Hello I want to enumerate a simple molecule having 4 substituents R with a list of ca. 100 SMILES. For reasons of simply synthesis, in each enumeration of R, the R should be the same in all four positions (no cross permutation). There is no reaction that covers all 100 SMILES.
I followed https://www.rdkit.org/docs/Cookbook.html#sidechain-core-enumeration and modified the code proposed by Earnshaw et al. accordingly: core = Chem.MolFromSmiles('[*]C(C=C1)=CC=C1C(C2=CC=C([*])C=C2)C(C3=CC=C([*])C=C3)C4=CC=C([*])C=C4') chains = ['C','CC','CCC','CCCC','CCCCC','CCCCCC'] chainMols = [Chem.MolFromSmiles(chain) for chain in chains] product_smi = [] for chainMol in chainMols: product_mol = Chem.ReplaceSubstructs(core,Chem.MolFromSmarts('[#4]'),chainMol) product_smi.append(Chem.MolToSmiles(product_mol[0])) print(product_smi) which results in ['*c1ccc(C(c2ccc(*)cc2)C(c2ccc(*)cc2)c2ccc(*)cc2)cc1', '*c1ccc(C(c2ccc(*)cc2)C(c2ccc(*)cc2)c2ccc(*)cc2)cc1', '*c1ccc(C(c2ccc(*)cc2)C(c2ccc(*)cc2)c2ccc(*)cc2)cc1', '*c1ccc(C(c2ccc(*)cc2)C(c2ccc(*)cc2)c2ccc(*)cc2)cc1', '*c1ccc(C(c2ccc(*)cc2)C(c2ccc(*)cc2)c2ccc(*)cc2)cc1', '*c1ccc(C(c2ccc(*)cc2)C(c2ccc(*)cc2)c2ccc(*)cc2)cc1’] This is six times the same compound with no enumeration. Python beginner here. Can anybody tell me what the mistake is or where I can find an example in the literature, please? Many thanks C.
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