Re: [Rdkit-discuss] smiles-mol-smiles roundtrip can change stereochemistry

O.K. More info now. It seems like MolFromSmiles works well. The problem is with MolToSmiles. Perhaps the ring closure marker digit is causing the problem. Attached is a simpler example. The input smiles is 'O/C=C1\\\\C1=N/F'. The bond info of the created molecule looks healthy. But MolToSmiles

Re: [Rdkit-discuss] smiles-mol-smiles roundtrip can change stereochemistry

I'll give you the original smiles too. Although it is longer, the round trip does not change the atom ordering. So perhaps it's easier to figure things out. "O=C1Nc2ccc(C(=O)N(F)CCF)cc2/C1=C1/Nc2c2/C1=N\OCCOF" Ling Chan 於 2021年11月6日週六 下午1:05寫道： > Dear colleagues, > > I have encountered an

[Rdkit-discuss] smiles-mol-smiles roundtrip can change stereochemistry

Dear colleagues, I have encountered an instance where MolToSmiles(MolFromSmiles()) resulted in a change of stereochemistry of a double bond. An attached figure illustrates this. The problematic input smiles is "C1Nc2ccc(C)cc2/C1=C1/Nc2c2/C1=N\OCCOF". The original smiles was even longer. I