IMPROVE GUI Allow gscript datsets to use dataset object or dataset name
NEW CMD Add extract method to dscript to extract a vector to a vector dataset
BUG CMD Setting up regions in SimData was overlapping regions that should not be The original method assumed regions were created in ppm order. Now search through existing regions to check for overlap
BUG GUI Fix setting up mapToDataset when P1 methods present. Phasing was failing
IMPROVE GUI Make Script pane non-editable. Will add a control to turn on/off
BUG CMD Fix setAcqOrder in JCAMP. Reading JCAMP files was failing
SKKKKKKKKKKkiP IMPROVE STR 1631222264 Update RNA attribute prediction data
IMPROVE CMD Change BucketedMatrix to use double for portability with Apache Commons Math * SMILE
BUG GUI Label color of peaks wasn't being set properly
SKKKKKKKKKKkiP IMPROVE STR 1628172551 Allow generating hose codes on polymer
BUG GUI Fix reading vector for 1D
BUG GUI Fix error with vector dims selector on 1D
SKKKKKKKKKKkiP NEW STR 1627911261 Add readMol2 to molio.py
IMPROVE GUI use getDlabel (instead of getLabel) in Dataset to get label for chart
IMPROVE CMD Change getStdLabel to return greek delta followed by supersripted nuclei
IMPROVE CMD Add toLatextString to Nuclei. REturns a superscripted latex format
IMPROVE GUI Change from spinner to choicebox for real/imaginary selector
IMPROVE GUI Move vecSpinner from status bar to be with row controllers
IMPROVE GUI More flexible sliding of FID display
IMPROVE GUI Add export TRACT data
SKKKKKKKKKKkiP IMPROVE STR 1623956842 Newly trained 2ndStr model
BUG GUI Fix loading indirect vectors that are not complex
SKKKKKKKKKKkiP NEW STR 1623776461 Add prediction resfactors and model for 2nd structure prediction SKKKKKKKKKKkiP NEW STR 1623714902 Add Protein2ndStructurePredictor
BUG CMD Fix writing ucsf header when saving memory files
IMPROVE CMD Add negateOdd to rft. And detect whether to use rft in autogen
NEW CMD Only adjust dwell if size different and not frequency domain
NEW CMD Add TPPI acq type to RS2DData
BUG GUI Fix problem with save/load stages on Windows. File path corrupted
SKKKKKKKKKKkiP BUG STR 1623034792 Allow names like stage_0 instead of 0_stage
NEW CORE Update to Java and JavaFX versions 15
NEW CORE Read T1/T2/NOE and order parameters from STAR files
NEW GUI Add new sequence display GUI with atom shift deltas and order/disorder calculation display
NEW STRUCTURE Add random coil chemical shift estimation based on concepts from Potenci
IMPROVE GUI Updates of code for peak path (titration and pressure) analysis
NEW GUI Add support for cd,pwd,ls commands to console
NEW GUI Add new simple Peak Assign Tool to toolbar at bottom of spectrum for entering peak assignments
NEW GUI Draw triangles at side of chart to show pivot position.
IMPROVE GUI Updates to interactive phasing controls.
IMPROVE GUI Set dataset name for processed dataset from an existing .nv/ucsf files or script in the FID directory
NEW GUI Automatically load an existing process.py script in FID directory
NEW STRUCTURE Add estimation of steric alignment tensor based on concepts similar to PALES
NEW PROCESS Add initial support for data files from RS2D consoles
IMPROVE STRUCTURE Update RNA shift training to use LASSO regression.
NEW GUI Add Projection display to show 1D projections on edges of 2D spectra.
NEW CORE Add tools for pulling data from remote server. Currently prototyped with nmrbox.
NEW GUI Add dataset browser to find NMR data (datasets and FIDs) in a directory and load them with button click.
NEW GUI Allow reading chemical shifts from a star file
NEW PROCESS First version of psglib for a library of processing scripts
NEW STRUCTURE Initial command line option for measuring PDB files.
NEW STRUCTURE Add doing ligand (small molecule) predictions
NEW STRUCTURE Allow output of rna attribute prediction information
NEW STRUCTURE Add -n option to generate a nef file from loaded restraints
NEW GUI Allow sliding in pseudo-3D datasets (like T1/T2). Uses first plane Should change to autodetect displayed plane
NEW GUI Add RING NMR Dynamics GUI to NMRFx
IMPROVE GUI Region measurement (from Scanner Tool) only worked with pseudo-2D. Now works with multiple 1D files.
