On Monday 7 February 2005 21:12, Nicolas Vervelle wrote: > From: "Miguel" <[EMAIL PROTECTED]> > > > The structure detection that is needed for FAH is at a level below this. > > The .xyz files do not have the amino acids identified. Therefore, we > > would need code which identifies amino acids from individual atoms & > > their bonds. > > > > I am sure that this is an interesting problem and that people have worked > > on it. It is essentially a pattern match on sub-structures. > > My knowledge in chemistry is somewhat limited so I may be wrong, > but it doesn't seem so much work to write code to identify amino acids from > atoms and bonds.
A real substructure search is complex, but I don't think we need that at this stage... > For example, each pattern that matches the following is alanine : a C > bonded to CH3, NH2 and COOH. Right, something like that is what I was thinking about... actually, just backbone was my first thought... > The algorithm must also deals with peptide bonds and disulfure bonds. The latter should be easy detectable too... just a S connected to another S... If we keep it simple like this, we have O(N). > It must also work when the H atoms are not int the xyz file. > > > It seems to me that it is the kind of thing that warrants a literature > > search prior to starting in on an implementation. It also seems to me > > that it would be a great project for a graduate student. > > If I have time this weekend, I will have a look at this and maybe make a > few tests. Thanx. Egon -- [EMAIL PROTECTED] GPG: 1024D/D6336BA6 ------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
