I've had similar problems; none of the claimed methods to switch off RDKit logging of warnings has worked for me.
I ended up just re-directing stderr when running the script like this: python myfile.py 2> myErrorLog.txt ==================== Dr. Steve O'Hagan, -----Original Message----- From: Jean-Marc Nuzillard [mailto:jm.nuzill...@univ-reims.fr] Sent: 21 January 2019 12:33 To: RDKit Discuss <rdkit-discuss@lists.sourceforge.net> Subject: [Rdkit-discuss] Warning as error Dear all, The minimalist python code: reader = Chem.SDMolSupplier('my_file.sdf') for mol in reader: pass gives me warning messages when run on a particular SD file. How can I simply run a specific action for the molecules that cause problem, possibly using try/catch statements? Best, Jean-Marc -- Jean-Marc Nuzillard Directeur de Recherches au CNRS Institut de Chimie Moléculaire de Reims CNRS UMR 7312 Moulin de la Housse CPCBAI, Bâtiment 18 BP 1039 51687 REIMS Cedex 2 France Tel : 03 26 91 82 10 Fax : 03 26 91 31 66 http://www.univ-reims.fr/ICMR http://eos.univ-reims.fr/LSD/CSNteam.html http://www.univ-reims.fr/LSD/ http://www.univ-reims.fr/LSD/JmnSoft/ --- L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast. https://www.avast.com/antivirus _______________________________________________ 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
