):
a.xyz_cartn[2] = leading_float(value)
_tr_atom_site_cartn_z = staticmethod(_tr_atom_site_cartn_z)
def _tr_atom_site_U_iso_or_equiv(a, value):
a.Uisoequiv = leading_float(value)
_tr_atom_site_U_iso_or_equiv = staticmethod(_tr_atom_site_U_iso_or_equiv)
def _tr_atom_site_B_iso_or_equiv(a, value):
a.Uisoequiv = P_cif.BtoU * leading_float(value)
_tr_atom_site_B_iso_or_equiv = staticmethod(_tr_atom_site_B_iso_or_equiv)
def _tr_atom_site_adp_type(a, value):
a.anisotropy = value not in ("Uiso", "Biso")
_tr_atom_site_adp_type = staticmethod(_tr_atom_site_adp_type)
_tr_atom_site_thermal_displace_type = _tr_atom_site_adp_type
def _tr_atom_site_occupancy(a, value):
a.occupancy = leading_float(value, 1.0)
_tr_atom_site_occupancy = staticmethod(_tr_atom_site_occupancy)
def _tr_atom_site_aniso_U_11(a, value):
a.U11 = leading_float(value)
_tr_atom_site_aniso_U_11 = staticmethod(_tr_atom_site_aniso_U_11)
def _tr_atom_site_aniso_U_22(a, value):
a.U22 = leading_float(value)
_tr_atom_site_aniso_U_22 = staticmethod(_tr_atom_site_aniso_U_22)
def _tr_atom_site_aniso_U_33(a, value):
a.U33 = leading_float(value)
_tr_atom_site_aniso_U_33 = staticmethod(_tr_atom_site_aniso_U_33)
def _tr_atom_site_aniso_U_12(a, value):
a.U12 = leading_float(value)
_tr_atom_site_aniso_U_12 = staticmethod(_tr_atom_site_aniso_U_12)
def _tr_atom_site_aniso_U_13(a, value):
a.U13 = leading_float(value)
_tr_atom_site_aniso_U_13 = staticmethod(_tr_atom_site_aniso_U_13)
def _tr_atom_site_aniso_U_23(a, value):
a.U23 = leading_float(value)
_tr_atom_site_aniso_U_23 = staticmethod(_tr_atom_site_aniso_U_23)
def _tr_atom_site_aniso_B_11(a, value):
a.U11 = P_cif.BtoU * leading_float(value)
_tr_atom_site_aniso_B_11 = staticmethod(_tr_atom_site_aniso_B_11)
def _tr_atom_site_aniso_B_22(a, value):
a.U22 = P_cif.BtoU * leading_float(value)
_tr_atom_site_aniso_B_22 = staticmethod(_tr_atom_site_aniso_B_22)
def _tr_atom_site_aniso_B_33(a, value):
a.U33 = P_cif.BtoU * leading_float(value)
_tr_atom_site_aniso_B_33 = staticmethod(_tr_atom_site_aniso_B_33)
def _tr_atom_site_aniso_B_12(a, value):
a.U12 = P_cif.BtoU * leading_float(value)
_tr_atom_site_aniso_B_12 = staticmethod(_tr_atom_site_aniso_B_12)
def _tr_atom_site_aniso_B_13(a, value):
a.U13 = P_cif.BtoU * leading_float(value)
_tr_atom_site_aniso_B_13 = staticmethod(_tr_atom_site_aniso_B_13)
def _tr_atom_site_aniso_B_23(a, value):
a.U23 = P_cif.BtoU * leading_float(value)
_tr_atom_site_aniso_B_23 = staticmethod(_tr_atom_site_aniso_B_23)
def _get_atom_setters(cifloop):
"""Find translators of CifLoop items to data in Atom instance.
Static method.
cifloop -- instance of CifLoop
Return a list of setter functions in the order of cifloop.keys().
"""
rv = []
for p in cifloop.keys():
lcname = "_tr" + p.lower()
fncname = P_cif._atom_setters.get(lcname, '_tr_ignore')
f = getattr(P_cif, fncname)
rv.append(f)
return rv
_get_atom_setters = staticmethod(_get_atom_setters)
# normal methods ---------------------------------------------------------
def __init__(self, eps=None):
"""Initialize the parser for CIF structure files.
eps -- fractional coordinates cutoff for duplicate positions.
When None use the default for ExpandAsymmetricUnit.
"""
StructureParser.__init__(self)
self.format = "cif"
self.ciffile = None
self.stru = None
self.spacegroup = None
self.eps = eps
self.eau = None
self.asymmetric_unit = None
self.labelindex = {}
self.cif_sgname = None
pass
def parse(self, s):
"""Create Structure instance from a string in CIF format.
Return Structure instance or raise StructureFormatError.
"""
self.ciffile = None
self.filename = ''
fp = six.StringIO(s)
rv = self._parseCifDataSource(fp)
return rv
def parseLines(self, lines):
"""Parse list of lines in CIF format.
lines -- list of strings stripped of line terminator
Return Structure instance or raise StructureFormatError.
"""
s = "\n".join(lines) + '\n'
return self.parse(s)
def parseFile(self, filename):
"""Create Structure from an existing CIF file.
filename -- path to structure file
Return Structure object.
Raise StructureFormatError or IOError.
"""
self.ciffile = None
self.filename = filename
fileurl = _fixIfWindowsPath(filename)
rv = self._parseCifDataSource(fileurl)
# all good here
return rv
def _parseCifDataSource(self, datasource):
"""\
Open and process CIF data from the specified `datasource`.
Parameters
----------
datasource : str or a file-like object
This is used as an argument to the CifFile class. The CifFile
instance is stored in `ciffile` attribute of this Parser.
Returns
-------
Structure
The Structure object loaded from the specified data source.
Raises
------
StructureFormatError
When the data do not constitute a valid CIF format.
"""
from CifFile import CifFile, StarError
self.stru = None
try:
with _suppressCifParserOutput():
self.ciffile = CifFile(datasource)
for blockname in self.ciffile.keys():
self._parseCifBlock(blockname)
# stop after reading the first structure
if self.stru is not None:
break
except (StarError, ValueError, IndexError) as err:
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = str(err).strip()
e = StructureFormatError(emsg)
six.reraise(StructureFormatError, e, exc_traceback)
return self.stru
def _parseCifBlock(self, blockname):
"""Translate CIF file block, skip blocks without _atom_site_label.
Updates data members stru, eau.
blockname -- name of top level block in self.ciffile
No return value.
"""
block = self.ciffile[blockname]
if '_atom_site_label' not in block: return
# here block contains structure, initialize output data
self.stru = Structure()
self.labelindex.clear()
# execute specialized block parsers
self._parse_lattice(block)
self._parse_atom_site_label(block)
self._parse_atom_site_aniso_label(block)
self._parse_space_group_symop_operation_xyz(block)
return
def _parse_lattice(self, block):
"""Obtain lattice parameters from a CifBlock.
This method updates self.stru.lattice.
block -- instance of CifBlock
No return value.
