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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.