On Friday 13 June 2003 22:59, Carl Resnikoff wrote:
> Hi Egon. That sounds like a great project. It may be too big to take on
> entirely on my own, but I would be happy to contribute to it.
Most other developers are very supporting in this regard... any question you
may have will be answered...
> 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.
Yes, that should be possible... This would require, though, a database of
> 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?
Yes, that is an option...
> 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.
Do you have access to the Encyclopedia of Computational Chemistry?
There is a chapter on "Three-dimensional Structure Generation:
It references to these programs:
CONCORD: Tripos, USA, lit.rev:R.S.Pearlman, Chem.Des.Auto.News, 1987, 2 1/5-6
ALCOGEN: Chemical Concepts, no lit.rev.
Chem-X: Chemical Design Ltd, lit.rev: K.Davies and R.Upton, Tetrahedron
Comp.Method., 1990, 3, 665-671
MOLGEO: E.V.Gordeeva, A.R.Katritzky, V.V.Shcherbukhin, and N.S.Zefirov,
J.Chem.Inf.Comput.Sci., 1993, 33, 102-111
COBRA: Oxford Molecular Ltd, lit.revs: A.R.Leach and K.Prout, J.Comput.Chem.,
1990, 11, 1193-1205, A.R. Leach, A.S.Smellie, J.Chem.Inf.Comput.Sci., 1992,
CORINA: lit.rev: J.Gasteiger, C.Rudolph and J.Sadowski, Tetrahedron
Comp.Method. 1990, 3, 537-547, J.Sadowski, C.Rudolph, J.Gasteiger,
Anal.Chim.Acta, 1992, 265, 233-241
CONVERTER: Biosym/MSI, no lit.rev.
> 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.
Yes, the graph is an AtomContainer, so not an efficient graph, but never the
less a graph... it has the Atom and Bond which can be retrieved with
getAtoms() and getBonds()... The Bond's have references to the Atoms, but
I do not think the other way around...
In the org.openscience.cdk.graph package are graph algorithms found. There is
also subgraph searching (i.e. is X a subgraph of Y) and graph matching
> BTW My sourceforge login is 'studiobamboo'.
Ok, I'll add you next week... BTW, what's the story behind the name ??