close to a working verision
created reduced library
fixed bug in motif_chain_task for level 2 solutions
added analysis scripts for motif chains
reworked MotifAssembler class seems to work better now
finishing analysis scripts for motif chain solutions
significant changes to perforance of MotifAssembler
expanded out the modify_3D_structure.py script still has some issues
added a lot more comments
added more comments
working verision of modify_3D_structure.py
added rna_elements.py
rearranged and added some more functionality with RNA_element
added script to find motif chains in pdbs and save them
added junctions and hairpin motifs
added motif_tree and dssr_parser modules
extremely minor implementation but dont want to lose it
more work done on motif tree task
added better tertiary contacts
more development on motif_tree_task, motif_tree and trying to precompute junction motifs