CHANGELOG

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    ===  TO DO  ==================================================================
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    ===  CHANGE LOG  =============================================================
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    ### 1.40 ###
    - Significant changes to MotifBuilder: allowed local files (not public_html) to
      be used, now outputs SubImpose commands to stdout, etc.
    - Tweaked MotifBuilder's output, & fixed -getn/-getc swap bug
    - VBC added FragmentParameterWriter to quickly analyze parameter set of loop
      endpoints
    - DAK added AltConfTracker to output simple info about residues in alt confs
    - VBC modified Sequence analyzer to give simple output for fragments sequences
      for use in making logos
    - DAK added StructureBasedSequenceAligner to get sequence alignments from pre-
      superimposed structures
    - DAK added AltConfEnsembler to make NMR-like PDB files from all alt conf combos
    - DAK modified AltConfEnsembler to fix network-merging bug & output kins

    ### 1.39 ### DAK
    - Added NeighborGreeter - simply finds both neighbors for each residue
    - Eliminated non-protein residues (e.g. HOH) from NeighborGreeter output
    - Added chain break check to NeighborGreeter as per VBC's suggestion
    - Removed some of my useless old kludgy classes
    - VBC improved fragmentlibrary maker to use DAK's molprobity mysql validation
      table to filter fragments.
    - Interdigitator: changes to -kin output, bb not OK for neighbors by default
      (but new -bbok flag to revert), new -okseqdiff flag for neighbors

    ### 1.38 ###
    - Removed KinImage (now king KinImagePlugin)
    - Added RotamerPCA -- currently a testing platform for rotasamp ideas
    - Added MotifBuilder for extracting substructures/motifs from Top5200 PDBs
    - Made default change in guanidinium normal 0 degrees in ArgFlipConfirmer
      (fixes bug w/ disordered sidechains).
    - Added -wholepdb output option and better output file naming to MotifBuilder
    - Changes to RotamerPCA -- still a very volatile testing ground
    - Added DisulfideParameterer for calculating geometry stats about disulfides;
      makes use of new disulfide treatment in driftwood.moldb2.*
    - Better safety check in DisulfideParameterer if either residue is not found
    - More changes and simplifications to DisulfideParameterer: just chi2, chi3,
      and chi2' (no phi, psi, chi1), alt confs, fraction through sequence
    - Minor changes to work with Vince's recent molikin changes (DAK 100130)

    ### 1.37 ###
    - Added KinImage (pun fully intended) to make flat kins from image files
    - Added Interdigitator to calculate degree of interpenetration of sidechains
    - Did something to CsvToKinner, presumably minor tweaks (?)

    ### 1.36 ###
    - Fixed SubImposeScripter to handle either : or , delimited input and the
      presence or absence of "Ncap " in the N-cap residue name token
    - Did something to CsvToKinner and GrepLines, presumably minor tweaks (?)
    - Added DatabaseGeometer for calculating geometry stuff like bond angles
      across populations stored in Bryan's MySQL database(s)
    - FragmentLibraryCreator can read gzipped files now.

    ### 1.35 ###
    - Changed RightNcapPsi to RightNcapPhiPsi (and added -phi flag)
    - Renamed FirstNLines to GrepLines

    ### 1.34 ###
    - Added new function for creating protein fragment 7 param libraries.
      Includes a few extra parameters now for looking at the first and last two
      peptides of a fragment.
    - bug fixes for dealing with alternate conformations and chain breaks.

