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smiles reaction 如何进行 Atom-mapping removal 及 canonicalization

郝杰
2023-12-01
from rdkit.Chem import rdChemReactions
from rdkit.Chem.rdChemReactions import RemoveMappingNumbersFromReactions

reaction = rdChemReactions.ReactionFromSmarts('[Br:1][c:2]1[cH:3][c:4]([C:11](=[O:12])[O:13][CH3:14])[c:5]2[cH:6][cH:7][nH:8][c:9]2[cH:10]1.[H-:19].[I:15][CH:16]([CH3:17])[CH3:18].[Na+:20].[O:21]=[CH:22][N:23]([CH3:24])[CH3:25].[OH2:26]>>[Br:1][c:2]1[cH:3][c:4]([C:11](=[O:12])[O:13][CH3:14])[c:5]2[cH:6][cH:7][n:8]([CH:16]([CH3:17])[CH3:18])[c:9]2[cH:10]1')

RemoveMappingNumbersFromReactions(reaction)

reaction = rdChemReactions.ReactionToSmiles(reaction)

reaction
#'CC(C)I.CN(C)C=O.COC(=O)c1cc(Br)cc2[nH]ccc12.O.[HH2-].[Na+]>>COC(=O)c1cc(Br)cc2c1ccn2C(C)C'

 

?结果应为

'CC(C)I.CN(C)C=O.COC(=O)c1cc(Br)cc2[nH]ccc12.O.[H-].[Na+]>>COC(=O)c1cc(Br)cc2c1ccn2C(C)C'[HH2-] 与[H-] 有出入
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