"""
if '_cell_length_a' not in block: return
# obtain lattice parameters
try:
latpars = (
leading_float(block['_cell_length_a']),
leading_float(block['_cell_length_b']),
leading_float(block['_cell_length_c']),
leading_float(block['_cell_angle_alpha']),
leading_float(block['_cell_angle_beta']),
leading_float(block['_cell_angle_gamma']),
)
except KeyError as err:
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = str(err)
e = StructureFormatError(emsg)
six.reraise(StructureFormatError, e, exc_traceback)
self.stru.lattice = Lattice(*latpars)
return
def _parse_atom_site_label(self, block):
"""Obtain atoms in asymmetric unit from a CifBlock.
This method inserts Atom instances to self.stru and
updates labelindex dictionary.
block -- instance of CifBlock
No return value.
"""
# process _atom_site_label
atom_site_loop = block.GetLoop('_atom_site_label')
# get a list of setters for atom_site values
prop_setters = P_cif._get_atom_setters(atom_site_loop)
# index of the _atom_site_label item for the labelindex dictionary
ilb = atom_site_loop.keys().index('_atom_site_label')
# loop through the values and pass them to the setters
sitedatalist = zip(*atom_site_loop.values())
for values in sitedatalist:
curlabel = values[ilb]
# skip entries that have invalid label
if curlabel == '?':
continue
self.labelindex[curlabel] = len(self.stru)
self.stru.addNewAtom()
a = self.stru.getLastAtom()
for fset, val in zip(prop_setters, values):
fset(a, val)
return
def _parse_atom_site_aniso_label(self, block):
"""Obtain value of anisotropic thermal displacements from a CifBlock.
This method updates U members of Atom instances in self.stru.
The labelindex dictionary has to be defined beforehand.
block -- instance of CifBlock
No return value.
"""
if '_atom_site_aniso_label' not in block: return
# was anisotropy processed in the _atom_site_label loop?
isotropy_done = _hasAtomSiteADPType(block)
# something to do here:
adp_loop = block.GetLoop('_atom_site_aniso_label')
# index of the _atom_site_label column
ilb = adp_loop.keys().index('_atom_site_aniso_label')
# get a list of setters for this loop
prop_setters = P_cif._get_atom_setters(adp_loop)
sitedatalist = zip(*adp_loop.values())
for values in sitedatalist:
idx = self.labelindex[values[ilb]]
a = self.stru[idx]
if not isotropy_done:
a.anisotropy = True
for fset, val in zip(prop_setters, values):
fset(a, val)
return
def _parse_space_group_symop_operation_xyz(self, block):
"""Process symmetry operations from a CifBlock. The method
updates spacegroup and eau data according to symmetry
operations defined in _space_group_symop_operation_xyz or
_symmetry_equiv_pos_as_xyz items in CifBlock.
block -- instance of CifBlock
No return value.
"""
from diffpy.structure.spacegroups import IsSpaceGroupIdentifier
from diffpy.structure.spacegroups import SpaceGroup, GetSpaceGroup
from diffpy.structure.spacegroups import FindSpaceGroup
self.asymmetric_unit = list(self.stru)
sym_synonyms = ('_space_group_symop_operation_xyz',
'_symmetry_equiv_pos_as_xyz')
sym_loop_name = [n for n in sym_synonyms if n in block]
# recover explicit list of symmetry operations
symop_list = []
if sym_loop_name:
# sym_loop exists here and we know its cif name
sym_loop_name = sym_loop_name[0]
sym_loop = block.GetLoop(sym_loop_name)
for eqxyz in sym_loop[sym_loop_name]:
opcif = getSymOp(eqxyz)
symop_list.append(opcif)
# determine space group number
sg_nameHall = (block.get('_space_group_name_Hall', '') or
block.get('_symmetry_space_group_name_Hall', ''))
sg_nameHM = (block.get('_space_group_name_H-M_alt', '') or
block.get('_symmetry_space_group_name_H-M', ''))
self.cif_sgname = (sg_nameHall or sg_nameHM or None)
sgid = (int(block.get('_space_group_IT_number', '0')) or
int(block.get('_symmetry_Int_Tables_number', '0')) or
sg_nameHM)
self.spacegroup = None
# try to reuse existing space group from symmetry operations
if symop_list:
try:
self.spacegroup = FindSpaceGroup(symop_list)
except ValueError:
pass
# otherwise lookup the space group from its identifier
if self.spacegroup is None and sgid and IsSpaceGroupIdentifier(sgid):
self.spacegroup = GetSpaceGroup(sgid)
# define new spacegroup when symmetry operations were listed, but
# there is no match to an existing definition
if symop_list and self.spacegroup is None:
new_short_name = "CIF " + (sg_nameHall or 'data')
new_crystal_system = (
block.get('_space_group_crystal_system') or
block.get('_symmetry_cell_setting') or
'TRICLINIC' ).upper()
self.spacegroup = SpaceGroup(
short_name=new_short_name,
crystal_system=new_crystal_system,
symop_list=symop_list)
if self.spacegroup is None:
emsg = "CIF file has unknown space group identifier {!r}."
raise StructureFormatError(emsg.format(sgid))
self._expandAsymmetricUnit(block)
return
def _expandAsymmetricUnit(self, block):
"""Perform symmetry expansion of self.stru using self.spacegroup.
This method updates data in stru and eau.
Parameters
----------
block : CifBlock
The top-level block containing crystal structure data.
"""
from diffpy.structure.symmetryutilities import ExpandAsymmetricUnit
corepos = [a.xyz for a in self.stru]
coreUijs = [a.U for a in self.stru]
self.eau = ExpandAsymmetricUnit(self.spacegroup, corepos, coreUijs,
eps=self.eps)
# setup anisotropy according to symmetry requirements
# was isotropy flag already processed
isotropy_done = (_hasAtomSiteADPType(block) or
'_atom_site_aniso_label' in block)
if not isotropy_done:
for ca, uisotropy in zip(self.stru, self.eau.Uisotropy):
ca.anisotropy = not uisotropy
# build a nested list of new atoms:
newatoms = []
for i, ca in enumerate(self.stru):
eca = [] # expanded core atom
for j in range(self.eau.multiplicity[i]):
a = Atom(ca)
a.xyz = self.eau.expandedpos[i][j]
if j > 0:
a.label += '_' + str(j + 1)
if a.anisotropy:
a.U = self.eau.expandedUijs[i][j]
eca.append(a)
newatoms.append(eca)
# insert new atoms where they belong
self.stru[:] = sum(newatoms, [])
return
# conversion to CIF ------------------------------------------------------
def toLines(self, stru):
"""Convert Structure stru to a list of lines in basic CIF format.
Return list of strings.
