Many examples could be moved to new modules or implemented as tests

[tlfobe]

The purpose of the example directory has mostly been to develop new code the objects I've developed. But we need to start thinking about how what examples will be relevant for end users when we publish this work. A number of examples can be converted to a module or test case. Below are a few suggested changes

Examples that could be moved to tests:

• read_in_pdb
• angle_minimization
• benchmarking?

Examples that could be moved to modules:

• parameter_scan
• create_random_distribution
• foldamer_cgmodel