... sounds like a good explanation. If this is indeed the case, it would be
reasonable to force flush to get guaranteed non-random behavior.
Thanks!
Best,
Dmitri
> On Jul 5, 2016, at 7:39 AM, Brian Kelley wrote:
>
> After some digging, it looks like the underlying C++ streams aren't flushing
After some digging, it looks like the underlying C++ streams aren't
flushing. This means that python might not actually have all the
information when you print them out. We may have to enable a "flush"
function for these streams for better error reporting on the python side,
I'll need to investig
Dmitri,
Could you send me the notebook that displays these issues? I can't
reproduce them.
Thanks,
Brian
On Tue, Jun 28, 2016 at 6:25 PM, Brian Kelley wrote:
> It looks like there may be an issue calling WrapLogs twice. If you see
> the error messages in the notebook, it's already been c
It looks like there may be an issue calling WrapLogs twice. If you see the
error messages in the notebook, it's already been called. Importing
IPythonConsole does this automatically.
This may be the cause of our confusion. I'll look into it.
Brian Kelley
> On Jun 28, 2016, at 3:54 PM,
Hi Brian,
First off, now I can capture the warnings, so for practical purposes my
question has been addressed, thank you for helping me get to this point.
Cool trick with StringIO. I can even just do:
Python 3.5.1 :: Anaconda 2.4.0 (x86_64), OSX 10.11.5, jupyter 4.1.0, Firefox
```
import io
Dmitri,
I admit to being a bit confused. What WrapLogs() does is simply redirect
the C++ errors into python's stderr. See attache png. I think you may
have noticed that, as you are capturing with sys.stderr.
These errors are output (at least for me) in the IPython notebook. I'm not
sure what
Brian - Thank you!
(on OSX 10.11.5, jupyter 4.1.0)
rdkit.Chem.WrapLogs() does hide the messages.
I could not figure out how to access them though once they are hidden.
To capture warnings, this mechanism seems to work - but it is ugly.
```
import os
## switch the streams
stderr_fn = 'stderr.lo
Dmitri, if you import rdkit.Chem.Draw.IPythonConsole the c++ errors and
warnings should be seen in IPython. This doesn't appear to work on Windows
yet, sadly.
This is enabled by the command
rdkit.Chem.WrapLogs()
We are also doing a second pass soon to get better exception details in python
w
Hi Greg -
Thank you very much for the clear and detailed explanation!
(and, now that I have a chance to say this, thank you for putting the project
together; being able to work with chemistry in the python notebook is great,
and having hooks into pandas is really cool)
In this case I was basi
Hi Dmitri,
The results that come back from the MCS in that examples really describe
queries, not necessarily stable molecules or things that can be accurately
translated into SMILES.
I'll describe below what's going on to cause the error, but the more
important question is: what are you trying to
Dear RDKitters,
I would appreciate any comments on the following:
I am looking at the 'SureChEMBL iPython Notebook Tutorial'
http://nbviewer.jupyter.org/github/rdkit/UGM_2014/blob/master/Notebooks/Vardenafil.ipynb
following along with rdkit '2016.03.1' on OSX
In Cell 142, there is this SMILE
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