Hi Jean-Marc, Just a thought, but SDMolSupplier has a lazy eval, if I am not mistaken. Technically you should get all the rdkit warnings and errors at the time of processing that bit of the sdf file. You can always read the stderror output, parse it and throw exception every time a 'funny' molecule comes in.
I use a routine similar to this: from io import StringIO import sys import rdkit saved_std_err = sys.stderr log = sys.stderr = StringIO() rdkit.Chem.WrapLogs() reader = Chem.SDMolSupplier('my_file.sdf') for mol in reader: error_msgs = log.getvalue() # check error_msgs content if it there are any particular errors and act accordingly, erhaps even flush the stream sys.stderr = saved_std_err Lukas On 21/01/2019, 13:24, "Jean-Marc Nuzillard" <jm.nuzill...@univ-reims.fr> wrote: Chem.SDMolSupplier _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss