Re: [Rdkit-discuss] Is there any way to protonate a molecule?

[Patrick W. <wpw...@gm...>]

I haven't tried it yet, but this recent paper in the Journal of
Cheminformatics looks interesting.  The authors supply a git repo with code
based on the RDKit.

Dimorphite-DL: an open-source program for enumerating the ionization states
of drug-like small molecules

https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0336-9

Pat

On Mon, Mar 25, 2019 at 5:13 AM HC.Ji <ji....@fo...> wrote:

> I m tring simulate the fragmentation of ESI mass spectra based on the
> [M+H]+ ions. Thus, I want to simulate the ionisation by the addition of one
> proton to heteroatoms. For example,
>
> from rdkit.Chem import AllChem
> from rdkit.Chem.Draw import rdMolDraw2D
> from IPython.display import SVG
> # read mol
> mol =
> Chem.MolFromSmiles('O=C(O)C1=CC(=NNC2=CC=C(C=C2)C(=O)NCCC(=O)O)C=CC1=O')
>
> # draw the mol
> dr = rdMolDraw2D.MolDraw2DSVG(800,800)
> dr.SetFontSize(0.3)
> op = dr.drawOptions()
> for i in range(mol.GetNumAtoms()) :
>   op.atomLabels[i] = mol.GetAtomWithIdx(i).GetSymbol() + str((i+1))
>   AllChem.Compute2DCoords(mol)
>   dr.DrawMolecule(mol)
>   dr.FinishDrawing()
>   svg = dr.GetDrawingText()
>   SVG(svg)
>
> If I want to add one proton to the N atom with the index of #17 and to
> ionize the molecule, what should I do in rdkit?
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