"""
import time
lines = []
# may be replaced with filtered Structure.title
# for now, we can add the title as a comment
if stru.title.strip() != "":
title_lines = stru.title.split('\n')
lines.extend([ "# " + line.strip() for line in title_lines ])
lines.append("")
lines.append("data_3D")
iso_date = "%04i-%02i-%02i" % time.gmtime()[:3]
lines.extend([
"%-31s %s" % ("_audit_creation_date", iso_date),
"%-31s %s" % ("_audit_creation_method", "P_cif.py"),
"",
"%-31s %s" % ("_symmetry_space_group_name_H-M", "'P1'"),
"%-31s %s" % ("_symmetry_Int_Tables_number", "1"),
"%-31s %s" % ("_symmetry_cell_setting", "triclinic"),
"" ])
# there should be no need to specify equivalent positions for P1
# _symmetry_equiv_posi_as_xyz x,y,z
lines.extend([
"%-31s %.6g" % ("_cell_length_a", stru.lattice.a),
"%-31s %.6g" % ("_cell_length_b", stru.lattice.b),
"%-31s %.6g" % ("_cell_length_c", stru.lattice.c),
"%-31s %.6g" % ("_cell_angle_alpha", stru.lattice.alpha),
"%-31s %.6g" % ("_cell_angle_beta", stru.lattice.beta),
"%-31s %.6g" % ("_cell_angle_gamma", stru.lattice.gamma),
"" ])
# build a list of site labels and adp (displacement factor) types
element_count = {}
a_site_label = []
a_adp_type = []
for a in stru:
cnt = element_count[a.element] = element_count.get(a.element,0)+1
a_site_label.append( "%s%i" % (a.element, cnt) )
if numpy.all(a.U == a.U[0,0]*numpy.identity(3)):
a_adp_type.append("Uiso")
else:
a_adp_type.append("Uani")
# list all atoms
lines.extend([
"loop_",
" _atom_site_label",
" _atom_site_type_symbol",
" _atom_site_fract_x",
" _atom_site_fract_y",
" _atom_site_fract_z",
" _atom_site_U_iso_or_equiv",
" _atom_site_adp_type",
" _atom_site_occupancy" ])
for i in range(len(stru)):
a = stru[i]
line = " %-5s %-3s %11.6f %11.6f %11.6f %11.6f %-5s %.4f" % (
a_site_label[i], a.element, a.xyz[0], a.xyz[1], a.xyz[2],
a.Uisoequiv, a_adp_type[i], a.occupancy )
lines.append(line)
# find anisotropic atoms
idx_aniso = [ i for i in range(len(stru)) if a_adp_type[i] != "Uiso" ]
if idx_aniso != []:
lines.extend([
"loop_",
" _atom_site_aniso_label",
" _atom_site_aniso_U_11",
" _atom_site_aniso_U_22",
" _atom_site_aniso_U_33",
" _atom_site_aniso_U_12",
" _atom_site_aniso_U_13",
" _atom_site_aniso_U_23" ])
for i in idx_aniso:
a = stru[i]
line = " %-5s %9.6f %9.6f %9.6f %9.6f %9.6f %9.6f" % (
a_site_label[i], a.U[0,0], a.U[1,1], a.U[2,2],
a.U[0,1], a.U[0,2], a.U[1,2] )
lines.append(line)
return lines
def write_cif(crystal, fname):
"""
Generate an atomic coordinates .cif file from a crystal structure.
.. versionadded:: 1.2.0
Parameters
----------
crystal : crystals.Crystal
Crystal to be converted.
fname : path-like
The CIF file will be written to this file. If the file already exists,
it will be overwritten.
comment : str or None, optional
Comment to include at the second line of ``fname``.
"""
cf = CifFile(strict=False)
a, b, c, alpha, beta, gamma = crystal.lattice_parameters
lattice_items = {
"_cell_length_a": a,
"_cell_length_b": b,
"_cell_length_c": c,
"_cell_angle_alpha": alpha,
"_cell_angle_beta": beta,
"_cell_angle_gamma": gamma,
}
sym = crystal.symmetry()
symmetry_items = {
"_symmetry_Int_Tables_number": sym["international_number"],
"_symmetry_space_group_name_Hall": sym["hall_symbol"],
}
block = CifBlock()
for key, val in lattice_items.items():
block[key] = val
for key, val in symmetry_items.items():
block[key] = val
# Note that we are using all atoms in the unit-cell,
# and not the asymmetric unit cell + symmetry operators
# This is valid CIF! And it is much simpler to implement
# TODO: how to determine asymmetric cell + symmetry operations?
atoms = list(crystal.primitive().unitcell)
symbols = [atm.symbol for atm in atoms]
xf = [atm.coords_fractional[0] for atm in atoms]
yf = [atm.coords_fractional[1] for atm in atoms]
zf = [atm.coords_fractional[2] for atm in atoms]
block.CreateLoop(
datanames=[
"_atom_site_type_symbol",
"_atom_site_fract_x",
"_atom_site_fract_y",
"_atom_site_fract_z",
],
length_check=False,
)
block["_atom_site_type_symbol"] = symbols
block["_atom_site_fract_x"] = xf
block["_atom_site_fract_y"] = yf
block["_atom_site_fract_z"] = zf
# Name of the block cannot be empty!
block_name = crystal.chemical_formula.replace(" ", "_")
cf[block_name] = block
# Converting to string writes to stdout for some reason
with redirect_stdout(StringIO()):
lines = str(cf).splitlines()
with open(fname, "w", encoding="utf-8") as f:
f.write(CIF_HEADER)
f.write("\n".join(lines[13::])) # Skip the fixed header
def get_cif(self, find_symmetry: bool = False):
""" Get CIF format string
:params find_symmetry: if use Spglib to find symmetry. Default: False
"""
lattice = np.array(self.cell) * self.lat0 * BOHR_TO_A # in Cartesian
positions = []
numbers = []
magmoms = []
label = []
type_symbol = []
for index, elem in enumerate(self.elements):
num = self.numbers[elem]
for n in range(num):
numbers.append(index)
label.append(f"{elem}{n+1}")
type_symbol.append(f"{elem}")
# fractional atomic positions
positions.append(self.scaled_positions[elem][n])
magmoms.append(self.magmoms[elem])
if sum(magmoms):
spgcell = (lattice, positions, numbers, magmoms)
else:
spgcell = (lattice, positions, numbers)
from CifFile import CifBlock, CifFile
cf = CifFile()
cb = CifBlock()
cb['_cell_length_a'], cb['_cell_length_b'], cb['_cell_length_c'], cb[
'_cell_angle_alpha'], cb['_cell_angle_beta'], cb[
'_cell_angle_gamma'] = self.cellpar
from abacuskit.postprocess.symmetry import Spacegroup
if find_symmetry:
from spglib import get_symmetry_dataset
dataset = get_symmetry_dataset(spgcell)
if dataset:
cb['_atom_site_label'] = [
self.elements[i] for i in dataset['std_types']
]
cb['_atom_site_type_symbol'] = [
f"{self.elements[i]}{i}" for i in dataset['std_types']
]
number = dataset['number']
cb['_symmetry_cell_setting'] = Spacegroup().get_crystal_system(
number)
cb['_space_group_IT_number'] = number
cb['_space_group_name_H-M_alt'] = dataset['international']
cb['_space_group_name_Hall'] = dataset['hall']
x, y, z = np.split(dataset["std_positions"], 3, axis=1)
else:
cb['_atom_site_label'] = label
cb['_atom_site_type_symbol'] = type_symbol
cb['_symmetry_cell_setting'] = Spacegroup().get_crystal_system(
1)
cb['_space_group_IT_number'] = 1
cb['_space_group_name_H-M_alt'] = "P1"
cb['_space_group_name_Hall'] = "P 1"
x, y, z = np.split(np.array(positions), 3, axis=1)
else:
cb['_atom_site_label'] = label
cb['_atom_site_type_symbol'] = type_symbol
cb['_symmetry_cell_setting'] = Spacegroup().get_crystal_system(1)
cb['_space_group_IT_number'] = 1
cb['_space_group_name_H-M_alt'] = "P1"
cb['_space_group_name_Hall'] = "P 1"
x, y, z = np.split(np.array(positions), 3, axis=1)
cb['_atom_site_fract_x'], cb['_atom_site_fract_y'], cb[
'_atom_site_fract_z'] = x.flatten(), y.flatten(), z.flatten()
cb.CreateLoop([
'_atom_site_label', '_atom_site_type_symbol', '_atom_site_fract_x',
'_atom_site_fract_y', '_atom_site_fract_z'
])
cf['stru_to_cif'] = cb
return str(cf)
def read_cif(fNameIn):
logger = logging.getLogger()
