On 01/07/2021 13:15, Hao wrote:
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.
Be careful, with some charge models the partial charges are
dependent on the conformer. For example, with AM1BCC (but this charge
model is not available in rdkit).
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 _______________________________________________
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