Re: [Rdkit-discuss] Getting to grips with Open3DAlign

Hi Tim, The below doesn't do what you think it does: On Wed, Jun 22, 2016 at 10:29 AM, Tim Dudgeon wrote: This line: AllChem.AddHs(mol1) > returns a new molecule with Hs added, it does not actually modify mol1. The consequence of that is that this: cids =

Re: [Rdkit-discuss] Getting to grips with Open3DAlign

Paolo, Greg Sereina, Thanks for your thoughts. In combination they do indeed resolve the problems. To clarify one other thing: better O3A alignments give higher scores. For the record here is my updated script: from rdkit import Chem, RDConfig from rdkit.Chem import AllChem, rdMolAlign ref

Re: [Rdkit-discuss] Getting to grips with Open3DAlign

Hi Sereina, I beg to differ on the advisability of minimisation, even after using the parameters you suggest to generate the conformation. I've recently been using the CCDC's excellent Python API to analyse the results of the generated conformations. This lets you very quickly assess whether any

Re: [Rdkit-discuss] Getting to grips with Open3DAlign

I just tried Tim’s example (or a version of it that Greg sent me, respectively). What is missing are the hydrogens for the torsion terms of ETKDG to work properly. Before generating the conformations AllChem.AddHs() should be called. Best, Sereina On 22 Jun 2016, at 06:48, Sereina

Re: [Rdkit-discuss] Getting to grips with Open3DAlign

Based on the code snippets, Paolo has not used the basic-knowledge terms whereas Tim did. When setting useExpTorsionAnglePrefs=True and useBasicKnowledge=True, a minimization is in principle not necessary anymore (unless there are aliphatic rings, because we currently don’t have torsion rules

Re: [Rdkit-discuss] Getting to grips with Open3DAlign

I don't have anything to add to the pieces about the alignment (Paolo is the expert there!), but one comment on the conformation generation: If you used the background knowledge terms in the embedding, I don't think you should be getting the really distorted aromatic rings. Since in this case that

Re: [Rdkit-discuss] Getting to grips with Open3DAlign

Dear Tim, the Align() method returns an RMSD value, which however is computed only on a limited number of atom pairs, namely those that the algorithm was able to match between the two molecules, so a low value is not particularly informative of the overall goodness of the alignment, as it

[Rdkit-discuss] Getting to grips with Open3DAlign

Hi All, I'm trying to get to grips with using Open3D Align in RDKit, but hitting problems. My approach is to generate random conformers of the probe molecule and align it to the reference molecule. My example is cobbled together from the examples in the cookbook. from rdkit import Chem,