Move parse_end_name above parse_name
Add check_sides function to check the polymerization paths
Add get_sides function to get the left, middle, and right sides
Fix missing var in check_sides and add test case for that problem
Update dataparser so that it is a little easier to use with an API

This change moves the curve fitting into a separate function so it
can be used in other parts of the code.

In addition, there is some simplification in writing the output.
This change adds an extra line before the error messages. This is
why there is the added line in output.txt