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. For example, each pattern that matches the following is alanine : a C bonded to CH3, NH2 and COOH. The algorithm must also deals with peptide bonds and disulfure bonds. 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. Nicolas ------------------------------------------------------- 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
