Lots of enhancements and bug fixes.  Very early beginnings of a UI.
The user can choose non-standard residues to leave unchanged
Bug fix
Fixed bugs when processing files that contain hydrogens
Preliminary support for adding missing residues
Added UI for adding missing residues.  Added option to delete chains.
Added option to add hydrogens
Improvements to the user interface
Further UI improvements
Displayed residue numbers match the ones in the PDB file.  User can select what amino acid to convert nonstandard ones to
Added templates for DNA, RNA, and terminal groups
Run some dynamics to improve the minimized structure
Fixed bug that sometimes caused exclusions to be added twice
Apply substitutions to added residues
Bug fix
Made energy minimization more robust
Fixed bug that would sometimes try to add an OXT to a non-protein residue