QED error Explicit valence for atom # 2 N, 5, is greater than permitted

[amir-tagh]

Hello,

I am using qed and rdkit to calculate the QED value for a set of SMILES. It seems there is a problem with some of the SMILES and calculations stop when encountering the problematic SMILES. Is there any way to continue the calculations and ignore the problematic SMILES?

Here is the code:

from qed import qed
from rdkit import Chem
import sys

for line in lines_1:
mol = Chem.MolFromSmiles(line)
#RDLogger.DisableLog('rdApp.*')
p = qed.properties(mol)

error message: Explicit valence for atom # 2 N, 5, is greater than permitted

I have 500k SMILES and calculations stop at 93395.

Thanks in forward.
Best,
Amir

[hansdewinter]

Dear Amir, I would catch the error with a try and except pair of statements: for line in lines_1: mol = Chem.MolFromSmiles(line) #RDLogger.DisableLog('rdApp.*’) try: p = qed.properties(mol) except: continue Bye for now, Hans On 28 Nov 2021, at 22:34, amir-tagh ***@***.******@***.***>> wrote: Hello, I am using qed and rdkit to calculate the QED value for a set of SMILES. It seems there is a problem with some of the SMILES and calculations stop when encountering the problematic SMILES. Is there any way to continue the calculations and ignore the problematic SMILES? Here is the code: from qed import qed from rdkit import Chem import sys for line in lines_1: mol = Chem.MolFromSmiles(line) #RDLogger.DisableLog('rdApp.*') p = qed.properties(mol) error message: Explicit valence for atom # 2 N, 5, is greater than permitted I have 500k SMILES and calculations stop at 93395. Thanks in forward. Best, Amir — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<https://github.com/UAMCAntwerpen/qed/issues/1>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AACVO25S2GTVXTBALTPQYATUOKN6XANCNFSM5I5XWRXA>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[amir-tagh]

Hello Hans, Thanks for the hint. Best, Amir On Mon, Nov 29, 2021 at 3:12 AM Hans De Winter ***@***.***> wrote:

…

Dear Amir, I would catch the error with a try and except pair of statements: for line in lines_1: mol = Chem.MolFromSmiles(line) #RDLogger.DisableLog('rdApp.*’) try: p = qed.properties(mol) except: continue Bye for now, Hans On 28 Nov 2021, at 22:34, amir-tagh ***@***.******@***.***>> wrote: Hello, I am using qed and rdkit to calculate the QED value for a set of SMILES. It seems there is a problem with some of the SMILES and calculations stop when encountering the problematic SMILES. Is there any way to continue the calculations and ignore the problematic SMILES? Here is the code: from qed import qed from rdkit import Chem import sys for line in lines_1: mol = Chem.MolFromSmiles(line) #RDLogger.DisableLog('rdApp.*') p = qed.properties(mol) error message: Explicit valence for atom # 2 N, 5, is greater than permitted I have 500k SMILES and calculations stop at 93395. Thanks in forward. Best, Amir — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub< https://github.com/UAMCAntwerpen/qed/issues/1>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AACVO25S2GTVXTBALTPQYATUOKN6XANCNFSM5I5XWRXA>. Triage notifications on the go with GitHub Mobile for iOS< https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android< https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/UAMCAntwerpen/qed/issues/1#issuecomment-981383935>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AS7GVKT7TEZNOZGMJR7KBA3UOMYXHANCNFSM5I5XWRXA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.