CHANGELOG

    ==============================================================================
    ===  TO DO  ==================================================================
    ==============================================================================
        Build wireframe version of Lathe tool

    VBC things to do:
      Check ColorGrouperPlugin.populateColorLists to see if there is a way to copy flags
        from one Klist to another.
      Check GeometryPlugin.doAll to make sure it still opens files correctly.
      Fix PlottingTool so it doesn't use old setDrawnXYZ KPoint functions. (Fixed, but changes
        coordinates of the points now).
      Check functionality in AutoBondRotTool; not sure if auto-updating of point parents
        messes anything up.
      FastaTool rewrite?
      LoopTool rewrite? (delete from file doesn't work)
      RNALineTracker desperately needs a rewrite.
      some loops get transfered over incorrectly in PatchGapPlugin: 107 models vs 111 found in hsp90
      PatchGapPlugin needs to wrap degree numbers!!!

    ==============================================================================
    ===  CHANGE LOG  =============================================================
    ==============================================================================
    ### 2.25 ###
    VBC:
    Added PDB Export tool as a separate option from the KinFudger tool.
    Fixed a bug in data PlottingTool.
    Added a separator field to HighDimSliders.

    ### 2.24 ###
    VBC:
    - Added counting tool.
    - Incorporated aspect tracking code from IWD into movie maker.
    DAK:
    - Added animate sequence to movie tool.
    - Made Kinimol respect PDB v2.3.
    - Added NikilomPlugin, a.k.a. "Kin->PDB 2.0","a new version of KinimolPlugin
      that still uses Kinimol but is more generic (?).
    - Added trianglelist support to Multi-list editor.
    ### 2.23 ###
    - Changed connectivityfinder to be able to keep singletons.
    - Fixed RnaMapWindow to reflect new constructor in EDMapWindow.
    - Added option to plotting tool to not add second column to point ids.
    - Fixed co-center tool recocenter button to cocenter when number is typed in.
    - Removed system.out messages from several tools.
    ### 2.22 ###
    VBC:
    - Fixed bugs in Plotting Tool, fixed up the gui a bit.
    - Added RnaRotator tool.
    - moved rdcplay plugin to rdcvis package
    - bugfixes in render exporter tool
    DAK:
    - Added "keep reference points" checkbox for 3-on-3, dock by pick range, and
      least-squares docking tools.
    - Added "Multi-list editor" tool.
    - Added ribbons, change color to Multi-list editor tool.
    - Added Multi-list editor tool manual entry.
    - Made Multi-list editor & Kin<-Image appear on the RHS of the KiNG window
    - Added turn off/on buttons to Multi-list editor
    - Added "Probe nearby" tool for Stuart - simply runs Probe on local region
    - Made "Probe nearby" threads more compatible w/ chiropraxis ScRot, etc.
    - Added water detection to "Probe nearby"
    - Added alt conf selection to "Probe nearby"
    ### 2.21 ###
    - Fixed RNAMapWindow to use minimizable tool windows.
    - Modified HighDimSliderTool to work with parallel coords, and improved
      interface a little.
    - Added documentation, fixed tools/plugins without toString() functions.
    - Fixed manual html file, using tth instead of lyx's built in HTML exporter.
    ### 2.20 ###
    DAK
    - Gave KinImagePlugin a major overhaul - new GUI, resol options
    - Started adding prev, curr, next trackers to cocenter tool.
    - Changed PointColorPlugin so extract points makes groups with select turned on.
    - Added export text to PointColorPlugin to export info of all visible points.
    - Modified PointColorPlugin to export colon-delimited output, and remove duplicate
      strings.
    ### 2.19 ###
    - Bug fixes in RenderExport (branched sidechains correct now, better shading on ribbons)
    - Cocenter jump uses parenthetical waypoints in point ids.
    - Cocenter jump can move smoothly.
    - ParenTool for more easy add/subtracting of paren points.
    - ParenTool bug fixes.
    ### 2.18 ###
    - Cocenter includes a jump function
    - Fixed bugs in RenderExport
    - Added Wrap function to plotting tool
    ### 2.17 ###
    - Added KinImagePlugin
    ### 2.16 ###
    -Moved RDCvis tools to RDCvis package
    -Cocentering now has undo.
    ### 2.15 ###
    - Changes to RdcVisTool, fatter curves, nicer colors.
    - Started putting in multimodel reading, but stopped in favor of standalone rdcvis.
    - Fixed bug in KinFudger PDB export where an extra space was getting put in.
    - Cocentering tool - translates all groups onto the same point ID, if in the group.
    - New functionality in AutoBondRotTool, averaging, zeroing. (for making Pro dist)
    ### 2.14 ###
    - RdcVisTool is working pretty well now, math seems to be mostly correct, but need
      to change the way the curves are drawn.
    - Fixed tabs in Framer
    - Added axis to RDCPlay tool.
    ### 2.13 ###
    - some bug fix in recolor tool, I think involving the spectral coloring mode.
    - new RdcVisTool, semi working at the moment, but needs a lot of work.

