: Greg Landrum
Sent: 14 September 2021 06:01
To: Mark Mackey
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Reaction SMARTS ring properties
Hi Mark,
You haven't shown how the molecules in reagentsRdMolList are constructed, but
from the error message I guess that they have been
Hi Mark,
You haven't shown how the molecules in reagentsRdMolList are constructed,
but from the error message I guess that they have been created without
running any of the sanitization code.
The example transformation you show includes ring information, so it will
generate errors if the
Hi all,
I'm trying to run some chemical reactions using the C++ API. Doing something
like
text = "
[cH1:1]1:[c:2](-[CH2:7]-[CH2:8]-[NH2:9]):[c:3]:[c:4]:[c:5]:[c:6]:1.[#6:11]-[CH1;R0:10]=[OD1]>>[c:1]12:[c:2](-[CH2:7]-[CH2:8]-[NH1:9]-[C:10]-2(-[#6:11])):[c:3]:[c:4]:[c:5]:[c:6]:1c1cc(CCN)ccc1";
Problem solved. Many Thanks,
Jean-Marc
Le 04/04/2019 à 06:54, Greg Landrum a écrit :
On Wed, Apr 3, 2019 at 8:26 PM Jean-Marc Nuzillard
mailto:jm.nuzill...@univ-reims.fr>> wrote:
Dear Greg,
In [10] and Out[10] of your answer below (thanks!) incited me to
believe that the
Dear Greg,
In [10] and Out[10] of your answer below (thanks!) incited me to believe
that the geometry of double bonds
outside of the reactive center in the reaction product is not lost for
ever, contrarily to what my example showed.
So, I went back to my example and printed the SMILES
Hi Jean-Marc,
Unfortunately not. The RDKit currently ignores stereo information from
"mapped bonds" (bonds for which both atoms are mapped) from the reactants.
If you include stereo info in the reaction itself, that will be copied over
in to the products, but that is not what you're looking for.
Hi Jean-Marc,
Try the reaction smarts '[C:1]([OH:2])=[N:3]>>[C:1](=[OH0:2])[NH:3]'. The
only difference is the addition of "H0" to product atom :2. The problem is
that the hydrogen count from the reactant atom gets copied over unless
specified otherwise.
Hope this helps,
Ivan
On Wed, Feb 6,
Hi Ivan,
I tried the SMARTS you sent and it worked.
Thank you!
Jean-Marc
Le 06/02/2019 à 15:46, Ivan Tubert-Brohman a écrit :
Hi Jean-Marc,
Try the reaction smarts '[C:1]([OH:2])=[N:3]>>[C:1](=[OH0:2])[NH:3]'.
The only difference is the addition of "H0" to product atom :2. The
problem is
Dear All,
I need to convert iminol functional groups into amides.
Being new to reaction SMARTS I wrote the following code:
*
from rdkit import Chem
from rdkit.Chem import AllChem
#from rdkit.Chem.Draw import IPythonConsole
sm1 = 'CNC(C)=O'
m1 = Chem.MolFromSmiles(sm1)
#m1
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