data = {}
# Open the CIF file and read all the lines into a list of strings.
try:
f = open(fNameIn, 'r')
lines = []
oko_fix = False
for line in f:
stripped = line.strip()
if (len(stripped) > 0):
#fix for OKO
#http://stackoverflow.com/questions/79968/split-a-string-by-spaces-preserving-quoted-substrings-in-python
import shlex
if stripped[0] == '_':
cols = shlex.split(stripped) #shlex protects the quotation
if len(cols) > 2:
stripped = "{0} '{1}'".format(cols[0]," ".join(cols[1:]))
logger.debug("Line (Fixed): {0}".format(stripped))
oko_fix = True
lines.append(stripped)
if oko_fix:
fixedfilename = fNameIn + ".fix"
fixedfile = open(fixedfilename,"w")
fixedfile.write("\n".join(lines)+"\n")
fixedfile.close()
fNameIn = fixedfilename
except:
logger.error("Failed to open CIF file '{0}'".format(fNameIn))
sys.exit()
# Use the CifFile parser to extract the data. Although there might be
# multiple data blocks, we'll only use the first one.
cif_file = CifFile(fNameIn)
for db in cif_file:
data_block = db
break
try:
# Extract some parameters, and convert them to floats.
data['_cell_length_a'] = float_with_error(data_block['_cell_length_a'])
data['_cell_length_b'] = float_with_error(data_block['_cell_length_b'])
data['_cell_length_c'] = float_with_error(data_block['_cell_length_c'])
data['_cell_angle_alpha'] = float_with_error(data_block['_cell_angle_alpha'])
data['_cell_angle_beta'] = float_with_error(data_block['_cell_angle_beta'])
data['_cell_angle_gamma'] = float_with_error(data_block['_cell_angle_gamma'])
if data_block.has_key('_cell_volume'):
data['_cell_volume'] = float_with_error(data_block['_cell_volume'])
# Get the symbolic operations that define the space group. In a CIF file
# that's the part that looks like:
#
# loop_
# _symmetry_equiv_pos_as_xyz
# 'x,y,z'
# 'y,x,2/3-z'
# '-y,x-y,2/3+z'
# '-x,-x+y,1/3-z'
# '-x+y,-x,1/3+z'
# 'x-y,-y,-z'
#
# In some cases it's called "_space_group_symop_operation_xyz" apparently?!?!
data['_symmetry_equiv_pos_as_xyz'] = []
try:
xyz = data_block["_symmetry_equiv_pos_as_xyz"]
except KeyError:
try:
xyz = data_block["_space_group_symop_operation_xyz"]
except KeyError:
logger.error("Missing item in CIF file: need either '_symmetry_equiv_pos_as_xyz' or '_space_group_symop_operation_xyz'.")
sys.exit()
# Copy the x,y,z symmetry group operations. Remove the quotes if there
# are any.
for op_xyz in xyz:
if (op_xyz[0] == '\''):
data['_symmetry_equiv_pos_as_xyz'].append(op_xyz[1:-1])
else:
data['_symmetry_equiv_pos_as_xyz'].append(op_xyz)
# Add x,y,z of the atoms to "data", but make sure to convert
# e.g. "0.1549(8)" to "0.1549".
data['_atom_site_label'] = data_block['_atom_site_label']
data['_atom_site_fract_x'] = []
for str_x in data_block['_atom_site_fract_x']:
data['_atom_site_fract_x'].append( float_with_error(str_x))
data['_atom_site_fract_y'] = []
for str_y in data_block['_atom_site_fract_y']:
data['_atom_site_fract_y'].append( float_with_error(str_y))
data['_atom_site_fract_z'] = []
for str_z in data_block['_atom_site_fract_z']:
data['_atom_site_fract_z'].append( float_with_error(str_z))
except KeyError as e:
logger.error("Error! Missing item in file.")
logger.error(e)
sys.exit()
#print "ALL DATA:"
#print data
#print
# Return the extracted data.
return data
def prepareGulpInput(cifFile, gulpFile, jobName, verbose = False, auto_fractions = False):
"""
Example file:
mgh2
cell
4.5168 4.5168 3.0205 90.0 90.0 90.0
frac
Mg 0.0 0.0 0.0
H 0.306 0.306 0.0
space
136
output xyz mgh2
"""
from CifFile import CifFile
if not os.path.exists(cifFile):
raise IOError("CIF file '%s' was not found!" % (cifFile))
cf = CifFile(cifFile)
if verbose:
print "------------------------------------------------------------------"
if len(cf) != 1:
raise StandardError("The cif file contains %i data blocks, while one was expected")
# A cif file can contain several "datablocks" that each start
# with "data_".
if verbose:
print "Reading data block '%s'..." % (cf.keys()[0])
cb = cf[cf.keys()[0]] # open the first block
AA = float(re.match('([0-9.e]*)',cb['_cell_length_a']).group(0))
BB = float(re.match('([0-9.e]*)',cb['_cell_length_b']).group(0))
CC = float(re.match('([0-9.e]*)',cb['_cell_length_c']).group(0))
alpha = float(cb['_cell_angle_alpha'])
beta = float(cb['_cell_angle_beta'])
gamma = float(cb['_cell_angle_gamma'])
# Spacegroup number (1-230)
# '_symmetry_Int_Tables_number' has been superseded by '_space_group_IT_number'
if '_space_group_IT_number' in cb.keys():
SG = int(cb['_space_group_IT_number'])
elif '_symmetry_Int_Tables_number' in cb.keys():
SG = int(cb['_symmetry_Int_Tables_number'])
else:
print "WARNING: No space group specified. Assuming P1."
