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View Code? Open in Web Editor NEWThe QED (Quantitative Estimation of Drug-likeness) molecular descriptor to use in combination with RDKit
License: The Unlicense
The QED (Quantitative Estimation of Drug-likeness) molecular descriptor to use in combination with RDKit
License: The Unlicense
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
Your commit to adding len() around getSSSR is not merged with the master branch so please merge it!!!
I had to debug a lot to start on your example case only.
Thanks in advance.
Traceback (most recent call last):
File "~/src/molenc/bin/molenc_qed.py", line 52, in <module>
main()
File "~/src/molenc/bin/molenc_qed.py", line 44, in main
score = qed.default(mol)
File "~/.local/lib/python3.10/site-packages/qed/qed.py", line 269, in default
return weights_mean(mol, gerebtzoff)
File "~/.local/lib/python3.10/site-packages/qed/qed.py", line 252, in weights_mean
return qed([0.66, 0.46, 0.05, 0.61, 0.06, 0.65, 0.48, 0.95], props, gerebtzoff)
File "~/.local/lib/python3.10/site-packages/qed/qed.py", line 227, in qed
d[i] = ads(p[i], pads1[i][0], pads1[i][1], pads1[i][2], pads1[i][3], pads1[i][4], pads1[i][5], pads1[i][6])
File "~/.local/lib/python3.10/site-packages/qed/qed.py", line 194, in ads
return ((a+(b/(1+exp(-1*(x-c+d/2)/e))*(1-1/(1+exp(-1*(x-c-d/2)/f))))) / dmax)
TypeError: unsupported operand type(s) for -: '_vectSt6vectorIiSaIiEE' and 'float'
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