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'''
Code from https://github.com/blender-nlp/MolT5
```bibtex
@article{edwards2022translation,
title={Translation between Molecules and Natural Language},
author={Edwards, Carl and Lai, Tuan and Ros, Kevin and Honke, Garrett and Ji, Heng},
journal={arXiv preprint arXiv:2204.11817},
year={2022}
}
```
'''
import argparse
import csv
import os.path as osp
import numpy as np
from rdkit import Chem
from rdkit.Chem import MACCSkeys
from rdkit import DataStructs
from rdkit.Chem import AllChem
from rdkit import RDLogger
RDLogger.DisableLog('rdApp.*')
def evaluate(input_file, morgan_r, verbose=False):
outputs = []
bad_mols = 0
with open(osp.join(input_file)) as f:
reader = csv.DictReader(f, delimiter="\t", quoting=csv.QUOTE_NONE)
for n, line in enumerate(reader):
try:
gt_smi = line['ground truth']
ot_smi = line['output']
gt_m = Chem.MolFromSmiles(gt_smi)
ot_m = Chem.MolFromSmiles(ot_smi)
if ot_m == None: raise ValueError('Bad SMILES')
outputs.append((line['description'], gt_m, ot_m))
except:
bad_mols += 1
validity_score = len(outputs)/(len(outputs)+bad_mols)
if verbose:
print('validity:', validity_score)
MACCS_sims = []
morgan_sims = []
RDK_sims = []
enum_list = outputs
for i, (desc, gt_m, ot_m) in enumerate(enum_list):
if i % 100 == 0:
if verbose: print(i, 'processed.')
MACCS_sims.append(DataStructs.FingerprintSimilarity(MACCSkeys.GenMACCSKeys(gt_m), MACCSkeys.GenMACCSKeys(ot_m), metric=DataStructs.TanimotoSimilarity))
RDK_sims.append(DataStructs.FingerprintSimilarity(Chem.RDKFingerprint(gt_m), Chem.RDKFingerprint(ot_m), metric=DataStructs.TanimotoSimilarity))
morgan_sims.append(DataStructs.TanimotoSimilarity(AllChem.GetMorganFingerprint(gt_m,morgan_r), AllChem.GetMorganFingerprint(ot_m, morgan_r)))
maccs_sims_score = np.mean(MACCS_sims)
rdk_sims_score = np.mean(RDK_sims)
morgan_sims_score = np.mean(morgan_sims)
if verbose:
print('Average MACCS Similarity:', maccs_sims_score)
print('Average RDK Similarity:', rdk_sims_score)
print('Average Morgan Similarity:', morgan_sims_score)
return validity_score, maccs_sims_score, rdk_sims_score, morgan_sims_score
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument('--input_file', type=str, default='caption2smiles_example.txt', help='path where test generations are saved')
parser.add_argument('--morgan_r', type=int, default=2, help='morgan fingerprint radius')
args = parser.parse_args()
evaluate(args.input_file, args.morgan_r, True)
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