[Molecularmechanics] Recycling CML

[Konrad Hinsen]

On Wednesday 05 November 2003 23:28, David van der Spoel wrote:

> The three options you describe are basically in my proposal. I don't see
> why my proposal should be limited to linear and/or peptide chains (as
> Konrad suggested), it is flexible in the sense that it defines a framework

First of all, because it has explicit element names that suggest such a 
restriction (macromolecules, residue). I don't see how I would define a water 
molecule, for example, although some provision could easily be added.

Second, because groups (residues in your terminology) cannot be nested. The 
tree structure has exactly three levels (molecule, residue, atom), with bonds 
inside residues and linkdefs in between residues.

There are, of course, advantages to such more rigid structures, in particular 
ease of handling. I would like to hear others' opinion on this.

Konrad.
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