Since the entire system is antiaromatic, why are any carbons at all shown
as aromatic in the SMILES?
-P.
On Thu, Jan 9, 2020 at 3:56 PM Andrew Dalke
wrote:
> Hi all,
>
> Could someone explain the following, which uses the SMILES from
> https://en.wikipedia.org/wiki/Acepentalene :
>
> >>> from
I wrote some code to do something like this that you might be able to start
from:
https://github.com/pstjohn/bde/blob/master/bde/fragment.py
Mine was mainly concerned with going to/from SMILES strings of the parent
mol and resulting radicals
On Wed, Jan 8, 2020 at 3:40 AM Puck van Gerwen
wrote:
Hi all,
Could someone explain the following, which uses the SMILES from
https://en.wikipedia.org/wiki/Acepentalene :
>>> from rdkit import Chem
>>> Chem.CanonSmiles("C1=CC2=CC=C3C2=C1C=C3")
'c1cc2ccc3ccc1-c=3-2'
>>> import rdkit
>>> rdkit.__version__
'2019.09.1'
I don't understand the aromatic
Hi Christian,
The topic of how to specify atom invariants came up recently on the list
here:
https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg09400.html
Here's a gist that shows how to specify your own atom invariants based
solely upon atomic number and, optionally,
Dear RDKit community,
Happy new year!
I am looking for a way to make the circular Morgen Fingerprints more SMILES
like. The background is that with the default definition of atom invariants
in the RDKit implementation, Morgan Fingerprints do not explicitly take
into account aromaticity, and use
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