except IOError, (errno, strerror): print "I/O error(%s): %s" % (errno, strerror) string = ifile.readlines() cell_params = [] cell_dict = {} for parser in cell_parsers: for data, dataStart, dataEnd in parser.scanString(string): cell_params.append(data[1]) cell_dict[data[0]]=data[1] ifile.close() ### end of fix t=Translator() t.filenameIn = fileInString ciflist = t.cifToAtomAndCoordinateList() cellvectors = MInv(cell_params) uc = UnitCell(cellvectors) for item in ciflist: X = item[0] pos = [float(x) for x in item[1:4]] uc.addAtom(Atom(symbol=X), pos, "") # Note: this only works if elements' symbols in CIF are "Ab" format
ifile = open(fileInString, 'r') except IOError, (errno, strerror): print "I/O error(%s): %s" % (errno, strerror) string = ifile.readlines() cell_params = [] cell_dict = {} for parser in cell_parsers: for data, dataStart, dataEnd in parser.scanString(string): cell_params.append(data[1]) cell_dict[data[0]] = data[1] ifile.close() ### end of fix t = Translator() t.filenameIn = fileInString ciflist = t.cifToAtomAndCoordinateList() cellvectors = MInv(cell_params) uc = UnitCell(cellvectors) for item in ciflist: X = item[0] pos = [float(x) for x in item[1:4]] uc.addAtom(Atom(symbol=X), pos, "") # Note: this only works if elements' symbols in CIF are "Ab" format