IMPROVE GUI Move setting of scan directories (Scanner Tool) to a preferenes pane (from menu items)
IMPROVE GUI Export slices (if currently displayed) to svg/pdf files
IMPROVE GUI Move clustering menu items to separate Cluster menu
IMPROVE GUI Draw lines between linked peaks using peak list color (they were always black)
IMPROVE GUI Allow turning off/on peak listening in PolyChart. Changing lots of peaks could slow display way down.
IMPROVE CMD Add code to remove diagonal peaks
IMPROVE GUI Show exception dialog if fid file not found rather than fail silently
IMPROVE GUI Clear datasets and remove datasets/peaks from chart when closing project
NEW GUI Add ability to extract vectors from chart and display them in a new chart that pops up.
IMPROVE GUI Add fit all and add all to peak path tool
NEW CMD Path Tool: Write all paths, not just ones with pars, to star file. This way we track parameters like confirmed on all paths
NEW CMD Fix saving Peak Path (titrations) to star file
NEW GUI Get display of clusters working for RunAboutX
NEW GUI Add Filter menu item
NEW GUI Add display of amino acids consistent with cluster shifts in RunAboutX.
NEW GUI Add panel for shifts for atom types for SpinSys in RunAboutX
IMPROVE GUI Speed 1D drawing with lots of multiplet labels
BUG GUI Fix control-scroll changing of 1D vertical scale
NEW CMD Fix saving multiplets to STAR file
IMPROVE CMD Add more multiplet conversions (to m, to s etc.)
NEW CMD Read/write norm from/to .par file
NEW CMD Write peakList scale to STAR file
NEW CMD More work on 1D analysis including multiplet info to STAR file and displaying journal format
IMPROVE GUI Work on analyzer functions split/extract/merge. Add support for mol menu
NEW CMD Work on 1D analyzer functions split/extract/merge
NEW GUI Add picking and moving molecule on canvas
IMPROVE GUI Lighten Ligand canvas background color
IMPROVE GUI Add Molecule and Region tools to SpectrumStatusBar tools
IMPROVE GUI Move Multiplet Analysis to tool in SpectrumStatusBar
IMPROVE GUI Move more tools to SpectrumStatusBar. Add method to add tools
IMPROVE GUI Get PDF Export working
BUG GUI Fix exporting large datasets to svg. Peaks were appearing in wrong postion in SVG output.
BUG GUI If one closed all spectral chart windows you couldn't open a project. Now a new stage with chart will be created on demand.
BUG GUI The nw.grid command would create a grid of windows, but they wouldn't appear immediately.
NEW GUI Add slider to control lvl,clm,nlvl,offset in the Spectrum attributes dataset table. Use a choice box to choose which parameter will be controlled. This applies to the selected dataset rows or all rows if none are selected.
NEW GUI Add aspect controls (slider in SpecAttrs) in view section of Spectrum Attributes. The axis shift range is scaled by the axis nucleis gyromagnetic ratio.
IMPROVE CMD Add reading sparky assignment (in Peak Tool File>Read Peaks menu). Type of file is automatically determined based on extension and content.
IMPROVE GUI Add "vp" pop view binding. Pops current chart into new toplevel chart.
BUG GUI Atom labels in peak navigator should use dim on x and y axis. Was using first/second dim of peak
IMPROVE GUI Make Peak Navigator width scaling uses the mean width of peak list, not the individual peaks width. Allows consistent view across all peaks of list.
BUG GUI Fix Peak Navigator move to peak code. Wasn't accounting for whether planes were ppm or pt
NEW GUI Add initial version of nw.bindKeys for user defined key bindings.
NEW GUI Add AutoCouple menu item. Collapses adjacent (coupled) peaks into single peak.
NEW GUI Add "Add Mirror Peaks" menu item. Generates peaks across diagonal from existing ones. Two D spectra only.
BUG GUI Fix offset of 1d integral display. Wasn't accounting for borders
BUG GUI Display of apodization on FID wasn't using chart borders correctly so was ooffset from correct position.
IMPROVE GUI Set title on window when loading from .yaml files
NEW CMD Add calculation of some measures used in NusCon for comparison of NUS processed datasets.
NEW GUI Add err field for intensity and volume in Peak Inspector
NEW CMD Add err value to peak measures
IMPROVE CMD Read/write noise value in dataset .par file
IMPROVE GUI Allow setting dataset RMS from Analyzer window
BUG CMD NvJ par file stores ref pt starting at 1, not 0 Change for compatability with NMRViewJ
BUG GUI Auto level wasn't being called when opening a processed dataset
BUG CMD Multiplet analysis: Removing peaks until multiplet is a singlet didn't update peak shift and intensity
NEW GUI Add Peak Table to show all the peaks in a list
IMPROVE GUI Remove NvJ button. Not very necessary now and didn't always work.
BUG CMD Read condition from .xpk file. Reading failed if .xpk file had a condition line
IMPROVE CMD Auto add a TRIM command for direct dimension of Jeol file when generating script.
