How is Net Charge computed?
The Net Charge of a protein sequence at a certain pH is computed using the following formulae.
In BioJava, the default pH used is 7.0.
pKa values used can be chosen between the following two sources with ExPASy being the default one.
1) ExPASy - ProtParam 1
2) A.Lehninger, Principles of Biochemistry, 4th Edition (2005), Chapter 3, page 78, Table 3-1. 2