============================================================================== === TO DO ================================================================== ============================================================================== ============================================================================== === CHANGE LOG ============================================================= ============================================================================== ### 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.