. Such an ASCII structure view method in RDKit would be great and
I would be interested in trying it.
Vin
From: Ivan Tubert-Brohman
Sent: Tuesday, September 1, 2020 9:29 AM
To: Scalfani, Vincent
Cc: rdkit-discuss@lists.sourceforge.net
Subject: [EXTERNAL] Re: [Rdkit
Hello,
Is it possible to display a molecule image directly in an IPython console (not
a Jupyter Notebook)? Or maybe I need to send the image file directly to my
image viewer? I would like to be able to quickly view the molecules without
using a Jupyter Notebook or having to save the PNGs. For
Hi Sebastian,
As far as I can tell, the latest version available in conda is 2020.03.3. As
Dave mentioned, I was able to get this version by specifying python 3.7:
More information on this method here:
http://rdkit.blogspot.com/2019/10/sharing-conda-environments.html
You can also specify the
Dear RDKit Community,
Greg and I are putting together an application for the Google Season of the
Docs program:
https://developers.google.com/season-of-docs
The program connects open source organizations with technical writers. A
technical writer would work with several RDKit community
Hello Ivan and all,
I found this old thread about counting rings in bicyclics and I would like to
add it to the RDKit Cookbook, however, I'm not able to get the fuse function to
work. I get a 'Mol object is not iterable' error.
Any help appreciated. Thanks.
Vin
Hi Macjek and Mike,
If I understand your question correctly, you can specify InChI option
parameters when calculating InChIs. Here is an example:
m = Chem.MolFromSmiles('CCC1=CN=C(NC1=O)NC')
Chem.MolToInchi(m)
'InChI=1S/C7H11N3O/c1-3-5-4-9-7(8-2)10-6(5)11/h4H,3H2,1-2H3,(H2,8,9,10,11)'
Now, try
Dear Navid,
RDKit rejects tetravalent Nitrogen by default. This thread below may help. It
shows how to load the SMILES with sanitization off, then perform a partial
sanitization.
https://sourceforge.net/p/rdkit/mailman/message/32589379/
Vin
From: Navid Shervani-Tabar
Sent: Tuesday,
Hi Jubi,
If you need the entire dataset and are not creating queries via the API, you
can download all PubChem Data via ftp here:
ftp://ftp.ncbi.nlm.nih.gov/pubchem/
Then download the SDFs, and extract out SMILES (I’ve used regular expressions
that match the appropriate data tag with good
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