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 experimental structures... > 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: Automation" see: http://www.wiley.com/legacy/wileychi/ecc/opening.html 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, 32, 379-385 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 implemented... > BTW My sourceforge login is 'studiobamboo'. Ok, I'll add you next week... BTW, what's the story behind the name ?? Egon ------------------------------------------------------- This SF.NET email is sponsored by: eBay Great deals on office technology -- on eBay now! Click here: http://adfarm.mediaplex.com/ad/ck/711-11697-6916-5 _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
