from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import rdkit
from rdkit import Chem
def canonicalize(smiles):
try:
tmp = Chem.MolFromSmiles(smiles)
except:
print('no mol')
return smiles
if tmp is None:
return smiles
tmp = Chem.RemoveHs(tmp)
[a.ClearProp('molAtomMapNumber') for a in tmp.GetAtoms()]
return Chem.MolToSmiles(tmp)
def get_weighted_f1(seq_pred, seq_gnd):
if seq_pred is None or seq_gnd is None:
return 0.0
pred = set(seq_pred.split('.'))
gnd = set(seq_gnd.split('.'))
t = pred.intersection(gnd)
w = len(t) / float(len(gnd))
precision = len(t) / float(len(pred))
recall = len(t) / float(len(gnd))
if precision + recall == 0.0:
return 0.0
return 2 * precision * recall * w / (precision + recall)
def get_score(pred, gnd, score_type):
x = canonicalize(gnd)
y = canonicalize(pred)
if score_type == 'mix_f1':
f1 = get_weighted_f1(y, x)
score = 0.75 * f1 + 0.25 * (x == y)
elif score_type == 'acc':
score = 1.0 * (x == y)
else:
raise NotImplementedError
return score
