Thanks Greg! That helps a lot, it was purely out of curiosity and understanding. I'm working with some legacy code that requires conformer generation before calculating partial charges. Now that I know it's unnecessary, I can speed up this process by quite a bit. It's good to know that there aren't really other RDKit descriptors that rely on conformers. In the future, I'll be using QM to generate partial charges as you have suggested.
Best, Hao On Wed, Jun 30, 2021 at 11:07 PM Greg Landrum <greg.land...@gmail.com> wrote: > Hi Hao, > > The reference for how the Gasteiger charges is calculated is in the > documentation for the function: > > https://www.rdkit.org/docs/source/rdkit.Chem.rdPartialCharges.html#rdkit.Chem.rdPartialCharges.ComputeGasteigerCharges > It does not use atomic coordinates. > > The MMFF charges are described in the MMFF94 papers (googling for MMFF94 > will turn these up). They also do not use atomic coordinates. > > If you really need partial charges which are dependent on the 3D conformer > (and I wonder why you do), the only option in the RDKit would be to use > it's implementation with the YAeHMOP package to do a semi-empirical QM > calculation: > > from rdkit import Chem > from rdkit.Chem import rdDistGeom > from rdkit.Chem import rdEHTTools > m = Chem.AddHs(Chem.MolFromSmiles('OCCN')) > rdDistGeom.EmbedMolecule(m) > ok,res = rdEHTTools.RunMol(m) > res.GetAtomicCharges() > > > Note that I call AddHs() there before generating the 3D coordinates. > Recent versions of the RDKit generate a warning if you don't do > this. That's not one which you should ignore: you generally need the Hs > there in order to get good conformations. > > There are many other methods out there which derive charges from quantum > mechanical calculations, but those all require using external software. > > Why do you want partial charges which are dependent on conformer? > > -greg > > > On Thu, Jul 1, 2021 at 3:53 AM Hao <shenha...@gmail.com> wrote: > >> Hi RDKit community, >> >> I am not familiar with how partial charges are calculated and I couldn't >> seem to find anything in my searches. >> >> If you run the code below, you'll see that the partial charges are always >> the same, even though the embedded mol is different - which leads me to >> believe these partial charge calculations are not dependent on conformers >> (which I always thought they were?) >> >> Can someone with more knowledge than me confirm my hypothesis? Also does >> rdkit have any partial charge calculators that are dependent on conformers? >> >> mol = Chem.MolFromSmiles('C[C@@](CC1=CC(O)=C(O)C=C1)(NN)C(O)=O') >> AllChem.EmbedMolecule(mol, AllChem.ETKDG()) >> AllChem.ComputeGasteigerCharges(mol) >> contribs = [float(mol.GetAtomWithIdx(i).GetProp('_GasteigerCharge')) for >> i in range(mol.GetNumAtoms())] >> fps = AllChem.MMFFGetMoleculeProperties(mol) >> mmff_partial_charges = [fps.GetMMFFPartialCharge(x) for x in >> range(mol.GetNumAtoms())] >> print(mmff_partial_charges) >> print(contribs) >> >> Thanks, >> Hao >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
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