Dear rdkit community,
I’m not quite sure if this is more of an rdkit or a chemistry related question.
I’d like to understand why a manganese ion has 3 radical electrons when
interpreted by rdkit. I have not seen radicals in any other metal ion so far.
The code to get the depiction looks like this:
from rdkit import Chem
from rdkit.Chem import Draw
width = 500
m = Chem.MolFromInchi('InChI=1S/Mn/q+2')
drawer = Draw.rdMolDraw2D.MolDraw2DSVG(width, width)
Draw.rdMolDraw2D.PrepareMolForDrawing(m, wedgeBonds=True, kekulize=True,
addChiralHs=True)
drawer.DrawMolecule(m)
drawer.FinishDrawing()
with open('2d_mol.svg', 'w') as f:
svg = drawer.GetDrawingText()
f.write(svg)
print('done')
and the depiction you get looks like the one on the page:
https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/MN Thank you in
advance for clarification.
rdkit through python 2020.03.4 on mac 10.15.6
Best,
Lukas
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