Drop unwanted molecules

[velocirraptor23]

Hi,

I was wondering if there is a way to drop unwanted molecules after the toxicity prediction. Just to filter before to perfomr the conformer generation or the optimization. Might reduce the time of run.

Best wishes,

Cesar

[bieniekmateusz]

This sounds like a useful feature.

ChemSpace has an attribute .df which is a pandas dataframe. That is basically its database. I think you should be able to overwrite it with:

cs.df = cs.df without all the toxicity

This could be a nice addition to the tutorial to show how to subtract the indices from the .toxicity(). Please let me know if you need help there, I should have a few minutes in the evening!

[velocirraptor23]

I will try this. I will let you know if it worked.

Cesar

[velocirraptor23]

I have tried this to drop bad molecules:

dft = pd.DataFrame(cs.toxicity())
list1 = dft.index[dft['has_unwanted_subs']==True].tolist()
list2 = dft.index[dft['has_pains']==True].tolist()
list3 = dft.index[dft['has_prob_fgs']==True].tolist()
list4 = dft.index[dft['synthetic_accessibility']< 6.5].tolist()
merged_list = list(set(list1+list2+list3+list4))
cs.df=cs.df.drop(merged_list, errors='ignore')

Seems to work at the moment.

Best wishes,

Cesar