def run_task(self, fw_spec):
db = SPStructuresMongoAdapter.auto_load()
tstructs = []
species = fw_spec['species']
t = fw_spec['threshold']
for p in SubstitutionPredictor(threshold=t).list_prediction(species):
subs = p['substitutions']
if len(set(subs.values())) < len(species):
continue
st = SubstitutionTransformation(subs)
target = map(str, subs.keys())
for snl in db.get_snls(target):
ts = TransformedStructure.from_snl(snl)
ts.append_transformation(st)
if ts.final_structure.charge == 0:
tstructs.append(ts)
transmuter = StandardTransmuter(tstructs)
f = RemoveDuplicatesFilter(structure_matcher=StructureMatcher(
comparator=ElementComparator(), primitive_cell=False))
transmuter.apply_filter(f)
results = []
for ts in transmuter.transformed_structures:
results.append(ts.to_snl([]).to_dict)
submissions = SPSubmissionsMongoAdapter.auto_load()
submissions.insert_results(fw_spec['submission_id'], results)
def __init__(self, threshold=1e-2, **kwargs):
"""
Args:
kwargs:
args for SubstitutionProbability class
lambda_table, alpha
"""
self._kwargs = kwargs
self._threshold = threshold
self._substitutor = SubstitutionPredictor(threshold=threshold,
**kwargs)
def test_prediction(self):
sp = SubstitutionPredictor(threshold = 8e-3)
result = sp.list_prediction(['Na+', 'Cl-'], to_this_composition = True)[5]
cprob = sp.p.cond_prob_list(result['substitutions'].keys(),
result['substitutions'].values())
self.assertAlmostEqual(result['probability'], cprob)
self.assertEqual(set(result['substitutions'].values()), set(['Na+', 'Cl-']))
result = sp.list_prediction(['Na+', 'Cl-'], to_this_composition = False)[5]
cprob = sp.p.cond_prob_list(result['substitutions'].keys(),
result['substitutions'].values())
self.assertAlmostEqual(result['probability'], cprob)
self.assertNotEqual(set(result['substitutions'].values()),
set(['Na+', 'Cl-']))
c = Composition({'Ag2+' : 1, 'Cl-' : 2})
result = sp.composition_prediction(c, to_this_composition = True)[2]
self.assertEqual(set(result['substitutions'].values()), set(c.elements))
result = sp.composition_prediction(c, to_this_composition = False)[2]
self.assertEqual(set(result['substitutions'].keys()), set(c.elements))
def __init__(self, threshold=1e-2, **kwargs):
self.kwargs = kwargs
self.threshold = threshold
self._substitutor = SubstitutionPredictor(threshold=threshold,
**kwargs)
