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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