ChEMBL_Structure_Pipeline icon indicating copy to clipboard operation
ChEMBL_Structure_Pipeline copied to clipboard

allow sanitization of the result molecules in standardize_mol()

Open greglandrum opened this issue 4 years ago • 3 comments

In order to help prevent users from getting themselves into trouble, we should add a standardize argument to standardize_mol() that defaults to True.

One argument against setting the default to True is that it does introduce the possibility that the sanitization might fail. But I think it's probably safer to go ahead and do it anyway.

This came up in the discussion of https://github.com/rdkit/rdkit/issues/3094.

greglandrum avatar Apr 15 '20 13:04 greglandrum

@eloyfelix : if you agree that this is a reasonable idea, I will go ahead and implement it and add a couple tests for it.

greglandrum avatar Apr 15 '20 13:04 greglandrum

Hi Greg, thanks for looking into this. Yes, it is definitely a good idea to do it.

eloyfelix avatar Apr 15 '20 14:04 eloyfelix

Ok. I will try to get a PR done in the next couple days. As usual, writing the tests will be the majority of the effort. :-)

greglandrum avatar Apr 15 '20 14:04 greglandrum

done in #45

eloyfelix avatar Nov 15 '22 16:11 eloyfelix