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.hongc...@foxmail.com> 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? > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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