[Molecularmechanics] Recycling CML

[Konrad Hinsen]

On Tuesday 04 November 2003 18:07, Jim Phillips wrote:

> Are atom ids not unique across the entire file?

If we want references to group templates, it is not possible to give each atom 
a unique id because there would not even be an explicit atom element for each 
atom.

> 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.

Then we have to list all atoms explicitly, meaning repetition of a lot of 
information.

It is true that my proposal requires a recursive parser, but on the plus side 
it generates smaller files and a clear indication of which molecules are 
chemically identical and which aren't.

For my code at least, the effort for reading such a file would be smaller than 
for reading a flat list from which I would have to reconstruct a set of 
unique molecule (and fragment) types.

Konrad.
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