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, DmitriR <xzf...@gmail.com> wrote:
>
> 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
> err = sys.stderr
> sys.stderr = io.StringIO()
>
> # capture errors/warnings
> Chem.MolFromSmiles('C1CC')
>
> msgs = sys.stderr.getvalue()
> sys.stderr = err
> print('Captured', msgs)
>
> # now errors show in the notebook again
> Chem.MolFromSmiles('C1CC')
> ```
>
> ==
>
> However, if you feel like digging a bit deeper, I'm a little confused too now
> :)
>
> What is the scope of WrapLogs() effects? (notebook-wide, or cell?) Or, by
> chance, does it set anything really persistent?
>
> In my prior notebook session, prior to trying WrapLogs() I could already see
> the warnings printed on red background (like in your screenshot, except that
> you have an ERROR msg, not WARNINGs as in my example).
>
> A call to WrapLogs() made warnings apparently disappear from the notebook.
>
> Upon reinitializing the session I could see the warnings on red background as
> before, wrote the code snippet in my prior email, and *without calling
> WrapLogs()* I could capture the warnings with it.
>
> So I assumed that RDKit messages went to the notebook's stderr by default,
> and WrapLogs() did something else.
>
> After getting your last email, I made a minimal test case (new notebook with
> just the RDKit call that generates warnings `dff['InChI'] =
> dff['ROMol'].map(Chem.MolToInchi)`, wrapped inside the stderr capture code
> snippet), killed all python instances, restarted the browser, loaded data
> from pickled dataframe.
>
> Now, *without ever having called WrapLogs()* I still get all RDKit warnings
> go to stderr, and I can still capture them using the snippet. Calls to
> WrapLogs() now appear to have no effect whatsoever.
>
> If this indicates to you any potential issue, we can look more into it.
> Otherwise I'm good.
>
> ==
>
> The other strange behavior that I described below (the number of warnings
> alternating between successive calls to the same code using Chem.MolToInchi)
> remains though. Maybe it's the underlying InChi code, I did not investigate.
>
> Thanks again.
> Dmitri
>
>
>
>> On Jun 28, 2016, at 2:14 PM, Brian Kelley <fustiga...@gmail.com> wrote:
>>
>> 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 is being hidden here. Perhaps the notebook has changed somehow?
>> Here is my version:
>>
>> Python 2.7.11 |Anaconda 2.1.0 (x86_64)| (default, Dec 6 2015, 18:57:58)
>> Type "copyright", "credits" or "license" for more information.
>>
>> IPython 4.0.0 -- An enhanced Interactive Python.
>>
>>
>> btw - you can use StringIO as opposed to a file
>>
>> from StringIO import StringIO
>>
>> err = sys.stderr
>> io = sys.stderr = StringIO()
>> ....
>> sys.stderr = err
>> print io.getvalue()
>>
>>
>>
>> On Tue, Jun 28, 2016 at 1:24 PM, DmitriR <xzf...@gmail.com> wrote:
>> 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.log'
>> orig_stderr = sys.stderr
>> sys.stderr = open(stderr_fn, 'w')
>>
>> ## RDKit code producing warnings goes here
>>
>> ## switch back stderr, process the warnings
>> sys.stderr.flush()
>> sys.stderr = orig_stderr
>> with open(stderr_fn, 'r') as f: err_data = f.read()
>> os.remove(stderr_fn)
>> print(len(err_data))
>> ```
>>
>> Assuming it is all even necessary, this could be made much nicer by using a
>> context manager/decorator to handle stderr capture and return the warnings
>> text in an extra argument, along the lines of
>> http://stackoverflow.com/questions/5136611/capture-stdout-from-a-script-in-python
>>
>> ==
>>
>> But also I noticed something weird:
>>
>> If I re-run the notebook cell with code that produces warnings, I get *no
>> warnings* every third or sometimes second invocation.
>>
>> And when I run this with data that produce a lot of warnings (hundreds), I
>> get different number of warnings between runs, at least with this call:
>>
>> ```
>> #dff is a pandas dataframe
>> dff['InChI'] = dff['ROMol'].map(Chem.MolToInchi)
>> ```
>>
>> it cycles higher-number -> lower-number -> higher-number ... Not sure what
>> to make of it. Something screwed up with my system?
>>
>> Dmitri
>>
>>
>>
>> > On Jun 28, 2016, at 8:24 AM, Brian Kelley <fustiga...@gmail.com> wrote:
>> >
>> > 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 which has been a pet peeve of mine for a while.
