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cifEditor.py
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cifEditor.py
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import pymongo
from pymatgen.io.cif import CifParser, CifFile
import re
import json
from pymatgen import DummySpecie, Composition
client = pymongo.MongoClient()
db = client.springer
def handle_missingdata(cif_string):
"""
Handles CIF parsing errors arising from missing elemental data.
:param cif_string: (str) cif file
:return: corrected cif string
"""
cif_lines = json.loads(json.dumps(cif_string)).splitlines()
noelemdata = True
for i, line in enumerate(cif_lines):
if '_sm_atomic_environment_type' in line:
if '? ?' not in cif_lines[i + 1]:
noelemdata = False
break
if noelemdata:
print 'Sucessful'
db['pauling_file_unique_Parse'].update({'key': doc['key']},
{'$addToSet': {'errors': ['cif missing element data']}})
else:
print 'Some other error in cif'
def handle_insufficientpowderdata(cif_string):
"""
Handles CIF parsing errors arising from too few or too many values in data loop for diffraction data.
:param cif_string: (str) cif file
:return: corrected cif string
"""
smlineno = 0
looplineno = 0
cif_lines = json.loads(json.dumps(cif_string)).splitlines()
powderdataline = False
loopdataline = False
cif_string_new = ''
for lineno, line in enumerate(cif_lines):
if '_sm_powderpattern_remark' in line:
powderdataline = True
smlineno = lineno + 1
break
else:
cif_string_new += line + '\n'
if powderdataline:
for line in cif_lines[smlineno:]:
line_list = line.split()
if len(line_list) > 10:
cif_string_new += line + '\n'
elif 1 < len(line_list) < 11:
cif_string_new += '#' + line + '\n'
try:
print CifParser.from_string(cif_string_new).get_structures()[0].as_dict()
return cif_string_new
except:
print 'UNSUCCESSFUL 1st attempt (uncommenting lines with insufficient or too many values for powder pattern)'
cif_string_new = ''
for lineno, line in enumerate(cif_lines):
if 'loop_' in line:
if '_sm_powderpattern' in cif_lines[lineno + 1]:
cif_string_new += '#' + line + '\n'
loopdataline = True
looplineno = lineno + 1
break
else:
cif_string_new += line + '\n'
else:
cif_string_new += line + '\n'
if loopdataline:
for line in cif_lines[looplineno:]:
cif_string_new += '#' + line + '\n'
try:
print CifParser.from_string(cif_string_new).get_structures()[0].as_dict()
return cif_string_new
except:
print 'UNSUCCESSFUL 2nd attempt (uncommenting all powder diffraction lines)'
return cif_string_new
def handle_partialocclables(cif_string):
"""
Handles CIF parsing errors arising from atom labels containing partial occupancy numbers
:param cif_string: (str) cif file
:return: corrected cif string
"""
cif_lines = json.loads(json.dumps(cif_string)).splitlines()
cif_string_new = ''
for line in cif_lines:
if ' + ' in line and len(line) < 150:
try:
newline = '#' + line
cif_string_new += newline + '\n'
matching_list = re.findall(r'\'(.+?)\'', line)
elemocc = matching_list[0].split('+')
elems = []
occupancies = []
for i in range(len(elemocc)):
occupancies.append('0' + re.findall('\.?\d+', elemocc[i].strip())[1])
if 'OH' in elemocc[i]:
c = re.findall('OH.*', elemocc[i].strip())
elems.append(c[0])
else:
c = re.findall('\D+', elemocc[i].strip())
elems.append(c[1])
occ_sum = 0
for i in range(len(occupancies)):
occ_sum += float(occupancies[i])
if occ_sum != 1:
sum_exc_last = 0
for i in range(len(occupancies) - 1):
sum_exc_last += float(occupancies[i])
occupancies[-1] = str(1 - sum_exc_last)
for i in range(len(elems)):
oldline = line
old_elemline = oldline.replace("'" + matching_list[0] + "'", "'" + elems[i] + "'")
new_elemline_list = old_elemline.split()
new_elemline_list[0] = elems[i]
new_elemline_list[7] = occupancies[i]
new_elemline_list.append('\n')
new_elemline = ' '.join(new_elemline_list)
cif_string_new += new_elemline
except:
break
else:
cif_string_new += line + '\n'
return cif_string_new
def handle_partialoccbracketlables(cif_string):
"""
Handles CIF parsing errors arising from atom labels containing partial occupancy numbers and brackets
:param cif_string: (str) cif file
:return: corrected cif string
"""
cif_lines = json.loads(json.dumps(cif_string)).splitlines()
cif_string_new = ''
for line in cif_lines:
if ' + ' in line:
newline = '#' + line
cif_string_new += newline + '\n'