NEW GUI Add some methods to gscript to make it easier to script GUI from Python.
IMPROVE GUI Autophase and manual phase interacted poorly in GUI. Now the PHASE op is added after an AUTOPHASE op. The phase sliders start with the auto generated phases and the phases added to the PHASE op are the amounts that will be added to the autophase amounts.
IMPROVE GUI Remove yAxis drawing on 1D spectra
IMPROVE GUI Change drawing of 1D titles to stack in top left. That way they avoid overlapping spectrum
BUG GUI Add ColorBy column to peak tab and fix ColorBy so it works. Color peaks by plane offset, status, assigned etc.
BUG GUI Fix color of integral value and height of region fill
BUG GUI Fix displaying peaks by nplanes. Now, as in NvJ, peaks that are off the displayed plane are drawn in the "off color"
IMPROVE GUI Add regions checkbox and cleanup integral controls
IMPROVE GUI You can now pan spectrum left/right up/down with mouse dragging in left/bottom border area (on top of axis).
IMPROVE GUI Allow scrolling with mouse when shift+alt keys down.
IMPROVE GUI Add titles on spectra (controlled by checkbox in Spectrum Attributes)
BUG GUI Fix offsets so using offset column menu (ramp etc.) in spec attributes work
BUG CMD Fix problem with processing to ucsf file format (header needed updating)
IMPROVE GUI Fix positioning of 1D integrals. Now they are autoscaled to always fit on display within a region specified with a range slider in spectrum attributes.
IMPROVE GUI Improve bindings to allow user to use mouse in selector cursor mode to zoom and to add regions.
IMPROVE GUI Fix drawing sum of multiplet / peaks
BUG GUI Fix picking mulitplets
NEW CMD Add something like Objective Deconvolution to automatically add peaks to optimially deconvolve a region.
IMPROVE CMD Various improvements to Multiplet analysis including better fitting and gui improvements
BUG CMD Fix reading Bruker vdlist with m, u and s suffixes on delays
IMPROVE GUI Add .jdf file type as option when choosing FID files (Jeol file)
IMPROVE CMD Add new types of low-level storage for datasets. Use in-memory mode for processing if data small enough
IMPROVE CMD Improvements to GRINS. Added as an OP.
IMPROVE CMD Simplify dataset/fid size code in pyproc and Processor.
NEW CMD Add Merge op (merge alternate real / imaginary pairs) to Complex values
IMPROVE GUI Stop using .tmp file when processing (now that we don't use mapped file) Mapped file could be hard to delete (especially on Windows). Now using cache file for processing
IMPROVE GUI Update TRACTGUI to work with changes in TRACTSimFit
IMPROVE GUI MOVE cursor on Linux is closed hand, so use HAND cursor instead Should eventually add custom cursor (pointer cursor)
NEW GUI New tools for titration and pressure analysis. Based on new PeakPath tool
NEW CMD Allow fitting pseudo-3D peak lists. Shape and position are common for a peak accross all planes. Intensity can be independetly fit for each plane, or fit to an exponential decay model using delays associated with the dataset.
NEW GUI Reorganize Fit menu and add "Fit Planes" and "Fit Planes(Exp)"
BUG CMD Processing would fail on Bruker datasets if DSP charge-up values were zero.
IMPROVE GUI Add menu triangle and tooltip to dataset table dim column so it is more clear that values for different dimensions can be seen and changed.
IMPROVE GUI Change space binding so peak inspector moves on top of spectrum
NEW GUI Add protein backbone experiments (hsqc, hnco, hnca etc.) to simulate peaks tab
NEW CMD Add support of a fixdsp method to processing scripts. Allows turning on/off fixing of DSP charge-up (Bruker fileds) when reading datasets. This was only working in GUI.
NEW ANALYST Add ability to get RNA secondary structure from a loaded 3D structure.
IMPROVE GUI Add check box to peak list attributes table to turn on/off display of link lines.
NEW ANALYST Show molecule viewer after reading molecule in
NEW ANALYST Add command/menu to read simple rdc text file.
NEW ANALYST Color constraint lines in SSViewer by peak intensity classes
NEW GUI Add new spectrum menu items for clustering along rows/columns and fitting rows, columns and planes.
NEW CMD Allow constrained (column, row) peak fitting. All peaks in linked column(row) get same shfit and width in that dimension.
NEW ANALYST Reset molecule transform so initial rotation is consistent with pymol
NEW GUI Add support for lineshape pick/fit from menu
IMPROVE CMD Change to use layers of peaks when fitting. Fit includes center peak and surrounding layer of peaks. Next layer is not fit , but intensities subtracted from region.