>> > ----
>> > Brian Kelley
>> >
>> > On Jun 28, 2016, at 4:04 AM, DmitriR <xzf...@gmail.com> wrote:
>> >
>> >> 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 basically just going through the example code and ran
>> >> into some behaviors that I did not understand (and you kindly explained).
>> >> So it's all clear now. Uppercase aromatic atoms in MCS output does appear
>> >> to be a bug; Hs on aromatic nitrogens I'll need to fix manually or with a
>> >> transform.
>> >>
>> >> ==
>> >>
>> >> Separately, on another thing that came up in my working through that data:
>> >>
>> >> I'd like to add my 2cents-equivalent of vote toward a bit fuller control
>> >> of warnings produced by the C++ backend. In that example's data I was
>> >> getting a lot of (fully valid, I think) warnings about stereochemistry,
>> >> but I could not do anything to catch or hide them - and in an ipython
>> >> notebook, it can get less than tidy. I did see this mentioned in other
>> >> threads, so I understand that logging is a known issue somewhere on the
>> >> stack. For now I just clean up manually.
>> >>
>> >> Thanks again!
>> >>
>> >> Kind regards,
>> >> Dmitri
>> >>
>> >>
>> >>
>> >>> On Jun 28, 2016, at 1:39 AM, Greg Landrum <greg.land...@gmail.com> wrote:
>> >>>
>> >>> 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 do?
>> >>>
>> >>> In this case there are two problems. One has to do with the aromatic
>> >>> bonds in the SMILES coming from C atoms that are written as capital
>> >>> letters. Here's a simplified version of your example:
>> >>>
>> >>> In [11]: Chem.MolFromSmiles('O=C1:[NH]:C:N:N2:C:*:C:C:1:2')
>> >>> [06:43:37] Explicit valence for atom # 1 C, 5, is greater than permitted
>> >>>
>> >>> If I rewrite the SMILES to have the atoms with aromatic bonds written
>> >>> with lower case letters everything is fine:
>> >>>
>> >>> In [12]: Chem.MolFromSmiles('O=c1:[nH]:c:n:n2:c:*:c:c:1:2')
>> >>> Out[12]: <rdkit.Chem.rdchem.Mol at 0x7f3204024440>
>> >>>
>> >>> This shouldn't make a difference in SMILES, so I'm inclined to think
>> >>> that it's a bug.
>> >>>
>> >>> The second problem was the missing hydrogen specification on the
>> >>> aromatic nitrogen that has an H (I fixed this in the SMILES above).
>> >>> Since the RDKit does not attempt to guess at chemistry, the general rule
>> >>> is that aromatic heteroatoms should have Hs specified if they have any.
>> >>> There have been a number of mailing list threads on this topic.
>> >>>
>> >>> Best,
>> >>> -greg
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> On Mon, Jun 27, 2016 at 8:26 PM, DmitriR <xzf...@gmail.com> wrote:
>> >>> 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 SMILES:
>> >>>
>> >>> MCS SMILES: O=C1:N:C(C2:C:C:C:C:C:2):N:N2:C:[*]:C:C:1:2
>> >>> This is a representation of a generalized structure, not any particular
>> >>> molecule.
>> >>>
>> >>> It was generated with Chem.MolToSmiles(mcsM,isomericSmiles=True)
>> >>>
>> >>> But when I try
>> >>> Chem.MolFromSmiles('O=C1:N:C(C2:C:C:C:C:C:2):N:N2:C:[*]:C:C:1:2')
>> >>>
>> >>> I get "RDKit ERROR: [14:11:32] Explicit valence for atom # 1 C, 5, is
>> >>> greater than permitted"
>> >>>
>> >>> So there is no "round-trip" possible here.
>> >>>
>> >>> Which behavior is "correct", given the aromaticity and structure as
>> >>> specified?
>> >>> Should this be rendering/creating molecule, or failing?
>> >>>
>> >>> Thanks!
>> >>>
>> >>> (MarvinSketch does display the SMILES without complaints.;
>> >>> image is attached)
>> >>>
>> >>> Dmitri
>> >>>
>> >>>
>> >>> <PastedGraphic-3.png>
>> >>>
>> >>> ------------------------------------------------------------------------------
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>> >>>
>> >>>
>> >>
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>>
>>
>> <IPythonError.png>
>
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