def does_match_composition(self, formula1, formula2):
c1 = Composition(formula1)
c2 = Composition(formula2)
return(c1.almost_equals(c2))
'Alphabetic Formula']
form = form.replace('[', '')
form = form.replace(']', '')
try:
redform = Composition(form).reduced_formula
except:
print 'Could not parse composition for key:{} with composition:{}'.format(
doc['key'], form)
y += 1
continue
alphaform_comp = Composition(redform).alphabetical_formula
alphaform_frac = Composition(alphaform_comp).fractional_composition
structure_comp = doc['metadata']['_structure'][
'reduced_cell_formula_abc']
structure_frac = Composition(structure_comp).fractional_composition
if alphaform_frac != structure_frac and not alphaform_frac.almost_equals(
structure_frac, 0.15):
for document in db['pauling_file'].find({'key': doc['key']}):
try:
struct_lst = CifParser.from_string(
document['cif_string']).get_structures()
except:
pass
if len(struct_lst) > 1:
matched = False
for struct in struct_lst[1:]:
another_frac = Composition(
struct.composition).fractional_composition
if alphaform_frac == another_frac or alphaform_frac.almost_equals(
another_frac, 0.15):
matched = True
# '''
form = doc['metadata']['_Springer']['geninfo']['Refined Formula']
else:
form = doc['metadata']['_Springer']['geninfo']['Alphabetic Formula']
form = form.replace('[', '')
form = form.replace(']', '')
try:
redform = Composition(form).reduced_formula
except:
print 'Could not parse composition for key:{} with composition:{}'.format(doc['key'], form)
y += 1
continue
alphaform_comp = Composition(redform).alphabetical_formula
alphaform_frac = Composition(alphaform_comp).fractional_composition
structure_comp = doc['metadata']['_structure']['reduced_cell_formula_abc']
structure_frac = Composition(structure_comp).fractional_composition
if alphaform_frac != structure_frac and not alphaform_frac.almost_equals(structure_frac, 0.15):
for document in db['pauling_file'].find({'key': doc['key']}):
try:
struct_lst = CifParser.from_string(document['cif_string']).get_structures()
except:
pass
if len(struct_lst) > 1:
matched = False
for struct in struct_lst[1:]:
another_frac = Composition(struct.composition).fractional_composition
if alphaform_frac == another_frac or alphaform_frac.almost_equals(another_frac, 0.15):
matched = True
# '''
db['pauling_file'].update({'key': doc['key']}, {'$set': {'structure': struct.as_dict()}})
db['pauling_file'].update({'key': doc['key']}, {
'$set': {'metadata._structure': get_meta_from_structure(struct)}})
