How to compute properties of peptides ?
Biopython and the other bio-programming languages typically have examples of how to do this kind of thing. 

For example here is some python code for calculating some of these:

http://biopython.org/w/index.php?title=ProtParam&amp;redirect=no

Many of the propensity scales are in this database:
http://www.genome.jp/aaindex/

And there are also biojava classes for accessing these. Essentially you will need to know what these physicochemical properties are and get access to a scale for converting the letter to a numerical value.