own, but I would be happy to contribute to it.
I assume for a first pass that one could either use the standard geometries for
single, double, triple bonds between atoms of various elements, plus some kind of lookup
table for the geometries of well known structures like aromatic rings,
and (as you mentioned) strained rings.
Or (better) one could do it entirely on the level of functional groups,
trying to recognize each functional group in the molecule
and then looking up its geometry in a table.
One would also have to some kind of pattern matching to find larger conjugated structures
like unsaturated ketones, since there geometry would be slightly altered, right?
Of course, chances are somebody somewhere has written algorithms
that do some of these tasks, so a little preliminary literature search would probably be advised
to avoid re-inventing the wheel.
Question: can I assume an in-memory connectivity graph of the molecule has already been built, or would I be parsing some compact form like Smiles and building the graph.
BTW My sourceforge login is 'studiobamboo'.
CarlI would like to propose to work on something which is much requested: a 3D structure generator... Such an algorithm creates a 3D model of a molecule based on the molecular connectivity alone. It does so by placing atoms such that it and the neighbouring atoms make expected angles and distances. Special things happen when ring systems (especially the smaller, strained one) are to be dealt with. Anyway, it is a big job, but will get you familiar with molecular chemistry.
The source needs to go into CDK (and will be used by Jmol) in the org.openscience.cdk.layout package, possibly in a sub package...
Does this sound like something you would like to work on?
BTW, do you also made a SF account? I will add you as a developer to both projects then...
Egon
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