This isn't so much an RDKit question as it is a python IO question. I'd look into the docs at https://docs.python.org/3/library/io.html as a starting point.
On Wed, Sep 25, 2019 at 2:13 AM <mi...@novadatasolutions.co.uk> wrote: > Hi. > Yes this works for me as per the RDKit docs. But I need to pipe it to a > file, any suggestions? > Thanks. > Mike > > Get Outlook for Android <https://aka.ms/ghei36> > > > > > On Tue, Sep 24, 2019 at 10:28 PM +0100, "Lukas Pravda" <lpra...@ebi.ac.uk> > wrote: > > 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 >> > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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