matching_list = re.findall(r'\'(.+?)\'', line)
try:
if '<sup>' in matching_list[0]:
elemocc_brackets = matching_list[0].split(' + ')
else:
elemocc_brackets = matching_list[0].split('+')
elemocc_list = []
for i in elemocc_brackets:
elemocc_list.append(re.sub('\([0-9]*\)', '', i.strip()))
elems = []
occupancies = []
for i in range(len(elemocc_list)):
occupancies.append('0' + re.findall('\.?\d+', elemocc_list[i].strip())[1])
c = re.findall('\D+', elemocc_list[i].strip())
elems.append(str(c[1]).replace('<sup>', ''))
except:
break
for i in range(len(elems)):
oldline = line
old_elemline = oldline.replace("'" + matching_list[0] + "'", "'" + elems[i] + "'")
new_elemline_list = old_elemline.split()
new_elemline_list[7] = occupancies[i]
new_elemline_list.append('\n')
new_elemline = ' '.join(new_elemline_list)
cif_string_new += new_elemline
else:
cif_string_new += line + '\n'
return cif_string_new
def handle_unparsablespecies(cif_string):
"""
Handles CIF parsing errors arising from unrecognizable species
:param cif_string: (str) cif file
:return: pymatgen structure object with appended unparsable species
"""
cif_string_new = ''
symbols = []
coords = []
occupancies = []
cif = CifFile.from_string(cif_string).data
for block in cif:
if 'standardized' in block:
cif_stdblock = cif[block]
break
for i, sym in enumerate(cif_stdblock['_atom_site_type_symbol']):
if 'OH' in sym:
symbols.append(sym)
coords.append([float(cif_stdblock['_atom_site_fract_x'][i]), float(cif_stdblock['_atom_site_fract_y'][i]),
float(cif_stdblock['_atom_site_fract_z'][i])])
occupancies.append(float(cif_stdblock['_atom_site_occupancy'][i]))
for key in cif:
cif_string_new += str(cif[key]) + '\n'
cif_string_new += '\n'
new_struct = CifParser.from_string(cif_string_new).get_structures()[0]
for specie_no in range(len(symbols)):
new_struct.append({DummySpecie('X'): occupancies[specie_no]}, coords[specie_no],
properties={"molecule": [symbols[specie_no]]})
return new_struct
if __name__ == '__main__':
d = 0
remove_keys = []
for unparsable_doc in db['unparsable_sds'].find().sort('_id', pymongo.ASCENDING).skip(d).limit(1):
if unparsable_doc['key'] in ['sd_1301665', 'sd_0456987', 'sd_1125437', 'sd_1125436']:
continue
d += 1
print '#######'
print 'On record # {} and key: {}'.format(d, unparsable_doc['key'])
for parsed_doc in db['pauling_file_unique_Parse'].find({'key': unparsable_doc['key']}):
doc = parsed_doc
if 'structure' in doc:
remove_keys.append(doc['key'])
else:
try:
structure = CifParser.from_string(doc['cif_string']).get_structures()[0].as_dict()
except:
print 'Error in parsing'
# print doc['cif_string']
new_cif_string = handle_partialocclables(doc['cif_string'])
# print new_cif_string
try:
# struct = CifParser.from_string(new_cif_string).get_structures()[0]
# struct_comp = CifParser.from_string(doc['cif_string']).get_structures()[
# 0].composition.reduced_formula
appended_struct = handle_unparsablespecies(new_cif_string)
print appended_struct
except Exception as e:
print e
print 'ERROR parsing NEW structure!'
continue
'''
try:
formula_comp = Composition(
doc['metadata']['_Springer']['geninfo']['Refined Formula']).get_el_amt_dict()
except Exception as e:
print e
continue
print 'Formula composition = {}'.format(formula_comp)
missing_element = False
for element in formula_comp:
if element not in appended_struct.composition:
missing_element = True
break
if missing_element:
print 'NO MATCH! - Element {} not in structure'.format(element)
continue
'''
# db['pauling_file_unique_Parse'].update({'key': doc['key']}, {
# '$set': {'structure': CifParser.from_string(new_cif_string).get_structures()[0].as_dict()}},
# upsert=False)
# db['pauling_file_unique_Parse'].update({'key': doc['key']},
# {'$rename': {'cif_string':
# 'metadata._Springer.cif_string_old'}})
# db['pauling_file_unique_Parse'].update({'key': doc['key']}, {'$set': {'cif_string':
# new_cif_string}})
# db['pauling_file_unique_Parse'].update({'key': doc['key']},
# {'$set': {'structure': appended_struct.as_dict()}}, upsert=False)
# db['pauling_file_unique_Parse'].update({'key': doc['key']}, {'$set': {'cif_string': new_cif_string}})
remove_keys.append(doc['key'])
print 'DONE!'
print remove_keys
print len(remove_keys)
# for key in remove_keys:
# db['unparsable_sds'].remove({'key': key})
##########