benstaf
commented
6 years ago It's an error with rdkit, so it's better to isolate this problem and ask this question in the rdkit project
On Feb 9, 2018 4:03 AM, "redBirdTx" notifications@github.com wrote:
Hi, I am trying to run the train_ogan, but getting the following. Any suggestions on getting over with it? Thanks!
Traceback (most recent call last):
File "", line 1, in runfile('C:/Users/AAA/Documents/Deep learning/GAN/ChemGAN- challenge-master/model/train_ogan.py', wdir='C:/Users/AAA/Documents/Deep learning/GAN/ChemGAN-challenge-master/model')
File "C:\ProgramData\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 710, in runfile execfile(filename, namespace)
File "C:\ProgramData\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 101, in execfile exec(compile(f.read(), filename, 'exec'), namespace)
File "C:/Users/AAA/Documents/Deep learning/GAN/ChemGAN- challenge-master/model/train_ogan.py", line 379, in return
File "C:/Users/AAA/Documents/Deep learning/GAN/ChemGAN- challenge-master/model/train_ogan.py", line 309, in main print('\t* LOAD_PRETRAIN was set to false.')
File "C:/Users/AAA/Documents/Deep learning/GAN/ChemGAN- challenge-master/model/train_ogan.py", line 193, in pretrain mm.compute_results(samples, train_samples, ord_dict, results)
File "C:\Users\AAA\Documents\Deep learning\GAN\ChemGAN- challenge-master\model\mol_metrics.py", line 176, in compute_results results[objective] = np.mean(func(verified_samples, train_data))
File "C:\Users\AAA\Documents\Deep learning\GAN\ChemGAN- challenge-master\model\mol_metrics.py", line 292, in batch_solubility vals = [logP(s, train_smiles) if verify_sequence(s) else 0 for s in smiles]
File "C:\Users\AAA\Documents\Deep learning\GAN\ChemGAN- challenge-master\model\mol_metrics.py", line 292, in vals = [logP(s, train_smiles) if verify_sequence(s) else 0 for s in smiles]
File "C:\Users\AAA\Documents\Deep learning\GAN\ChemGAN- challenge-master\model\mol_metrics.py", line 299, in logP logp = Crippen.MolLogP(Chem.MolFromSmiles(smile))
File "C:\ProgramData\Anaconda3\lib\site-packages\rdkit\Chem\Crippen.py", line 170, in MolLogP = lambda *x, *y: rdMolDescriptors.CalcCrippenDescriptors(x, **y)[0]
ValueError: Sanitization error: Explicit valence for atom # 3 O, 3, is greater than permitted
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/mostafachatillon/ChemGAN-challenge/issues/1, or mute the thread https://github.com/notifications/unsubscribe-auth/AHzfFMRUEEXWrU8YTLmE1ZDyQ7HbYlzMks5tS6dsgaJpZM4R_T5y .
redBirdTx
Hi, I am trying to run the train_ogan, but getting the following. Any suggestions on getting over with it? Thanks!
Traceback (most recent call last):
File "", line 1, in
runfile('C:/Users/AAA/Documents/Deep learning/GAN/ChemGAN-challenge-master/model/train_ogan.py', wdir='C:/Users/AAA/Documents/Deep learning/GAN/ChemGAN-challenge-master/model')
File "C:\ProgramData\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 710, in runfile execfile(filename, namespace)
File "C:\ProgramData\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 101, in execfile exec(compile(f.read(), filename, 'exec'), namespace)
File "C:/Users/AAA/Documents/Deep learning/GAN/ChemGAN-challenge-master/model/train_ogan.py", line 379, in
return
File "C:/Users/AAA/Documents/Deep learning/GAN/ChemGAN-challenge-master/model/train_ogan.py", line 309, in main print('\t* LOAD_PRETRAIN was set to false.')
File "C:/Users/AAA/Documents/Deep learning/GAN/ChemGAN-challenge-master/model/train_ogan.py", line 193, in pretrain mm.compute_results(samples, train_samples, ord_dict, results)
File "C:\Users\AAA\Documents\Deep learning\GAN\ChemGAN-challenge-master\model\mol_metrics.py", line 176, in compute_results results[objective] = np.mean(func(verified_samples, train_data))
File "C:\Users\AAA\Documents\Deep learning\GAN\ChemGAN-challenge-master\model\mol_metrics.py", line 292, in batch_solubility vals = [logP(s, train_smiles) if verify_sequence(s) else 0 for s in smiles]
File "C:\Users\AAA\Documents\Deep learning\GAN\ChemGAN-challenge-master\model\mol_metrics.py", line 292, in
vals = [logP(s, train_smiles) if verify_sequence(s) else 0 for s in smiles]
File "C:\Users\AAA\Documents\Deep learning\GAN\ChemGAN-challenge-master\model\mol_metrics.py", line 299, in logP logp = Crippen.MolLogP(Chem.MolFromSmiles(smile))
File "C:\ProgramData\Anaconda3\lib\site-packages\rdkit\Chem\Crippen.py", line 170, in
MolLogP = lambda *x, *y: rdMolDescriptors.CalcCrippenDescriptors(x, **y)[0]
ValueError: Sanitization error: Explicit valence for atom # 3 O, 3, is greater than permitted