SG = 1
# CCTBX:
#unit_cell = uctbx.unit_cell([AA,BB,CC,alpha,beta,gamma])
#space_group_info = sgtbx.space_group_info(symbol=cb['_symmetry_space_group_name_H-M'])
#crystal_symmetry = crystal.symmetry(unit_cell=unit_cell,space_group_info=space_group_info)
#print "CIF file read successfully:"
#crystal_symmetry.show_summary()
if verbose:
print " Space group:",SG
print " a=%s, b=%s, c=%s, alpha=%s, beta=%s, gamma=%s" % (AA,BB,CC,alpha,beta,gamma)
atomTypes = []
atoms = ''
fracOccFound = False
firstAtom = True
atoms = ""
# The coordinates of the atom (_atom_site_fract_x/y/z) may have
# a last digit in parenthesis, like "-0.6636(7)". Therefore we
# extract the part consisting of only digits and a decimal separator:
coordsMatch = re.compile('[0-9.e-]*');
for atom in cb.GetLoop('_atom_site_label'):
atomKeys = dir(atom)
if '_atom_site_type_symbol' in atomKeys:
m = re.match('[a-z]*',atom._atom_site_type_symbol,re.I)
atomType = m.group(0)
else:
m = re.match('[a-z]*',atom._atom_site_label,re.I)
atomType = m.group(0)
if '_atom_site_occupancy' in atomKeys:
occ = float(coordsMatch.match(atom._atom_site_occupancy).group())
if not occ == 1.0:
if not fracOccFound:
print " "
print " WARNING: Fractional occupancy (" + str(occ) +") " \
+ "found for atom of type " + atomType + "."
fracOccFound = True
else:
occ = 1.0
# Some crystal structures obtained by neutron diffraction use D for H:
if atomType == 'D':
atomType = 'H'
if '_atom_site_symmetry_multiplicity' in atomKeys and '_atom_site_Wyckoff_symbol' in atomKeys:
atomTypes.append(atomType+' at '+atom._atom_site_symmetry_multiplicity+atom._atom_site_Wyckoff_symbol)
else:
atomTypes.append(atomType)
atomX = coordsMatch.match(atom._atom_site_fract_x).group()
atomY = coordsMatch.match(atom._atom_site_fract_y).group()
atomZ = coordsMatch.match(atom._atom_site_fract_z).group()
atomPos = [atomX, atomY, atomZ]
for i in range(3):
pp = atomPos[i].split(".")
if len(pp) is 2:
decimals = pp[1]
if len(decimals) > 3 and len(decimals) < 6 and decimals[0] == decimals[1] and decimals[0] == decimals[2] and decimals[-1] != "0":
if auto_fractions:
oldPos = atomPos[i]
atomPos[i] = "%.6f" % (float(eval('1.*'+float2fraction(atomPos[i]))))
print " Notice: Converted %s into %s" %(oldPos,atomPos[i])
else:
print "\n"\
+ " ! Warning: The coordinate "+atomPos[i]+" looks similar to the fraction %s, but\n" % float2fraction(atomPos[i]) \
+ " ! has insufficient decimals to be recognized as so by GULP. If you want\n" \
+ " ! this coordinate to be recognized as a special high-symmetry position,\n" \
+ " ! you need to specify at least six digits. If you run cif2vasp with the \n" \
+ " ! -f switch, cif2vasp will try to add the necessary decimals automaticly."
atoms += "%s %s %s %s %f %f\n" % (atomType, atomPos[0], atomPos[1], atomPos[2], 0.0, occ)
firstAtom = False
if fracOccFound:
print " "
print "ERROR: Fractional occupancies are not currently supported.\n"
exit()
if verbose:
print " Atom types: " + ', '.join(atomTypes)
gulpFile = open(gulpFile,'w') #Create and write the GULP
gulpFile.writelines([jobName+'\n',
'cell\n',
'%s %s %s %s %s %s\n' % (AA,BB,CC,alpha,beta,gamma),
'frac\n',
atoms,
'space\n',
str(SG)+'\n',
'output xyz '+jobName+'\n'
])
def readCifFile(cifFile):
from CifFile import CifFile
if not os.path.exists(cifFile):
raise IOError("CIF file '%s' was not found!" % (cifFile))
cf = CifFile(cifFile)
print "------------------------------------------------------------------"
if len(cf) != 1:
raise StandardError("The cif file contains %i data blocks, while one was expected")
# A cif file can contain several "datablocks" that each start
# with "data_".
cb = cf[cf.keys()[0]] # open the first block
AA = float(re.match('([0-9.]*)',cb['_cell_length_a']).group(0))
BB = float(re.match('([0-9.]*)',cb['_cell_length_b']).group(0))
CC = float(re.match('([0-9.]*)',cb['_cell_length_c']).group(0))
alpha = float(cb['_cell_angle_alpha'])
beta = float(cb['_cell_angle_beta'])
gamma = float(cb['_cell_angle_gamma'])
SG = int(cb['_symmetry_Int_Tables_number']) # spacegroup
atomTypes = []
atoms = ''
fracOccFound = False
firstAtom = True
atoms = []
for atom in cb.GetLoop('_atom_site_label'):
atomKeys = dir(atom)
if '_atom_site_type_symbol' in atomKeys:
m = re.match('[a-z]*',atom._atom_site_type_symbol,re.I)
atomType = m.group(0)
else:
m = re.match('[a-z]*',atom._atom_site_label,re.I)
atomType = m.group(0)
atomLabel = atom._atom_site_label
if '_atom_site_occupancy' in atomKeys:
occ = float(atom._atom_site_occupancy)
if not occ == 1.0:
if not fracOccFound:
print " "
print " WARNING: Fractional occupancy (" + str(occ) +") " \
+ "found for atom of type " + atomType + "."
fracOccFound = True
else:
occ = 1.0
# Some crystal structures obtained by neutron diffraction use D for H:
if atomType == 'D':
atomType = 'H'
atomLabel.replace('H','D')
if '_atom_site_symmetry_multiplicity' in atomKeys and '_atom_site_Wyckoff_symbol' in atomKeys:
atomTypes.append(atomType+' at '+atom._atom_site_symmetry_multiplicity+atom._atom_site_Wyckoff_symbol)
else:
atomTypes.append(atomType)
atomPos = [atom._atom_site_fract_x, atom._atom_site_fract_y, atom._atom_site_fract_z]
for p in atomPos:
pp = p.split(".")
if len(pp) is 2:
decimals = p.split(".")[1]
if len(decimals) > 3 and len(decimals) < 6 and decimals[0] == decimals[1] and decimals[-1] != "0":
print "\n ---------------------\n"\
+ " Warning: If the fractional coordinate "+p+" is a recurring decimal, such as 1/3,\n" \
+ " then it is necessary to specify this value to six decimal places to be sure of \n" \
+ " it being recognised correctly as a spcecial position.\n ------------------"
# The coordinates of the atom (_atom_site_fract_x/y/z) may have
# a last digit in parenthesis, like "0.6636(7)". Therefore we
# extract the part consisting of only digits and a decimal separator:
p = re.compile('[0-9.]*');
atomX = float(p.match(atom._atom_site_fract_x).group())
atomY = float(p.match(atom._atom_site_fract_y).group())
atomZ = float(p.match(atom._atom_site_fract_z).group())
#atoms += "%s %f %f %f %f %f\n" % (atomType, atomX, atomY, atomZ, 0.0, occ)
atoms.append({'label': atomLabel, 'type': atomType, 'pos': (atomX,atomY,atomZ) })
firstAtom = False
if fracOccFound:
print " "
print "ERROR: Fractional occupancies are not currently supported.\n"
exit()
print " Atom types: " + ', '.join(atomTypes)
return {'spacegroup': SG, 'unit_cell': [AA,BB,CC,alpha,beta,gamma], 'scatterers': atoms}
# prepare a cursor object using cursor() method
cursor = db.cursor()
sql = "select file from data"
cursor.execute(sql)
allFiles = cursor.fetchall()
for i in range(0, len(allFiles)):
fileNum = str(allFiles[i][0])
fileName = "%s.cif" % fileNum
dir_level1 = fileNum[0]
dir_level2 = fileNum[1:3]
dir_level3 = fileNum[3:5]
cif_full_dir = os.path.join(cif_dir, dir_level1, dir_level2, dir_level3)
cif_full_file = os.path.join(cif_full_dir, fileName)
if (not os.path.exists(cif_full_file)):
raise IOError("CIF file '%s' was not found!" % (fileName))
else:
cf = CifFile(cif_full_file)
cb = cf[cf.keys()[0]]
cb['_symmetry_cell_setting']
cb['_symmetry_space_group_name_Hall']
cb['_symmetry_space_group_name_H-M']
cb['_atom_site_label']
cb['_atom_site_fract_x']
cb['_atom_site_fract_y']
cb['_atom_site_fract_z']
class P_cif(StructureParser):
"""Simple parser for CIF structure format.
