Hi,
Thanks for the pointers and taking to time to read and respond to my questions.
This is what I was doing before, however, despite all the on-line docs and the
help from the RDKit Docs, there is nothing mentioned about capturing the
WARNINGS adequately from the program, although I see that some years ago there
was a thread about this, but it was never addressed to completeness.
The issue is that RDkit at the cmd line generates WANRING: Omitted undefined
stereo and other related warnings, these messages are not going to stderr or
stdout.
There is a way to change the log reporting, that didn’t seem to work either.
Thoughts and suggestions are welcome – code snippets are gratefully accepted.
I’ve enclosed the challenging SDF if anyone wants to have a play.
Cheers,
mike
From: Lukas Pravda <lpra...@ebi.ac.uk>
Sent: 26 September 2019 00:20
To: Brian Lee <brian.kihoon....@gmail.com>; mi...@novadatasolutions.co.uk
Cc: RDKIT mailing list <rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] Fwd: sending warnings to stderr/stdout to files
That’s true, but I always hated ‘do your homework’ kind of answers, especially
when I was completely lost and did not know where to start from (which may not
be your case).
import sys
from rdkit import Chem
saved_std_err = sys.stderr
log = sys.stderr = open('test_log.log', mode='w')
Chem.WrapLogs()
mol = Chem.MolFromSmiles('c1ccccc1(C)(C)')
log.close()
sys.stderr = saved_std_err
works
Lukas
From: Brian Lee <brian.kihoon....@gmail.com <mailto:brian.kihoon....@gmail.com>
>
Date: Wednesday, 25 September 2019 at 20:55
To: <mi...@novadatasolutions.co.uk <mailto:mi...@novadatasolutions.co.uk> >
Cc: RDKIT mailing list <rdkit-discuss@lists.sourceforge.net
<mailto:rdkit-discuss@lists.sourceforge.net> >, Lukas Pravda <lpra...@ebi.ac.uk
<mailto:lpra...@ebi.ac.uk> >
Subject: Re: [Rdkit-discuss] Fwd: sending warnings to stderr/stdout to files
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
<mailto: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
<mailto: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 <mailto:mi...@novadatasolutions.co.uk> >
Date: Tuesday, 24 September 2019 at 16:52
To: RDKIT mailing list <rdkit-discuss@lists.sourceforge.net
<mailto: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
Error! Filename not specified.
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 <mailto:mi...@novadatasolutions.co.uk>
www.novadatasolutions.co.uk <http://www.novadatasolutions.co.uk/>
skype michael.mazanetz
NovaData Solutions Ltd.
PO Box 639
Abingdon-on-Thames
Oxfordshire
OX14 9JD
United Kingdom
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SDF Test_Concat.sdf
Description: chemical/mdl-sdfile
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