Re: [Rdkit-discuss] Reaction SMARTS ring properties

2021-09-13 Thread Greg Landrum
Hi Mark, You haven't shown how the molecules in reagentsRdMolList are constructed, but from the error message I guess that they have been created without running any of the sanitization code. The example transformation you show includes ring information, so it will generate errors if the

[Rdkit-discuss] Reaction SMARTS ring properties

2021-09-13 Thread Mark Mackey via Rdkit-discuss
Hi all, I'm trying to run some chemical reactions using the C++ API. Doing something like text = " [cH1:1]1:[c:2](-[CH2:7]-[CH2:8]-[NH2:9]):[c:3]:[c:4]:[c:5]:[c:6]:1.[#6:11]-[CH1;R0:10]=[OD1]>>[c:1]12:[c:2](-[CH2:7]-[CH2:8]-[NH1:9]-[C:10]-2(-[#6:11])):[c:3]:[c:4]:[c:5]:[c:6]:1c1cc(CCN)ccc1";

Re: [Rdkit-discuss] SMILES from sdf file

2021-09-13 Thread Anthony Nash
Hi Patrick, Thank you for the code and the links, both are very helpful and exactly what I needed. Many thanks Anthony Kind regards Dr Anthony Nash PhD MRSC Senior Research Scientist Nuffield Department of Clinical Neurosciences RMCR Kellogg College University of Oxford