Aside from the autogenerated docs:
Here is a [wiki:EMAN1To2Translation Table of translations from EMAN1 functions -> EMAN2]
Programming Internals:
EMAN2 uses [http://www.boost.org/libs/python/doc/ Boost.python] to wrap c++ functions to Python.
[http://www.boost.org/libs/python/pyste/ Pyste] is a Boost.Python code generator to automate this process.
In EMAN2 there is a script create_boost_python in /eman2/libpyEM directory calls Pyste to create c++ wrapping files libpy***.cpp.
Then the c++ compiler will create libraries which contain all the Python function call of EMAN2. Current release of Pyste has a dificit for the default argument handling. So please replace two of your Pyste files in Python site-packages with attached files.