/
fix_incorrect_structures.py
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/
fix_incorrect_structures.py
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import pymongo
from pymatgen.io.cif import CifParser, CifFile
import re
import json
from pymatgen import Composition
client = pymongo.MongoClient()
db = client.springer
def fix_incorrectlyparsedstructures_labels(cif_string):
"""
Fixes already parsed CIF files with structures that have sites with partial occupancies WITHOUT BRACKETS,
but unlike other CIF files with partial occupancies, have atomic labels with atomic symbols separated by commas,
which makes them parsable by CifParser but only uses the first element in the structure, ignoring other elements
on this site.
: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:
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])
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 fix_incorrectlyparsedstructures_braclabels(cif_string):
"""
Fixes already parsed CIF files with structures that have sites with partial occupancies WITH BRACKETS,
but unlike other CIF files with partial occupancies, have atomic labels with atomic symbols separated by commas,
which makes them parsable by CifParser but only uses the first element in the structure, ignoring other elements
on this site.
: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:
try:
# print line
newline = '#' + line
cif_string_new += newline + '\n'
matching_list = re.findall(r"\'(.+?)\'", line)
elemocc_brac = matching_list[0].split('+')
elemocc_list = []
for i in elemocc_brac:
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(c[1])
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
# print new_elemline
except:
break
else:
cif_string_new += line + '\n'
return cif_string_new
def fix_incorrectlyparsedstructures_sup(cif_string):
"""
Fixes already parsed CIF files with structures that have sites with partial occupancies WITH <SUP>,
but unlike other CIF files with partial occupancies, have atomic labels with atomic symbols separated by commas,
which makes them parsable by CifParser but only uses the first element in the structure, ignoring other elements
on this site.
: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:
try:
# print line
newline = '#' + line
cif_string_new += newline + '\n'
matching_list = re.findall(r"\'(.+?)\'", line)
if '<sup>' in matching_list[0]:
elemocc_brac = matching_list[0].split(' + ')
else:
elemocc_brac = matching_list[0].split('+')
elemocc_list = []
for i in elemocc_brac:
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())
if '<sup>' in c[1]:
elems.append(c[1].strip('<sup>'))
else:
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
# print new_elemline
except:
break
elif '<sup>' in line and ' + ' not in line:
try:
# print line
newline = '#' + line
cif_string_new += newline + '\n'
matching_list = re.findall(r"\'(.+?)\'", line)
elem = matching_list[0][:2]
oldline = line
old_elemline = oldline.replace("'" + matching_list[0] + "'", "'" + elem + "'")
new_elemline_list = old_elemline.split()
new_elemline_list[0] = elem
new_elemline_list.append('\n')
new_elemline = ' '.join(new_elemline_list)
cif_string_new += new_elemline
# print new_elemline
except:
break
else:
cif_string_new += line + '\n'
return cif_string_new
def fix_incorrectlyparsedstructures_symbols(cif_string):
"""
Fixes already parsed CIF files with structures that have data with either incorrect labels. This function will
replace the labels with symbols.
:param cif_string: (str) cif file
:return: corrected cif string
"""
cif_string_new = ''
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 sym != cif_stdblock['_atom_site_label'][i]:
cif_stdblock['_atom_site_label'][i] = sym
for key in cif:
cif_string_new += str(cif[key]) + '\n'
cif_string_new += '\n'
return cif_string_new
def fix_incorrectlyparsedstructures_manually(cif_string):
"""
Fixes already parsed CIF files with random errors in them (used for last 8 incorrectly parsed structures).
:param cif_string: (str) cif file
:return: corrected cif string
"""
cif_string_new = ''
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 sym == 'Mn':
cif_stdblock['_atom_site_occupancy'][i] = 0.76
elif sym == 'Ti':
cif_stdblock['_atom_site_occupancy'][i] = 0.12
elif sym == 'V':
cif_stdblock['_atom_site_occupancy'][i] = 0.12
for key in cif:
cif_string_new += str(cif[key]) + '\n'
cif_string_new += '\n'
return cif_string_new
if __name__ == '__main__':
d = 0
remove_keys = []
for incorrect_doc in db['incorrect_structs'].find().batch_size(75).sort('_id', pymongo.ASCENDING).skip(d).limit(1):
d += 1
print '#########################'
print 'On record # {} and key {}'.format(d, incorrect_doc['key'])
for parsed_doc in db['pauling_file_unique_Parse'].find({'key': incorrect_doc['key']}):
doc = parsed_doc
# if 'cif_string_old' in doc['metadata']['_Springer']:
# print doc['cif_string']
# print doc['metadata']['_Springer']['cif_string_old']
new_cif_string = fix_incorrectlyparsedstructures_labels(doc['metadata']['_Springer']['cif_string_old'])
new_cif_string = fix_incorrectlyparsedstructures_manually(new_cif_string)
# new_cif_string = fix_incorrectlyparsedstructures_symbols(new_cif_string)
# new_cif_string = fix_incorrectlyparsedstructures_sup(doc['metadata']['_Springer']['cif_string_old'])
# new_cif_string = fix_incorrectlyparsedstructures_symbols(doc['metadata']['_Springer']['cif_string_old'])
# new_cif_string = fix_incorrectlyparsedstructures_sup(doc['cif_string'])
# new_cif_string = fix_incorrectlyparsedstructures_symbols(doc['cif_string'])
print new_cif_string
try:
struct_comp = CifParser.from_string(new_cif_string).get_structures()[0].composition.reduced_formula
# struct_comp = CifParser.from_string(doc['cif_string']).get_structures()[0].composition.reduced_formula
except Exception as e:
print e
print 'ERROR parsing NEW structure!'
