Hi Shani
This should work
rxn = AllChem.ReactionFromSmarts('[C:1]=[C:2]>>[*:1][*+:2]')
m = Chem.MolFromSmiles('CC(C)C1=CC[C@H]2C(=C1)CC[C@@H]3[C@@]2(CCCC3(C)C)C')
ps = rxn.RunReactants((m,))
mols = [x[0] for x in ps]
Best regards, Jan
On 2 Feb 2020, at 11.34, Shani Levi
<levishan...@gmail.com<mailto:levishan...@gmail.com>> wrote:
Hi,
I would like to create a carbocation "database" from my existing database of
unsaturated molecules.
The idea is as follows:
For each double bond, I would like to attach one Hydrogen, for each carbon in
the double bond.
So for example, if I have a molecule with one double bond, I will end up with
two different carbocations,
if I have a molecule with 2 double bonds, I would like to get 4 different
carbocations.
I tried using GetSubstructMatch for ('C=C') and SetFormalCharge to 1.
e.g:
mol = Chem.MolFromSmiles('CC(C)C1=CC[C@H]2C(=C1)CC[C@@H]3[C@@]2(CCCC3(C)C)C')
func = Chem.MolFromSmiles('C=C')
matches = mol.GetSubstructMatches(func)
mol.GetAtomWithIdx(matches[0][1]).SetFormalCharge(1)
The result is:
CC(C)C1=[C+]C[C@H]2C(=C1)CC[C@H]1C(C)(C)CCC[C@@]12C
I would like to get rid of the double bond.
(and get CC(C)C1[C+]C[C@H]2C(=C1)CC[C@H]1C(C)(C)CCC[C@@]12C )
How can I do that?
Thanks a lot in advance,
Shani
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