Displaying molecules with a 3d shape

[dan2097]

Original report by Anonymous.

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Hi
I'm not sure but there might be an issue with displaying organic molecules that have some 3d structure. They are not the same as the images on e.g. wikipedia, here some examples:

https://en.wikipedia.org/wiki/Octanitrocubane
https://en.wikipedia.org/wiki/Twistane also a large dissimilarity
https://en.wikipedia.org/wiki/2.2.2-Propellane
https://en.wikipedia.org/wiki/1.1.1-Propellane
https://en.wikipedia.org/wiki/Bicyclo(1.1.1)pentane
https://en.wikipedia.org/wiki/Adamantane displays some CH_2
https://en.wikipedia.org/wiki/Iceane I don't know how you'd render that
https://en.wikipedia.org/wiki/Cubane

I've also filed this issue to lambdacasserole/avogadrio#30 where I originally stumbled upon this.

Can you improve on this?

[dan2097]

Original comment by Daniel Lowe (Bitbucket: dan2097, GitHub: dan2097).

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Both OPSIN and Avogadrio are using the same structue depiction library, Indigo (http://lifescience.opensource.epam.com/indigo/). There are other free depiction libraries e.g. http://www.simolecule.com/cdkdepict/depict.html, but for the type of molecules you are interested I don't think any depiction libraries do a good job unless the handling of the particular molecules has been special cased. The diagrams you're seeing on Wikipedia have almost certainly been manually drawn in a sketcher like ChemDraw. ChemDraw actually may be able to depict some of these molecules better, especially as it correctly removes part of a bond when two bonds cross, so as to make it clear that the crossing point is not an additonal carbon, but it isn't free and its library functionality is limited anyway.

The bottom line is that I can't really improve the situation.