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ljmartin/syngenta-rdkit-indigo-rxn-parse.ipynb

Last active February 9, 2024 03:37
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ljmartin commented Feb 9, 2024

after all this, note that this works too (on the hydrogen issue, not aromaticity):

reactant = Chem.MolFromSmarts('[#6]1(=[#7])-[#6](=[#7])-[#7](-[#1])-[#6]=,:[#7]-[#7]-1-[#1]')
product = Chem.MolFromSmarts('[#6]1(-[#7])-[#6](-[#7])=[#7]-[#6]:[#7]-[#7]=1')
rxn = rdChemReactions.ReactionFromSmarts(
    Chem.MolToSmarts(reactant)+'>>'+Chem.MolToSmarts(product)
)
from rdkit.Chem import AllChem
AllChem.SanitizeRxn(rxn)

mol = Chem.MolFromSmiles('N=C1NC=NNC1=N')
Chem.Kekulize(mol, clearAromaticFlags=True)
rxn.RunReactant(mol, 0)[0][0]

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