Ideas over representation in chemistry

This section starts with a collection of open points about the research about representation methods for chemistry. I’s an open ended activity for now.

Bonds representations

Besides the usual bonds and H-bonds, which other bonds type are useful (or necessary)? I'm speaking about:

1. Multiple bonds (double, triple)
2. Other “simple” bonds? Like resonance bonds or fractional order bonds (what are they?)
3. Aromatic cycles
4. Salt bridges
5. Disulphur bridges
6. Metallocene-like bonds

Other questions: which file format support them? How reliably are they computed?

Simplification methods

How to identify, extract and isolate important structures?

• How to extract rings.
• Other global structures highlighting methods: least-squares mean planes, etc.
• Other summarizing methods for groups of atoms or sets of surface vertices: for example they may be represented by ellipsoids that enclose them while having minimal volume.

Unusual representations

The paper: Molecular Morphing by Felice Frankel cites a new method of structure representation. See also A new framework for non-photorealistic rendering and a nice movie.