[Molecularmechanics] Recycling CML

[Jim Phillips]

Hi,

On Tue, 4 Nov 2003, Konrad Hinsen wrote:

> Look at
>
>   http://dirac.cnrs-orleans.fr/fsatom_wiki/StructuralData
>
> and compare the last representation ("generic tree") with the molecule element
> in CML, it is an almost perfect fit. What doesn't seem possible, however, is
> to define bonds between "submolecules" (what I called "group"), as the atom
> reference must be a simple atom id. In a hierarchic arrangement, atom
> references need to be paths into substructures.

Are atom ids not unique across the entire file?

This would be a useful requirement in my book.  One reason is that if the
molecule is represented as a generic tree of nested groups that eventually
contain atoms, it would be nice if the parser could ignore the groups and
treat all of the atoms as a single flat list.

If you want path-based naming, then also assign names to groups and atoms,
so you can get to the same atom as "a4329" or "/BPTI/CA43/CA",

-Jim