[Biojava-l] Find Epitope and CDR3?

[Ashika Umanga Umagiliya]

Greetings all,

This is kind of off the topic , but since I am from a computer science 
background and I have very little knowledge in bioinformatics ,i thought 
I can get some help form here.
In the project I am working with, I have to find the 'epitope' sequence 
in a PDB file.At the moment they have implemented some logic (not very 
good, as they say) for it using Perl ,but for the requirements they ask 
I need to do it in Java.
And also there is a requirement to highlight CRD3 region in JMol.
Any tips where I found start?

Thanks in advance.
umanga