CHANGELOG

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    ===  TO DO  ==================================================================
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    Crash with 1h0v?
    Kin to show source?
    BUG with model numbers and TER records not having the same number??

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    ===  CHANGE LOG  =============================================================
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    ### 1.12 ###
    - Added -*range flags to control what ranges to search on parameters.
    - Changed kin output to show PDB names of fragments.
    ### 1.11 ###
    - Usability enhancements: better file names, fragments in kins have PDB source
      identity info.
    - Added -tighter to give option for tighter parameters.
    ### 1.10 ###
    - Changed FragFiller to use new database setup, with each fragment length in a
      separate table.
    ### 1.09 ###
    - Added jiffiloop.changes and help files.
    - Added -fragment to limit number of fragments generated.
    - Added -sequence to keep residue name info.
    - Changed functionality to renumber and rename residues by default.
    ### 1.08 ###
    - Scorer function for scoring the jiffiloop-ness of a protein.
    - Output changed to spit out each individual gap score.
    ### 1.07 ###
    - Added option for superimposing using just N-term of a fragment.
    - Found some issues with residues/fragments not being complete.
    - Moved some exception handling around to be a little smarter and with more useful bug reports.
    ### 1.06 ###
    - Moved DatabaseManager to driftwood.
    ### 1.05 ###
    - Fixed a bug in database "select" construction.
    - Added a system.out for printing out gap parameters.
    ### 1.04 ###
    - Added a way to simulate gaps in structures.
    - Output pdbs get labeled with model name and chain.
    ### 1.03 ###
    - Input pdb gets output in the output kin.
    - Output pdbs include information past column 80 on where the files came from.
    - Added ability for tool to obtain fragment data from a database.
    - Added a ProteinGap class to hold all info on gaps.

    ### 1.02 ###
    - added a way to parse arguments, specifying locations for the libraries.
    - fixed bugs in how it deals with arguments.

    ### 1.01 ###
    - fixed main so it uses the absolute path of the arguments.

    ### 1.00 ###
    - initial build of fragment filler program, based on PatchGapPlugin