Add connection types to constants
Update structure and molecule code

This is a major change to restructure all of the molecule backend code
so that it is nicer to use. This is a halfway point that keeps the
interfaces to the molecules mostly the same.
Remove GJFWriter class all together
Remove commented out section
Cleanup names in chemtools.structure
Fix typo in polymerize
Remove unneeded molecule module
Add get_exact_name to Benzobisazole
Add masses and atomic numbers to chemtools constants
Add properties to structure
Add misssing imports
Add functions to convert z-matrix to cartesian coords
Move get_full_rotation and get_angle to utils module
Fix fileparser geometry parsing to work with windows outputs
Fix regression in old chemtools.utils test cases
Fix typos in z matrix functions
Add tests for z matrix functions
Remove all \r chars from log at start of parsing
Continue adding windows support for log parser
Add tests for new windows log parsing