Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

[Cameron Pye]

 I know this isn't a particularly sexy job for a budding cheminformatician
but...

Work on the Python documentation!!!

I love rdKit and occasionally think I'm pretty savvy but I can't tell you
how often I'm scrolling through the documentation (or source) and either:

a) discover something that exists but doesn't have anything documentation
but the function signature
or
b) discover some some functionality that exists (and i've wanted) but
didn't know it was there!

I think this mailing list and Greg do a superb job of keeping the community
informed and creating and maintaining the codebase but I think having some
more "Pythonic" API documentation would be great.

One shining example is the scikit-learn documentation
 that has a quick start,
tutorials etc.  and then in the well categorized and explanatory API ref
has links for examples in the User Guide (akin to the "Getting Started with
the RDKit in Python" doc) .

Just my 2 cents!

Thanks for all the hard work as always,
Cam


On Mon, Jan 15, 2018 at 12:52 PM <
rdkit-discuss-requ...@lists.sourceforge.net> wrote:

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>1. Re: RDKit and Google Summer of Code 2018 (Jason Biggs)
>2. Re: RDKit and Google Summer of Code 2018 (Tim Dudgeon)
>3. Re: RDKit and Google Summer of Code 2018 (Tim Dudgeon)
>
>
> --
>
> Message: 1
> Date: Mon, 15 Jan 2018 09:20:48 -0600
> From: Jason Biggs 
> To: Greg Landrum 
> Cc: RDKit Discuss 
> Subject: Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018
> Message-ID:
> 

[Rdkit-discuss] Can't stifle warnings / logs

[Cameron Pye]

Hi There,

I'm a longtime rdkit user but a first time mailing list user.

One thing that has always haunted me is the warnings and errors that get
thrown whilst reading in a dirty sd file or smiles list. I've tried to no
avail to silence the warnings and errors many times and normally just live
with the endless scroll on my terminal but today I've finally had enough.

Any help would be appreciated!!

I've tried wrapping a ForwardSDMolSupplier with the following :

from io import StringIO
import sys
Chem.WrapLogs()

def silent_supplier(supplier):
sio = sys.stderr = StringIO()
for m in supplier:
sio = sys.stderr = StringIO()
if m is None:
continue
else:
yield m

but still get a stream of these sorts of errors:
[11:39:24]  S group DAT ignored on line 143364
[11:39:24] Can't kekulize mol.  Unkekulized atoms: 5 6 7 8 9 10 11 13 14

[11:39:24] ERROR: Could not sanitize molecule ending on line 143370
[11:39:24] ERROR: Can't kekulize mol.  Unkekulized atoms: 5 6 7 8 9 10 11
13 14

[11:39:24]  S group DAT ignored on line 145111
[11:39:24] Can't kekulize mol.  Unkekulized atoms: 3 4 5 6 26

[11:39:24] ERROR: Could not sanitize molecule ending on line 145117
[11:39:24] ERROR: Can't kekulize mol.  Unkekulized atoms: 3 4 5 6 26

[11:39:24]  S group DAT ignored on line 159380
[11:39:24] Can't kekulize mol.  Unkekulized atoms: 5 6 7 8 9 10 11 12 13

[11:39:24] ERROR: Could not sanitize molecule ending on line 159386
[11:39:24] ERROR: Can't kekulize mol.  Unkekulized atoms: 5 6 7 8 9 10 11
12 13
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