[Rdkit-discuss] Problems minimising

I'm seeing lots of failures when minimising molecules using MMFFOptimizeMolecule. A large proportion of seemingly valid molecules seem to fail. Am I doing something stupid here? Example: from rdkit import Chem from rdkit.Chem import AllChem molblock = ''' RDKit 3D 5 4 0 0 0

Re: [Rdkit-discuss] Problems minimising

Worked it out for myself. I needed to use: Chem.AddHs(mol, addCoords=True) Doh! On Tue, Dec 14, 2021 at 5:45 PM Tim Dudgeon wrote: > I'm seeing lots of failures when minimising molecules using > MMFFOptimizeMolecule. > A large proportion of seemingly valid molecules seem to fail. > Am I doing

[Rdkit-discuss] Query on a failed molecule from SureChEMBL

Hi All, Reading molecules from a bulk download of SureChEMBL, I come across a fair few molecules that fail to parse. Not sure whether they SHOULD parse or not. Here is an example: https://www.surechembl.org/chemical/SCHEMBL386 with SMILES code: COC(=O)C1=C(C=CC=C1)C1=CC=C(C[N+]#[N]=[N-])C=C1 Even

Re: [Rdkit-discuss] Query on a failed molecule from SureChEMBL

Hi Lewis, Dealing with all the strange chemical representations that show up "in the wild" is an ongoing struggle. Your first example is pretty clearly intended to be an azide and we can certainly add a rule to normalize that one to what the RDKit expects it to be (there already is a rule for C-N