On Mon, Oct 22, 2012 at 11:42 PM, Andrew Dalke <[email protected]>wrote: > > > I thought that I could switch to RDKit to do the same depiction, only > with the ability to control the bond highlighting. I want the > matched atoms and bonds to be in one color, and the others to > be in another color. > > I have failed. What I get looks like this: > > Pretty much my code doesn't work. Even if I could get it to work, > you can see that the wedge bonds are in black, when I expected > them to be in one of the two colors I chose. >
There was a bug in the drawing code that caused it to not highlight wedged or dashed bonds (https://sourceforge.net/p/rdkit/bugs/262/). I just checked in a fix: m=Chem.MolFromSmiles('C1N[C@@]1(Cl)Br') Draw.MolToImage(m,highlightAtoms=(2,3,4)) [image: Inline image 2] > Also, most of the reasons for MCS confusion in my data set is because > I'm working with structures with different aromaticity perception. While > chemists hate the aromatic ring, I would like to see it. Is there an option > to enable that? > You can't get a ring, but you can have it draw dashed lines for the "extra" line of aromatic bonds by setting the optional kekulize argument to False when you call Draw.MolToImage: m = Chem.MolFromSmiles('c1ccccc1') Draw.MolToImage(m,kekulize=False) [image: Inline image 1] Is that close enough? -greg
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