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Does anyone know if this type of rendering in RDKIT ver. 2020.03.3.0 is normal #4391

Answered by ptosco
Lhx0108 asked this question in General
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RDKit will depict an explicit C atom when the are neither multiple bonds nor substituents that help showing the presence of a carbon atom, and the two contiguous single bonds are almost collinear, making it very difficult to figure out that there is indeed a carbon atom in between the two bonds.
If you switch to the CoordGen depiction you will get a nicer layout that does not require those explicit carbons as it has 120 degree angles between sp3 carbons:

from rdkit.Chem.Draw import rdDepictor
rdDepictor.SetPreferCoordGen(True)

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@Lhx0108
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Answer selected by greglandrum
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