I don't know of any protein specific programming books but I can tell you a few
things to get you started. There are two basic ways that proteins structure
data can be represented. One way is simply a list (array) of XYZ cartesian
coordinates representing the atom postitions. A second method often used is
a system of "internal" coordinates. In this case an array of bond lengths,
angles and torsions can describe a protein structure. Most programs that use
internal coordinates also use cartesian coordinates and can easily convert
between the two.
I hope this helps a little. You should search out all the code you can find
(and there is a lot) that deals with proteins and see what others have done.
Jeffrey S. Taylor Molecular Modeling
The Wistar Institute and Software development
The University of Pennsylvania Molecular Biology
Philadelphia, PA 19104 E-Mail Jeff at aries.wistar.upenn.edu
(215) 898-2202 WWW http://adeno.wistar.upenn.edu