Dear rdkitters,
I am trying to use rdkit descriptors to investigate protonation of
molecules in the gas phase
while testing my procedure on Ritalin, I try to calculate the protonation
energy on different functional groups in the molecule
although my understanding tells me protonation should occur
Hello to all,
I am trying to write a RDkit reaction, using Recursive SMARTS to better
define the atoms participating in the reaction.
For example, in this fragmentation reaction:
rxn = AllChem.ReactionFromSmarts('[C:1][O:2][C:3]>>[C:1].[O:2]=[C:3]')
I would like for [C:1] to define the carbon a
Hello all,
I am working on reactions in generalized form, such as
rxn = AllChem.ReactionFromSmarts('[C:1]=[N,O,S:2]>>[C:1]-[*:2]')
Is there an easy way to find out what were the elements in the reactant?
Was the second atom an oxygen, nitrogen or sulfur?
I hope someone can help me with this issu
Hello,
I am trying to formulate a reaction that describes a disconnection of a
terminal methyl group from a sulfide while leaving two ions - [S+] and
[CH3-].
Herein is my code:
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem.Descriptors import *
mo
Hello,
I am trying to formulate a reaction that describes a disconnection of a
terminal methyl goup from a sulfide while leaving to ions - [S+] and [CH3-].
Herein is my code:
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem.Descriptors import *
mol =
Hi,
I am using rdkit to emulate fragmentation of molecules, and it is working
great.
While working with opening of aromatic rings, it seems to me that it would
be simpler to work on the molecule after it was kekulized.
My question is: how do I write a reaction on a kekulized molecule.
For example
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