Hi Greg,
I was trying the following reaction in rdkit and it returns a product's
smiles that is invalid and can't be converted back into a valid molecule.
Any thoughts what's missing in my code?
>>rxn =
AllChem.ReactionFromSmarts('[#6:5][CH1:6]([#6:4])[NH1:2][C:7]([#6:8])=[O:9]>>[#6:8][C:7]#[N:2].[#6:4][C:6]=[C:5].[#8:9]')
>> reactants = [Chem.MolFromSmiles('CC(NC(=O)C(N)F)C(C)=O')]
>> ps = rxn.RunReactants(tuple(reactants))
>> or p in ps:
...: for m in p:
...: print Chem.MolToSmiles(m, isomericSmiles = True)
...:
N#CC(N)F
C=CC(C)=O
O
N#CC(N)F
CC=[C](C)=O
O
As you can see CC=[C](C)=O is an invalid smiles ( carbon has explicit
valence greater than permitted) which you can't convert back into a valid
molecule.
Any comments how this can be solved?
Thanks
*Syeda Sabrina*
*Graduate Assistant*
*Department of Chemical Engineering, Penn State University*
*University Park, PA*
*
*
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