finished implementing new structure class, benchmarking rotations now compared to prody
testing consistency with motif
got bp align to work with new reworked core structure
minor change to how pds are printed
another minor change to pdb printing
found a bug that atoms were not being added to residues with alt name such as O1P instead of OP2
more improvements, working on getting sterics workign again in the rework
more changes in motif chain sterics
gave up reimplementing calculating reference frame cant get it close enough consistently
finished implementing faster copy for structure and motif objects
minor changes, was not using previous transform correctly
major updates
added motif score function to judge which motifs to use for thermo optimization
got a working BuildDenovoTwoWayJunction class
finished refactoring dssr parser
finished algorithm for parsering tertiary contacts
fixed minor for generating chain names in structure.py
added script to find tertiary contact duplicates
finished updating new object structure added all tertiary contacts
merged new basic structure