Reads Structure from the first block containing _atom_site_label key.
Following blocks, if any are ignored.
Data members:
format -- structure format name
ciffile -- instance of CifFile from PyCifRW
stru -- Structure instance used for cif input or output
Data members used for input only:
spacegroup -- instance of SpaceGroup used for symmetry expansion
eps -- resolution in fractional coordinates for non-equal
positions. Use for expansion of asymmetric unit.
eau -- instance of ExpandAsymmetricUnit from SymmetryUtilities
asymmetric_unit -- list of atom instances for the original asymmetric
unit in the CIF file
labelindex -- dictionary mapping unique atom label to index of atom
in self.asymmetric_unit
cif_sgname -- space group name obtained by looking up the value of
_space_group_name_Hall, _symmetry_space_group_name_Hall,
_space_group_name_H-M_alt, _symmetry_space_group_name_H-M
items. None when neither is defined.
"""
# static data and methods ------------------------------------------------
# dictionary set of class methods for translating CIF values
# to Atom attributes
_atom_setters = dict.fromkeys((
'_tr_ignore',
'_tr_atom_site_label',
'_tr_atom_site_type_symbol',
'_tr_atom_site_fract_x',
'_tr_atom_site_fract_y',
'_tr_atom_site_fract_z',
'_tr_atom_site_cartn_x',
'_tr_atom_site_cartn_y',
'_tr_atom_site_cartn_z',
'_tr_atom_site_U_iso_or_equiv',
'_tr_atom_site_B_iso_or_equiv',
'_tr_atom_site_adp_type', '_tr_atom_site_thermal_displace_type',
'_tr_atom_site_occupancy',
'_tr_atom_site_aniso_U_11',
'_tr_atom_site_aniso_U_22',
'_tr_atom_site_aniso_U_33',
'_tr_atom_site_aniso_U_12',
'_tr_atom_site_aniso_U_13',
'_tr_atom_site_aniso_U_23',
'_tr_atom_site_aniso_B_11',
'_tr_atom_site_aniso_B_22',
'_tr_atom_site_aniso_B_33',
'_tr_atom_site_aniso_B_12',
'_tr_atom_site_aniso_B_13',
'_tr_atom_site_aniso_B_23',
))
# make _atom_setters case insensitive
for k in list(_atom_setters.keys()):
_atom_setters[k] = _atom_setters[k.lower()] = k
del k
BtoU = 1.0/(8 * numpy.pi**2)
def _tr_ignore(a, value):
return
_tr_ignore = staticmethod(_tr_ignore)
def _tr_atom_site_label(a, value):
a.label = str(value)
# set element when not specified by _atom_site_type_symbol
if not a.element:
P_cif._tr_atom_site_type_symbol(a, value)
_tr_atom_site_label = staticmethod(_tr_atom_site_label)
# 3 regexp groups for nucleon number, atom symbol, and oxidation state
_psymb = re.compile(r'(\d+-)?([a-zA-Z]+)(\d[+-])?')
def _tr_atom_site_type_symbol(a, value):
rx = P_cif._psymb.match(value)
smbl = rx and rx.group(0) or value
smbl = str(smbl)
a.element = smbl[:1].upper() + smbl[1:].lower()
_tr_atom_site_type_symbol = staticmethod(_tr_atom_site_type_symbol)
def _tr_atom_site_fract_x(a, value):
a.xyz[0] = leading_float(value)
_tr_atom_site_fract_x = staticmethod(_tr_atom_site_fract_x)
def _tr_atom_site_fract_y(a, value):
a.xyz[1] = leading_float(value)
_tr_atom_site_fract_y = staticmethod(_tr_atom_site_fract_y)
def _tr_atom_site_fract_z(a, value):
a.xyz[2] = leading_float(value)
_tr_atom_site_fract_z = staticmethod(_tr_atom_site_fract_z)
def _tr_atom_site_cartn_x(a, value):
a.xyz_cartn[0] = leading_float(value)
_tr_atom_site_cartn_x = staticmethod(_tr_atom_site_cartn_x)
def _tr_atom_site_cartn_y(a, value):
a.xyz_cartn[1] = leading_float(value)
_tr_atom_site_cartn_y = staticmethod(_tr_atom_site_cartn_y)
def _tr_atom_site_cartn_z(a, value):
a.xyz_cartn[2] = leading_float(value)
_tr_atom_site_cartn_z = staticmethod(_tr_atom_site_cartn_z)
def _tr_atom_site_U_iso_or_equiv(a, value):
a.Uisoequiv = leading_float(value)
_tr_atom_site_U_iso_or_equiv = staticmethod(_tr_atom_site_U_iso_or_equiv)
def _tr_atom_site_B_iso_or_equiv(a, value):
a.Uisoequiv = P_cif.BtoU * leading_float(value)
_tr_atom_site_B_iso_or_equiv = staticmethod(_tr_atom_site_B_iso_or_equiv)
def _tr_atom_site_adp_type(a, value):
a.anisotropy = value not in ("Uiso", "Biso")
_tr_atom_site_adp_type = staticmethod(_tr_atom_site_adp_type)
_tr_atom_site_thermal_displace_type = _tr_atom_site_adp_type
def _tr_atom_site_occupancy(a, value):
a.occupancy = leading_float(value, 1.0)
_tr_atom_site_occupancy = staticmethod(_tr_atom_site_occupancy)
def _tr_atom_site_aniso_U_11(a, value):
a.U11 = leading_float(value)
_tr_atom_site_aniso_U_11 = staticmethod(_tr_atom_site_aniso_U_11)
def _tr_atom_site_aniso_U_22(a, value):
a.U22 = leading_float(value)
_tr_atom_site_aniso_U_22 = staticmethod(_tr_atom_site_aniso_U_22)
def _tr_atom_site_aniso_U_33(a, value):
a.U33 = leading_float(value)
_tr_atom_site_aniso_U_33 = staticmethod(_tr_atom_site_aniso_U_33)
def _tr_atom_site_aniso_U_12(a, value):
a.U12 = leading_float(value)
_tr_atom_site_aniso_U_12 = staticmethod(_tr_atom_site_aniso_U_12)
def _tr_atom_site_aniso_U_13(a, value):
a.U13 = leading_float(value)
_tr_atom_site_aniso_U_13 = staticmethod(_tr_atom_site_aniso_U_13)
def _tr_atom_site_aniso_U_23(a, value):
a.U23 = leading_float(value)
_tr_atom_site_aniso_U_23 = staticmethod(_tr_atom_site_aniso_U_23)
def _tr_atom_site_aniso_B_11(a, value):
a.U11 = P_cif.BtoU * leading_float(value)
_tr_atom_site_aniso_B_11 = staticmethod(_tr_atom_site_aniso_B_11)
def _tr_atom_site_aniso_B_22(a, value):
a.U22 = P_cif.BtoU * leading_float(value)
_tr_atom_site_aniso_B_22 = staticmethod(_tr_atom_site_aniso_B_22)
def _tr_atom_site_aniso_B_33(a, value):
a.U33 = P_cif.BtoU * leading_float(value)
_tr_atom_site_aniso_B_33 = staticmethod(_tr_atom_site_aniso_B_33)
def _tr_atom_site_aniso_B_12(a, value):
a.U12 = P_cif.BtoU * leading_float(value)
_tr_atom_site_aniso_B_12 = staticmethod(_tr_atom_site_aniso_B_12)
def _tr_atom_site_aniso_B_13(a, value):
a.U13 = P_cif.BtoU * leading_float(value)
_tr_atom_site_aniso_B_13 = staticmethod(_tr_atom_site_aniso_B_13)
def _tr_atom_site_aniso_B_23(a, value):
a.U23 = P_cif.BtoU * leading_float(value)
_tr_atom_site_aniso_B_23 = staticmethod(_tr_atom_site_aniso_B_23)
def _get_atom_setters(cifloop):
"""Find translators of CifLoop items to data in Atom instance.
