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.
Besides the usual bonds and H-bonds, which other bonds type are useful (or necessary)?
I'm speaking about:
- Multiple bonds (double, triple)
- Other “simple” bonds? Like resonance bonds or fractional order bonds (what are they?)
- Aromatic cycles
- Salt bridges
- Disulphur bridges
- Metallocene-like bonds
Other questions: which file format support them? How reliably are they computed?
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.
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.