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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