Static method.
cifloop -- instance of CifLoop
Return a list of setter functions in the order of cifloop.keys().
"""
rv = []
for p in cifloop.keys():
lcname = "_tr" + p.lower()
fncname = P_cif._atom_setters.get(lcname, '_tr_ignore')
f = getattr(P_cif, fncname)
rv.append(f)
return rv
_get_atom_setters = staticmethod(_get_atom_setters)
# normal methods ---------------------------------------------------------
def __init__(self, eps=None):
"""Initialize the parser for CIF structure files.
eps -- fractional coordinates cutoff for duplicate positions.
When None use the default for ExpandAsymmetricUnit.
"""
StructureParser.__init__(self)
self.format = "cif"
self.ciffile = None
self.stru = None
self.spacegroup = None
self.eps = eps
self.eau = None
self.asymmetric_unit = None
self.labelindex = {}
self.cif_sgname = None
pass
def parse(self, s):
"""Create Structure instance from a string in CIF format.
Return Structure instance or raise StructureFormatError.
"""
self.ciffile = None
self.filename = ''
fp = six.StringIO(s)
rv = self._parseCifDataSource(fp)
return rv
def parseLines(self, lines):
"""Parse list of lines in CIF format.
lines -- list of strings stripped of line terminator
Return Structure instance or raise StructureFormatError.
"""
s = "\n".join(lines) + '\n'
return self.parse(s)
def parseFile(self, filename):
"""Create Structure from an existing CIF file.
filename -- path to structure file
Return Structure object.
Raise StructureFormatError or IOError.
"""
self.ciffile = None
self.filename = filename
fileurl = _fixIfWindowsPath(filename)
rv = self._parseCifDataSource(fileurl)
# all good here
return rv
def _parseCifDataSource(self, datasource):
"""\
Open and process CIF data from the specified `datasource`.
Parameters
----------
datasource : str or a file-like object
This is used as an argument to the CifFile class. The CifFile
instance is stored in `ciffile` attribute of this Parser.
Returns
-------
Structure
The Structure object loaded from the specified data source.
Raises
------
StructureFormatError
When the data do not constitute a valid CIF format.
"""
from CifFile import CifFile, StarError
self.stru = None
try:
with _suppressCifParserOutput():
self.ciffile = CifFile(datasource)
for blockname in self.ciffile.keys():
self._parseCifBlock(blockname)
# stop after reading the first structure
if self.stru is not None:
break
except (StarError, ValueError, IndexError) as err:
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = str(err).strip()
e = StructureFormatError(emsg)
six.reraise(StructureFormatError, e, exc_traceback)
return self.stru
def _parseCifBlock(self, blockname):
"""Translate CIF file block, skip blocks without _atom_site_label.
Updates data members stru, eau.
blockname -- name of top level block in self.ciffile
No return value.
"""
block = self.ciffile[blockname]
if '_atom_site_label' not in block: return
# here block contains structure, initialize output data
self.stru = Structure()
self.labelindex.clear()
# execute specialized block parsers
self._parse_lattice(block)
self._parse_atom_site_label(block)
self._parse_atom_site_aniso_label(block)
self._parse_space_group_symop_operation_xyz(block)
return
def _parse_lattice(self, block):
"""Obtain lattice parameters from a CifBlock.
This method updates self.stru.lattice.
block -- instance of CifBlock
No return value.
"""
if '_cell_length_a' not in block: return
# obtain lattice parameters
try:
latpars = (
leading_float(block['_cell_length_a']),
leading_float(block['_cell_length_b']),
leading_float(block['_cell_length_c']),
leading_float(block['_cell_angle_alpha']),
leading_float(block['_cell_angle_beta']),
leading_float(block['_cell_angle_gamma']),
)
except KeyError as err:
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = str(err)
e = StructureFormatError(emsg)
six.reraise(StructureFormatError, e, exc_traceback)
self.stru.lattice = Lattice(*latpars)
return
def _parse_atom_site_label(self, block):
"""Obtain atoms in asymmetric unit from a CifBlock.
This method inserts Atom instances to self.stru and
updates labelindex dictionary.
block -- instance of CifBlock
No return value.
"""
# process _atom_site_label
atom_site_loop = block.GetLoop('_atom_site_label')
# get a list of setters for atom_site values
prop_setters = P_cif._get_atom_setters(atom_site_loop)
# index of the _atom_site_label item for the labelindex dictionary
ilb = atom_site_loop.keys().index('_atom_site_label')
# loop through the values and pass them to the setters
sitedatalist = zip(*atom_site_loop.values())
for values in sitedatalist:
curlabel = values[ilb]
# skip entries that have invalid label
if curlabel == '?':
continue
self.labelindex[curlabel] = len(self.stru)
self.stru.addNewAtom()
a = self.stru.getLastAtom()
for fset, val in zip(prop_setters, values):
fset(a, val)
return
def _parse_atom_site_aniso_label(self, block):
"""Obtain value of anisotropic thermal displacements from a CifBlock.
This method updates U members of Atom instances in self.stru.
The labelindex dictionary has to be defined beforehand.
block -- instance of CifBlock
No return value.
"""
if '_atom_site_aniso_label' not in block: return
# was anisotropy set in the _atom_site_label loop?
atom_site_loop = block.GetLoop('_atom_site_label')
anisotropy_already_set = (
'_atom_site_adp_type' in atom_site_loop or
'_atom_site_thermal_displace_type' in atom_site_loop)
# something to do here:
adp_loop = block.GetLoop('_atom_site_aniso_label')
# index of the _atom_site_label column
ilb = adp_loop.keys().index('_atom_site_aniso_label')
# get a list of setters for this loop
prop_setters = P_cif._get_atom_setters(adp_loop)
sitedatalist = zip(*adp_loop.values())
for values in sitedatalist:
idx = self.labelindex[values[ilb]]
a = self.stru[idx]
if not anisotropy_already_set:
a.anisotropy = True
for fset, val in zip(prop_setters, values):
fset(a, val)
return
def _parse_space_group_symop_operation_xyz(self, block):
"""Process symmetry operations from a CifBlock. The method
updates spacegroup and eau data according to symmetry
operations defined in _space_group_symop_operation_xyz or
_symmetry_equiv_pos_as_xyz items in CifBlock.
block -- instance of CifBlock
No return value.
