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>
Date: Thursday, 22 February 2018 at 13:32
To: Lukas Pravda <lpra...@ebi.ac.uk>
Cc: RDKit Discuss <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> 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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