The mol produced is correctly depicted in Jupyter, including dotted aromatic bonds, if SVG is used. Thus, in summary, RDKit can create the mol from some particular valid SMILES, but it cannot parse its own canonicalized SMILES to create a mol. ...
For the case of calling SanitizeMol after MolFromSmiles you can force rdkit to calculate the correct InChI key by calling AllChem.AssignStereochemistry(m1, cleanIt=True, force=True) before calculating the key. This behavior was unexpected since it would seem that sanitize=True should be equivalen...
Draw.MolsToGridImage(mol_scaffolds[:9], molsPerRow=3, subImgSize=(300,300)) 基于Murcko骨架聚类 scaffolds={}clusters_list=[]idx=1formol in mol_list:scaffold_smi=MurckoScaffold.MurckoScaffoldSmiles(mol=mol, includeChirality=False)ifscaffold_smi not in scaffolds.keys():scaffolds[scaffold_smi]=id...