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
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