I have been thinking about putting together a good set of objects for
dealing with molecular structures for about two years now. Grad
school has not left me the time I would like to work on it though (Get
to see my wife about 5th weekend or so). There are some ideas I would like
to discuss though before I force time into my schedule. I propose that
a publicly available set of objects should be extensible, so that widely
varying purposes could be met, but at the same time a mechanism for
limiting the extensions for certain purposes. For example, someone wanting
to look at a protein structure would like the code to know about helix and
beta sheet conformations and would probably not worry about the individual
atomic masses, whereas doing certain typpes of calculations one might
need the reverse. Should separate objects e developed that could be
associated with one another, or should a control mechanism be established,
along with guidelines for making extensions to the standard?
Tom Branham
branham at binah.cc.brandeis.edu
