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qed's Issues

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

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

Please merge the len of getSSSR commit

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.

does this work with python3? 

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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