RDKit 縮合環のコンフォメーション探索

例：C[C@@H]1CN2C(=O)[N-]C(=O)[C@@]1(c1ccccc1)C2=O

code:embed_mol_small.py

mol = Chem.MolFromSmiles("CC@@H1CN2C(=O)N-C(=O)C@@1(c1ccccc1)C2=O")

mol = Chem.AddHs(mol)

params = AllChem.ETKDGv3()

params.useSmallRingTorsions = True # 縮合環などねじれ対策

res = AllChem.EmbedMolecule(mol, params)

assert res !=-1

mol

https://scrapbox.io/files/68dbf66355d193776d6f8cf7.png