[Rdkit-discuss] UFFTYPE error in MMFF minimization

Hello In order to bypass errors in UFF typing I am using MMFF94 as a minimization forcefield. However errors about UFF atom type are still occurring for Boron. staring MMFF94 minimization CHEMBL2374533 [15:59:34] UFFTYPER: Unrecognized atom type: B_1 (26) [15:59:34] UFFTYPER: Unrecognized atom

Re: [Rdkit-discuss] Question regarding 3D pharmacophores

Greg, Outstanding - thanks! This looks to be as close to what I wanted as I could have dared hope. I had no idea where to even begin looking. Fine work. Very fine. Best, Andy On Fri, Oct 20, 2017 at 5:21 PM, Greg Landrum wrote: > Assuming I'm understanding correctly

Re: [Rdkit-discuss] Question regarding 3D pharmacophores

Assuming I'm understanding correctly what you're asking for, the RDKit actually has code for doing exactly this. That's the good news. The bad news is that there's pretty much no documentation for it. Since it's kind of interesting code (at least I think so) and it came up in an earlier

[Rdkit-discuss] Question regarding 3D pharmacophores

Hi, I'm curious if anyone has figured out a way to compare two molecules based upon their pharmacophore similarities. Specifically, I want to compare 2 molecules in their _absolute_ locations, and not simply see if they have 2 pharmacophores that match well via a translation/rotation. From what I

Re: [Rdkit-discuss] SetBondDir not Affecting Chiral Centers

That's a nice Python implementation of the logic that's used in prepareMolForDrawing that does the same thing. It probably makes sense for there to be an easy single function that you can call to do this, but that should definitely work. -greg On Thu, Oct 19, 2017 at 6:43 PM, Chris Murphy