Re: [Rdkit-discuss] PyMOL from RDKit? (Resurrection)

On Sat, Apr 23, 2016 at 8:37 PM, Robert DeLisle wrote: > > > In working with this, I found myself wanting to save some PyMOL files > programatically, but I see that there is not a Save option in the RDKit > PyMOL code. I added the snip below to the MolViewer class and it

Re: [Rdkit-discuss] Protonation and deprotonation

Dear Mark, you may wish to have a look at the SetFormalCharge() method, which operates on Atom objects: http://www.rdkit.org/docs/api/rdkit.Chem.rdchem.Atom-class.html#SetFormalCharge E.g., to protonate a piperidine: import rdkit from rdkit import Chem # create molecule from SMILES mol =

[Rdkit-discuss] Protonation and deprotonation

Dear RDkit community I have been experimenting with the RDkit toolkit for a little while, and I must say it offers an amazingly flexible and powerful set of chemical functionality. It is enough to finally get me to move to Python I think! So first of all, thanks for creating and supporting this.