Fixed up the get_sides_plus section
Fixed the unit tests for get_flanking_region
Tests for get_flanking_sequence
Tests for flanking handles in interior loops.
Allow the initializtion with a sequence
Added are_adjacent_stems()
Added a function to output to a file
Added the multiloops_count flag to are_adjacent_stems
Added a test for rmsd.py
Fixed the stem_length function
Fixes to get_bulge_dimensions
Added a test for the multiloop sides
Some debug statements
Added some previously missing files
Sort the elements and test the connection_type
Added visualize_pdb.py
Add long range interactions
Load longrange interactions into the CoarseGrainRNA data structure
Handle hairpins of length 0
Random subgraph and radius of gyration