Improve documentation

[jlmaccal]

We currently only have rudimentary documentation.

We need to:

• make sure that all public modules, classes, methods, and functions are properly documented
• develop a written guide and tutorials

This should all be done using restructured text. This will automatically be parsed and uploaded to http://meld-md.org.

[alberto99]

Yeah, I need to help out more with this.

[jlmaccal]

I'll try to chip in here too. This is boring stuff, but we need to do it if we're going to continue to push MELD.

[jlmaccal]

We should use the Numpy/Scipy documentation convention: https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt.

It's easy to read and write, and can be interpreted by sphinx to auto generate html documentation.

We will have to convert the existing docstrings, but this shouldn't be too hard.

[GoldEagle93]

I'm working on a tutorial for protein-DNA systems with meld. In the future I will also do it for using dummy particles.

[arupmondal835]

I would like to write tutorial(s) about protein-peptide binding and protein folding using data.