Added a Python interface and some tools.

Multiple replicas can run in parallel.

There are some examples of use.

Some ignore files also added.
Style and readability.
Increased heavy atom mass cutoff.

Increased to 3.5 to exclude all isotopes of hydrogen from heavy atoms.
Merge pull request #7 from OndrejMarsalek/python-PR

Python interface and Python tools
Merge pull request #14 from OndrejMarsalek/heavy_atoms

Increased heavy atom mass cutoff