    ### 1.33 ### (dak)
    - Made small edit to SubImposeBashScriptMaker.help
    - Started to expand ArgFlipConfirmer to other aa types; may complete later
    - Added simple utility FirstNLines

    ### 1.32 ### (dak)
    - Added a weighted-averaging method to PCAPlotter using the SVD S matrix
    - Added a -color flag (& possibly something else?) to CsvToKinner

    ### 1.31 ### (dak)
    - Fixed a 'columns vs. rows' bug in PCAPlotter

    ### 1.30 ### (dak)
    - Added PCAPlotter to make principal component motion kinemage from BRD lab's
      K* and/or MD data in the form of an SVD U matrix

    ### 1.29 ### (dak)
    - Changed prekin script lines in SubImposeBashScripter

    ### 1.28 ### (dak)
    - Realized I didn't 'svn add' AtomicDisplMatrixMaker before -- it's there now!

    ### 1.27 ### (dak)
    - Fixed a dumb bug I'd just submitted in AtomicDisplMatrixMaker

    ### 1.26 ### (dak)
    - Added AtomicDisplMatrixMaker class to help with PCA analysis of ensembles

    ### 1.25 ### (dak)
    - Made some changes to CsvToKinner including help file
    - Added SubImposeBashScripter to make bash script that runs Ian's chiropraxis.
      mc.SubImpose on a set of helices in a HelixBuilder output file

    ### 1.24 ### (dak)
    - Made some changes to CsvToKinner help and flags

    ### 1.23 ###
    - Fixed -scalez handling of axes and labels in CsvToKinner

    ### 1.22 ###
    - Fixed rotaballs pointids when flag -___all used (___ = some aa)
    - Added 9d RNA kin-style frame to CsvToKinner

    ### 1.21 ###
    - Fixed some minor output bugs in CsvToKinner

    ### 1.20 ###
    - Fixed -rotaballs option so balls, not dots in CsvToKinner
    - Added support for desired pointids in CsvToKinner output kin (e.g. PDB ID)

    ### 1.19 ###
    - Added rota common-atom balls option and some extra dimension fxnality to
      CsvToKinner

    ### 1.18 ###
    - Added flexibility with axes and extra dimension to CsvToKinner

    ### 1.17 ###
    - Added new class, DiffFractions, for comparing pre- and post-Coot refits

    ### 1.16 ###
    - Added SequenceAnalyzer for analyzing sequences of fragments that come out of fragmentfiller.

    ### 1.15 ###
    - Added -nokin and other similar flags to CsvToKinner

    ### 1.14 ###
    - Changed single SQL query handling in MySqlLiaison

    ### 1.13 ###
    - Set up MySqlLiaison so single queries can be called w/out intention of
      superimposing resulting residues in a kinemage

    ### 1.12 ###
    - Changed scaling properties and flags for CsvToKinner

    ### 1.11 ###
    - Made note of this extremely cool version number
    - Edited scaling on Z axis in CsvToKinner so axis labels actually correspond
      to data; other minor tweaks

    ### 1.10 ###
    - Added axes, flags, etc. to CsvToKinner

    ### 1.09 ###
    - Made quick change to CsvToKinner -h output

    ### 1.08 ###
    - Added new CsvToKinner to take generic csv file and generate kin

    ### 1.07 ###
    - Fixed bug in ArgFlipConfirmer so chain Strings of " " aren't trimmed

    ### 1.06 ###
    - Changed ArgFlipConfirmer so no junk input needed; just handles all Args in
      the orig PDB and compares to those Args in the second PDB

    ### 1.05 ###
    - Fixed bug in ArgFlipConfirmer so chain A...Z or " " handled

    ### 1.04 ###
    - Amended ArgFlipConfirmer class to allow for diff output more compatible with
      Bob's Coot refitting Perl script
    - Added a Test file for testing random stuff (currently chiropraxis ramalyze)

    ### 1.03 ### (DK)
    - Added new ArgFlipConfirmer class for testing whether Arg refits done by Bob
      Immormino's Coot refitting Perl script are flips or some other type of refit

    ### 1.02 ### (DK)
    - New MultiPdbSuperimposer and MySqlLiaiason for running a MySql query and
      superimposing the single-residue results in a kinemage (options available).

    ### 1.01 ###
    - New FragmentRotator for testing effects of rotating a fragment on the NMR RDC RMSDs.

    ### 1.00 ###
    - New ParameterCalcRmsd for calculating distance metric for affinity propagation clustering.
    - Added changelog.
    - Bug in LibraryFilterer? RMSD calculation seemed to be doing an unnecessary extra square root
      when doing the sum.