README

EMAN2 README

How to install EMAN2
    see instructions in INSTALL.

What is the file structure for EMAN2 source code

  - libEM       core libEM library
  - libpyEM     boost python wrapper of libEM
  - programs    python programs
  - utils       utility-level programs
  - examples	Pyton sample programs
  - pyemtbx     python library modules toolbox
  - plugins     c++ templates and sample code for EMAN2 developments
  - doc         documentation
  - rt          regression tests
  
Where is the documentation

    EMAN2 documentation are in doc directory, has 2 kinds of documentation source:
    1) The hand-written documentation, for example: INSTALL.
    
    2) The code-based auto-generated documentation, which will be built and 
    installed in the EMAN2 building process if ENABLE_AUTODOC option is set.
    	a) EMAN2 uses Doxygen (ver 1.4.3+ prefered) to maintain its code-embedded 
       	documentations. To generate the Doxygen-based documentation.
       	b) EMAN2 has a set of latex based documentation in /doc/latex directory, 
       	which will create same content in dvi, ps, pdf and html format.
       	c) There is a docgen.py Python program which can create two html files to 
       	describe processors.

What's the coding style of EMAN2
    1) EMAN2 follows the GNU coding style with minor differences. We use
       GNU indent to make the proper indentation. The indent options are:
       -br -nce -i4  -npcs -nprs  -npsl -l100  -ts4

    2) The naming styles are:
       a) All source code files use lower cases.
       b) All classes and data types use uppercase in the first letter.
       c) All functions use lower cases with '_' as the word separator.
       d) All parameter names for modular class use lower cases with '_' 
       as the word separator.
     
How do I make my code to follow the EMAN2 coding style
    Suppose your code is in file 'input.cpp', then run:
      % indent -br -nce -i4  -npcs -nprs  -npsl -l100  -ts4 input.cpp -o output.cpp
    The output is saved in 'output.cpp'.