    ### 2.12 ###
    - revised KinFudgerTool to disable the move points button until there are points to move.

    ### 2.11 ###
    - revamped KinFudgerTool to be much more user-friendly, and be more descriptive about its behavior.
      It highlights the points it is going to move, and gives users a chance to reconsider a move.

    ### 2.10 ###
    - added king.tools.vr.VRKinTool to communicate from KiNG to the Duke DIVE

    ### 2.09 ###
    - Added a (commented) line in PatchGapPlugin for outputting RMSD of superimposed CA points of fragments.
    - Added a label to RdcPlayPlugin.

    ### 2.08 ###
    - PatchGapPlugin fixed so it takes angle wrapping (i.e. 180 == -180) into account.
    - RdcPlayPlugin created so I can see how Rhombicity affects RDC curves.

    ### 2.07 ###
    - New HighLowSliders to make it easier to specify a range of numbers to do stuff with.
    - New LoopRMSDTool to make it easy to correlate loops with RDC RMSD information.
    - New HighDimSliderPlugin to adjust different dimensions on the fly.
    Changes in PatchGapPlugin:
    - Attempts to get a progress bar don't seem to work yet, but it doesn't flash the
    opening kin progress bar repeatedly anymore.
    Changes in PointComparator:
    - Changed getAtomName to only look at the beginning of pointIDs because it would occasionally
    find valid atom names in the pdbIDs.
    Changes in PlottingTool:
    - Fixed so if no kinemage is open, it creates a new one and puts the plotted points into it.

    ### 2.06 ###
    - added "Select by color" plugin to emulate Mage's selection tools

    ### 2.041 (2.05) ###
    PatchGapPlugin changes:
    - Made a little faster by reducing the number of Double.parseDoubles it does.
    - Finally deletes waters.
    - Doesn't include extra atoms past the endpoints of superimposed loops.
    - Trying out different methods of superimposing the loops, currently uses only the Ca of endpoints.
    - Adds residue numbers to PDB appended to end of the lines of PDB exports, temporarily fixes a problem
      where if two or more matches were found from one PDB, they'd get stuck together in one model.
    - GeometryPlugin fixed so it (again) scans 30 degrees around 0 for the peptide dihedral; I thought it was wrong
      before and changed it to 20.
    - RamaTool fixed so it uses KinUtil.get functions.

    ### 2.04 ###
    - PatchGapPlugin created, automatically fills in gap in protein structures.
      Searches database for appropriate matches, based on loop framework.
    - DockConnTool added help.
    - LoopTool added help.
    - PatchGapPlugin added help, and added ability to export loops to pdb format.
    - GeometryPlugin added help, and fixed onDoAll to ask for a directory.
    - KinFudger fixed to use KinUtil.get functions.
    - PointComparater fixed to use KinUtil.get functions.
    - KinUtil cleaned up a little, added new get functions.
    Tools were reorganized in their menus a little bit as well.
    - Kinimol and Kinimol plugin added.

    ### 2.03 ###
    - Undo (one step only) for RecolorTool!

    ### 2.02 ###
    - GeometryPlugin AnalyzeCurrent seems to be working normally...
    - LoopTool updated to use some Java 1.5 features.
    - RecolorTool being updated to Java 1.5 features.
    - RecolorTool converted all getResNum calls to use KinUtil.
    - RecolorTool ribbon recoloring fixed.
    - RecolorTool no longer stores lists that have been clicked; seems like the program/computers
      are fast enough now that this isn't necessary.
    - Buildfile updated to use -Xlint:unchecked flag so unchecked errors show up now.

    ### 2.01 ###
    - ColorGrouperPlugin updated to use new King 2.0 code and Java 1.5 features.
    - GeometryPlugin updated to use new King 2.0 code and Java 1.5 features.
    - KinFudgerTool updated to use new King 2.0 code.
    - PlottingTool updated to use new King 2.0 code.
    - AutoBondRotTool updated to use new King 2.0 code.
    The following tools were updated to use new King 2.0 code.
    - RecolorTool and associated objects, FastaTool, RamaTool, RMSDTool, FramerTool, LoopTool, LoopDockingTool
      RNAMapTool and associated (still needed?), GuilloTool (still needed?), RNAExtractTool (still needed?)

    ### 2.00 ###
    - changed to Java 1.5
    - changes to work with KiNG 2.x code

    ### 1.03 ###
    - added SkylightPlugin, based on rendering ideas from QuteMol

    ### 1.02 ###
    - updated DockLsqTool, DockConnTool, LoopDockingTool to new SuperPoser API
    - added pointID as last field of DiveExport

    ### 1.01 ###
    - moved documentation for these tools into this package

    ### 1.00 ###
    - migrated tools out of main king.jar into separate build project (this one)