Hello Lukas,
The file rdkit/TestRunner.py contains a class/context manager called
OutputRedirectC. If I remember correctly, this allowed capturing these
messages. It's not used anywhere in the RDkit code base, so it not work
anymore. Anyway, give it a try and if it works, you can modify it to redirect
the output into a variable or StringIO.
Best,
Peter
> On 9 Mar 2018, at 9:34 AM, Lukas Pravda <lpra...@ebi.ac.uk> wrote:
>
> Hello Greg,
>
> I’m very sorry for the late reply. Thank you for the hint on disabling the
> log message, it works on my end. However, I was more interested in catching
> the other bit i.e. which part of the structure is wrong, rather than which
> part of the sanitization process failed. That is accessing the message
> ‘Explicit valence for atom # 1 O, 3, is greater than permitted’ in form to
> find out that it is the misbehaving oxygen which causes failure of the
> sanitization process. Perhaps piping the log information into a variable or
> something like that.
>
> Best,
> Lukas
>
>
>
> From: Greg Landrum <greg.land...@gmail.com <mailto:greg.land...@gmail.com>>
> Date: Thursday, 22 February 2018 at 13:32
> To: Lukas Pravda <lpra...@ebi.ac.uk <mailto:lpra...@ebi.ac.uk>>
> Cc: RDKit Discuss <Rdkit-discuss@lists.sourceforge.net
> <mailto:Rdkit-discuss@lists.sourceforge.net>>
> Subject: Re: [Rdkit-discuss] Programatic access to the mol sanitation process
> results
>
> Hi Lukas,
>
> On Thu, Feb 22, 2018 at 1:14 PM, Lukas Pravda <lpra...@ebi.ac.uk
> <mailto:lpra...@ebi.ac.uk>> wrote:
>> Dear rdkiters,
>>
>> I’m constructing molecules from scratch using python 3.5.4 and RDKit
>> 2017.09.2 and due to the variety of reasons some of them are violating
>> general principles of chemistry in a way implemented in rdkit, so I’m
>> getting information like:
>>
>> Explicit valence for atom # 14 N, 4, is greater than permitted etc.
>>
>> I wonder if there is a way how to retrieve this piece of information in a
>> programmatic way. In order to work with it. Presently, rdkit only prints
>> this out into terminal and Chem.SanitizeMol() only returns first
>> sanitization flag with the issue. Ideally, I’d like no information to be
>> printed into console, while keeping the log info ‘Explicit valence for atom
>> # 14 N, 4, is greater than permitted’ preferably in a structured way (in a
>> property/method?), in order to further deal with those erroneous cases.
>
> At last part of this is pretty straightforward.
>
> There are two parts:
> - making it so error messages don't go to the console
> - capturing the failed operation.
>
> The first is a bit fragile (i.e. doesn't always work), so you will sometimes
> end up still seeing error messages (as here), but the second should be
> reliable:
>
> In [30]: rdBase.DisableLog('rdApp.*')
>
> In [31]: m = Chem.MolFromSmiles('c1cccc1',sanitize=False)
>
> In [32]: Chem.SanitizeMol(m,catchErrors=True)
> [14:29:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
>
> Out[32]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_KEKULIZE
>
> In [35]:
> Chem.SanitizeMol(Chem.MolFromSmiles('CO(C)C',sanitize=False),catchErrors=True)
> [14:31:37] Explicit valence for atom # 1 O, 3, is greater than permitted
> Out[35]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_PROPERTIES
>
>
> You can see that the return value indicates what went wrong in the
> sanitization.
>
> I hope this helps,
> -greg
>
>
>
>
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