"""
from diffpy.structure.spacegroups import IsSpaceGroupIdentifier
from diffpy.structure.spacegroups import SpaceGroup, GetSpaceGroup
self.asymmetric_unit = list(self.stru)
sym_synonyms = ('_space_group_symop_operation_xyz',
'_symmetry_equiv_pos_as_xyz')
sym_loop_name = [n for n in sym_synonyms if n in block]
# recover explicit list of symmetry operations
symop_list = []
if sym_loop_name:
# sym_loop exists here and we know its cif name
sym_loop_name = sym_loop_name[0]
sym_loop = block.GetLoop(sym_loop_name)
for eqxyz in sym_loop[sym_loop_name]:
opcif = getSymOp(eqxyz)
symop_list.append(opcif)
# determine space group number
sg_nameHall = (block.get('_space_group_name_Hall', '') or
block.get('_symmetry_space_group_name_Hall', ''))
sg_nameHM = (block.get('_space_group_name_H-M_alt', '') or
block.get('_symmetry_space_group_name_H-M', ''))
self.cif_sgname = (sg_nameHall or sg_nameHM or None)
sgid = (int(block.get('_space_group_IT_number', '0')) or
int(block.get('_symmetry_Int_Tables_number', '0')) or
sg_nameHM)
# try to reuse existing space group
self.spacegroup = None
if sgid and IsSpaceGroupIdentifier(sgid):
sgstd = GetSpaceGroup(sgid)
oprep_std = [str(op) for op in sgstd.iter_symops()]
oprep_std.sort()
oprep_cif = [str(op) for op in symop_list]
oprep_cif.sort()
# make sure symmetry operations have the same order
if oprep_std == oprep_cif:
self.spacegroup = copy.copy(sgstd)
self.spacegroup.symop_list = symop_list
# use standard definition when symmetry operations were not listed
elif not symop_list:
self.spacegroup = sgstd
# define new spacegroup when symmetry operations were listed, but
# there is no match to an existing definition
if symop_list and self.spacegroup is None:
new_short_name = "CIF " + (sg_nameHall or 'data')
new_crystal_system = (
block.get('_space_group_crystal_system') or
block.get('_symmetry_cell_setting') or
'TRICLINIC' ).upper()
self.spacegroup = SpaceGroup(
short_name=new_short_name,
crystal_system=new_crystal_system,
symop_list=symop_list)
if self.spacegroup is None:
emsg = "CIF file has unknown space group identifier {!r}."
raise StructureFormatError(emsg.format(sgid))
self._expandAsymmetricUnit()
return
def _expandAsymmetricUnit(self):
"""Perform symmetry expansion of self.stru using self.spacegroup.
This method updates data in stru and eau.
No return value.
"""
from diffpy.structure.symmetryutilities import ExpandAsymmetricUnit
# get reverse-ordered unique indices
corepos = [a.xyz for a in self.stru]
coreUijs = [a.U for a in self.stru]
self.eau = ExpandAsymmetricUnit(self.spacegroup, corepos, coreUijs,
eps=self.eps)
# build a nested list of new atoms:
newatoms = []
for i, ca in enumerate(self.stru):
eca = [] # expanded core atom
for j in range(self.eau.multiplicity[i]):
a = Atom(ca)
a.xyz = self.eau.expandedpos[i][j]
if j > 0:
a.label += '_' + str(j + 1)
if a.anisotropy:
a.U = self.eau.expandedUijs[i][j]
eca.append(a)
newatoms.append(eca)
# insert new atoms where they belong
self.stru[:] = sum(newatoms, [])
return
# conversion to CIF ------------------------------------------------------
def toLines(self, stru):
"""Convert Structure stru to a list of lines in basic CIF format.
Return list of strings.
"""
import time
lines = []
# may be replaced with filtered Structure.title
# for now, we can add the title as a comment
if stru.title.strip() != "":
title_lines = stru.title.split('\n')
lines.extend([ "# " + line.strip() for line in title_lines ])
lines.append("")
lines.append("data_3D")
iso_date = "%04i-%02i-%02i" % time.gmtime()[:3]
lines.extend([
"%-31s %s" % ("_audit_creation_date", iso_date),
"%-31s %s" % ("_audit_creation_method", "P_cif.py"),
"",
"%-31s %s" % ("_symmetry_space_group_name_H-M", "'P1'"),
"%-31s %s" % ("_symmetry_Int_Tables_number", "1"),
"%-31s %s" % ("_symmetry_cell_setting", "triclinic"),
"" ])
# there should be no need to specify equivalent positions for P1
# _symmetry_equiv_posi_as_xyz x,y,z
lines.extend([
"%-31s %.6g" % ("_cell_length_a", stru.lattice.a),
"%-31s %.6g" % ("_cell_length_b", stru.lattice.b),
"%-31s %.6g" % ("_cell_length_c", stru.lattice.c),
"%-31s %.6g" % ("_cell_angle_alpha", stru.lattice.alpha),
"%-31s %.6g" % ("_cell_angle_beta", stru.lattice.beta),
"%-31s %.6g" % ("_cell_angle_gamma", stru.lattice.gamma),
"" ])
# build a list of site labels and adp (displacement factor) types
element_count = {}
a_site_label = []
a_adp_type = []
for a in stru:
cnt = element_count[a.element] = element_count.get(a.element,0)+1
a_site_label.append( "%s%i" % (a.element, cnt) )
if numpy.all(a.U == a.U[0,0]*numpy.identity(3)):
a_adp_type.append("Uiso")
else:
a_adp_type.append("Uani")
# list all atoms
lines.extend([
"loop_",
" _atom_site_label",
" _atom_site_type_symbol",
" _atom_site_fract_x",
" _atom_site_fract_y",
" _atom_site_fract_z",
" _atom_site_U_iso_or_equiv",
" _atom_site_adp_type",
" _atom_site_occupancy" ])
for i in range(len(stru)):
a = stru[i]
line = " %-5s %-3s %11.6f %11.6f %11.6f %11.6f %-5s %.4f" % (
a_site_label[i], a.element, a.xyz[0], a.xyz[1], a.xyz[2],
a.Uisoequiv, a_adp_type[i], a.occupancy )
lines.append(line)
# find anisotropic atoms
idx_aniso = [ i for i in range(len(stru)) if a_adp_type[i] != "Uiso" ]
if idx_aniso != []:
lines.extend([
"loop_",
" _atom_site_aniso_label",
" _atom_site_aniso_U_11",
" _atom_site_aniso_U_22",
" _atom_site_aniso_U_33",
" _atom_site_aniso_U_12",
" _atom_site_aniso_U_13",
" _atom_site_aniso_U_23" ])
for i in idx_aniso:
a = stru[i]
line = " %-5s %9.6f %9.6f %9.6f %9.6f %9.6f %9.6f" % (
a_site_label[i], a.U[0,0], a.U[1,1], a.U[2,2],
a.U[0,1], a.U[0,2], a.U[1,2] )
lines.append(line)
return lines
