Separate bindings for HHblits2 and HHblits3

HHblits2 is considered to be deprecated. If the raw hhblits binding
is imported, the module autodetects the hhblits version and imports
the appropriate version of the binding.

modules/bindings/pymod/CMakeLists.txt

@@ -9,6 +9,8 @@ clustalw.py
 utils.py
 naccess.py
 hhblits.py
+hhblits2.py
+hhblits3.py
 blast.py
 cadscore.py
 kclust.py