continue
print 'Structure composition = {}'.format(struct_comp)
try:
formula_comp = Composition(doc['metadata']['_Springer']['geninfo']['Standard 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 struct_comp:
missing_element = True
break
if missing_element:
print 'NO MATCH! - Element {} not in structure'.format(element)
continue
print 'SUCCESS'
# 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']}, {'$set': {'cif_string': new_cif_string}})
# db['pauling_file_unique_Parse'].update({'key': doc['key']}, {'$addToSet': {'errors': 'incorrect occupancies in cif file'}})
# db['pauling_file_unique_Parse'].update({'key': doc['key']}, {'$unset': {'structure': ''}})
remove_keys.append(doc['key'])
#####################
print 'FINISHED!'
print remove_keys
print len(remove_keys)
# for key in remove_keys:
# db['incorrect_structs'].remove({'key': key})
# Partial occupancy (maybe bracket?) labels (with incorrect label): "sd_0462521", "sd_0560149", "sd_1320784",
# "sd_1414947"
# Partial occupancy (bracket in symbol) labels (with incorrect label): "sd_1811457", "sd_1622133", "sd_1928405"
# Partial occupancy (maybe bracket?) labels (with correct label): "sd_1011081", "sd_1908491", "sd_1810366"
# Partial occupancy (bracket in label) labels (with incorrect label): "sd_1615854"
# Partial occupancy (maybe bracket?) labels (with incorrect label) and <sup>: "sd_1902347"
# (this one had comments in the original CIF)
# structural composition and refined/alphabetic formula do not match: "sd_1211858",
# "sd_1212949", "sd_1521691" (last two do not match compostion for unknown reasons - probably because
# of coordinate matching)
# Insufficient powder diffraction data: "sd_1704003", "sd_1002871"
# Unparsable species ("molecular species added as species X"): "sd_1500382", "sd_1601634" (found 2)
# (of course, structure and Springer formula don't match)
'''
# for doc in coll.find({'metadata._Springer.cif_string_old': {'$exists': True}}).skip(40).limit(10):
# for doc in coll.find({'errors': {'$in': ['structural composition and refined/alphabetic formula do not match']}})
.limit(10):
# print doc['key']
# fixed_keys.append(doc['key'])
# coll = db['pauling_file']
for doc in coll.find({'errors': {'$in': ['cif missing element data']}}).limit(1):
print doc['key']
print doc['cif_string']
for doc in coll.find({'errors': {'$in': ['cif missing one element data']}}).limit(1):
print doc['key']
for doc in coll.find({'errors': {'$in': ['incorrect occupancies in cif file']}}).limit(1):
print doc['key']
print doc.keys()
print doc['metadata']['_Springer'].keys()
# print doc['metadata']['_Springer']['cif_string_old']
'''
'''
for doc in coll.find({'key': {'$in': ['sd_1500382', 'sd_1601634']}}):
# for doc in coll.find({'key': {'$in': ['sd_0462521', 'sd_0560149', 'sd_1320784', 'sd_1414947', 'sd_1811457',
# 'sd_1622133', 'sd_1928405', 'sd_1011081', 'sd_1908491', 'sd_1810366', 'sd_1615854']}}):
# for doc in coll.find({'key': {'$in': ['sd_1002871', 'sd_1704003']}}):
print '--------'
print doc['key']
print doc['cif_string']
# print doc['metadata']['_Springer']['cif_string_old']
# struct = CifParser.from_string(doc['cif_string']).get_structures()[0]
for k in CifParser.from_string(doc['cif_string']).get_structures():
print k.formula
# struct_old = CifParser.from_string(doc['metadata']['_Springer']['cif_string_old']).get_structures()[0]
# print struct.formula
# print struct.composition
# print struct_old.formula
'''