Hi Markus, The automatic substructure highlighting is one of the features of the RDKit-Jupyter integration. It works by monkey patching the substructure matching functions to store the results on the molecule being queried in a data member called __sssAtoms. If you want to get rid of the highlights in particular molecules you can just set the __sssAtoms attribute to None: mol.__sssAtoms = None
There's not a function to disable the saving of substructure search results entirely, but if you want to do that it's easy enough: Chem.Mol.GetSubstructMatch = Chem.Mol.__GetSubstructMatch Chem.Mol.GetSubstructMatches = Chem.Mol.__GetSubstructMatches All of this is demonstrated in this gist: https://gist.github.com/greglandrum/5d45b56afe75603b955103cdd0d8e038 -greg On Thu, Nov 14, 2019 at 8:13 AM Markus Heller <mhel...@admarebio.com> wrote: > Follow-up after some digging: > > I did do a substructure search in the affected Jupyter notebooks, > specifically while calculating ESOL (using the function calc_esol() in > esol.py from Pat Walters' github: https://github.com/PatWalters/solubility). > This seems to explain why the matches are highlighted in the molecule > column in my dataframe. > > I still haven't figured out how to turn this highlighting off though. > Neither web searches nor searches in the RDkit docs were successful, or I > have searched using the wrong terms ... How can this be done? > > Cheers > Markus > > From: Markus Heller <mhel...@admarebio.com> > > Sent: November 13, 2019 5:01 PM > > To: rdkit-discuss (rdkit-discuss@lists.sourceforge.net) < > rdkit-discuss@lists.sourceforge.net> > > Subject: [Rdkit-discuss] Random (?) highlighting in pandas dataframe > > > > > Hi all, > > > > I have an issue with molecule rendering in a pandas dataframe. I read a > csv file with SMILES strings and names into a dataframe, and add a mol > column to the dataframe based on the SMILES. I then display the molecules > in the dataframe like so: > > > > from IPython.display import HTML > > HTML(df.to_html()) > > > > What happens is that most of the molecules have a substructure > highlighted, but not all. My questions are: why is there a substructure > highlighted, and how can I turn it off? > > > > > More details: it happens in a new Jupyter notebook with compounds I save > as SMILES or SDF that I obtained from a substructure search done with RDkit > in a *different* notebook. In the notebook where the issue arises, I have > not performed any searches, nor have > I specified a substructure for highlighting. I'm confused. > > > > Thanks > > Markus > > > > > > > > _______________________________________________ > > Rdkit-discuss mailing list > > Rdkit-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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