Hi Mike,
The following code works for me: import sys from io import StringIO from rdkit import Chem saved_std_err = sys.stderr log = sys.stderr = StringIO() Chem.WrapLogs() # do whatever you want with rdkit whatever_used_to_be_printed_by_rdkit_in_console_as_str = log.getvalue() sys.stderr = saved_std_err This populated the stream in memory, if you replace StringIO with FileIO I think you can directly redirect it to file, but have not tested that. Let me know if this works for you. Lukas From: <mi...@novadatasolutions.co.uk> Date: Tuesday, 24 September 2019 at 16:52 To: RDKIT mailing list <rdkit-discuss@lists.sourceforge.net> Subject: [Rdkit-discuss] Fwd: sending warnings to stderr/stdout to files Hi Rdkit forum, Easy question, perhaps difficult to answer… I’ve been reading a lot of support messages, many a very old about how to get warnings (only visible at the cmd line) to be send to files. I can get error messages sent, but not warnings. The type I’m trying to capture are – which I can see when I run code at the cmd line, but not in jupyter-notebook. “charges were rearranged” “Omitted undefined stereo” Ideally I’d like to run the code in jupyter-notebook and also at the cmd line with python script.py etc and get the warnings into a file. Can you provide me with a simple example as to how to do this? Thanks, mike Dr Mike Mazanetz, FRSC Director Honorary Lecturer School of Natural and Computing Sciences University of Aberdeen +44 (0) 141 533 0930 +44 (0) 7780 672509 mi...@novadatasolutions.co.uk www.novadatasolutions.co.uk skype michael.mazanetz NovaData Solutions Ltd. PO Box 639 Abingdon-on-Thames Oxfordshire OX14 9JD United Kingdom _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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