NEW CMD Add new LorentzGausNDWithCatalog Line shape fitting using lineshape catalog
NEW CMD Add refinePickWithLSCat (start of something like INFOS)
NEW CMD Add linksDrawn (and get/set). Used in drawing link lines (lines between peaks that are linked)
NEW ANALYST Add original, molecular SVD, and RDC rotated axes in molecule viewer.
NEW CMD Add pick (peakpick) to dataset scripting (nd command)
NEW GUI Add GUI support for generating line shape catalog during processing
NEW CMD Add get method to return a dataset based on name
NEW CMD Add support for generating lineshape catalog. Generated during processing based on apodization etc. Read in when loading a dataset.
NEW ANALYST Add SVG plot export to RDC interface.
NEW ANALYST Add interface for RDC analysis.
NEW GUI Initial add of new path tool for following peaks in titration (etc.) experiments
NEW GUI Add tool for doing TRACT analysis
IMPROVE GUI Add button for closing dataset to datasets table window.
NEW GUI Get Styles tab working with settings for grid lines, colors and fonts
NEW CMD Initial creation of pscript to provide python interface (read/write etc.) to peaklists (npk command)
IMPROVE GUI Switch to using ppm for planes. Add nplanes tol to peak display
IMPROVE GUI Fix freezing of drawing with too many charts.
BUG CMD Close dataset when there is processing error. Fixes bug where processing stops working, even loading new file and setting correct processing parameters. Failure would happen, for example, with setting invalid (non-power-2) zf size.
BUG CMD Change spaces in dataset names to "_". Prevents various issues. Was a problem writing STAR files. We could quote it in STAR file, but seems simpler to work without spaces in dataset names.
BUG CMD DatasetPhaser wasn't saving correct phase values to dataset. Wasn't adding new phase correction to existing phase values
NEW GUI Add TRIM processing op to gui list
NEW CMD Initial attempt at getting Jeol Data reading working. Basic functionality, but needs work
NEW CMD Add TRIM op (to trim off edges of spectra)
NEW ANALYST Allow choice of dist or ring-current prediction for RNA in gui
NEW ANALYST Initial version of ligand scanner in NMRFx
NEW GUI Add menu item to save peak list to sparky format
NEW GUI Add button to save parameter file to Datasets table
NEW CMD Add Equation Fitter (with support for janino compilation) and use from Tract code
NEW CMD Add MatrixAnalyzer (used for PCA comparison of bucketed dataset)
NEW CMD Initial tools for new version of ligand scanner (analyzing effects of ligands on HSQC (etc.) spectra.
NEW CMD Add writePeaksToSparky
IMPROVE CMD When doing an alignmnent of 1D spectra calculate the alignment position of max intensity with interpolated polynomial. Alignment still done with integer shift, but report of fractional shift useful for analysis.
IMPROVE GUI When measuring peak intensities check if peak list has an associated dataset. If not, try to add one.
IMPROVE CMD When measuring 2D peak intensity/volume try to find a match of peak list and dataset dims if they don't have exact match.
BUG GUI Showing spectrum pop-up menu was deselecting any selected peaks.
IMPROVE GUI Auto add peak lists to spectra in RunAboutX
NEW GUI Add menu item (in spectrum pop-up menu, Reference section) for shifting peak lists to align with dataset
IMPROVE GUI Reduce the range of sliders for phasing (in both the Phaser tool and in the operations display) so that its easier to make fine adjustments
IMPROVE GUI Changing phase (ph0,ph1) values in the PHASE operation dialog now updates the sliders in the Phaser tool, and changing ph1 uses the pivot position set on active spectrum.
IMPROVE GUI Update Java to 8.0.202
NEW GUI Right clicking on the Color column of the Dataset table (in Spectrum Attributes window) now gives a menu item that allows you to set a color scheme that applies to multiple datasets (useful for titrations etc.)
IMPROVE CMD Allow using units (Hz, PPM, pts, Fraction) in CSHIFT
IMPROVE CMD Add adjref argument to CSHIFT and SHIFT. When set to true the reference value for vector will be changed to compensate for the shift.
NEW GUI Add new referencing methods and menu items, Set Reference and Shift Reference, to the spectrum pop-up menu.
NEW GUI Add a server mode that creates a socket-listener that can respond to commands from another program. Used for the CoMD dynamics software.
BUG GUI Fix showing new chart targets for adding new spectra to window. The bottom and top targets were missing since switch to canvas mode) mode)
IMPROVE GUI Add delete icons to data columns in the Scanner Table
NEW GUI Scanner table now has menu items for measuing regions in the pseudo-2D spectra. Similar to what in dCSM
IMPROVE CMD Set non-processed (arrayed dims to be not complex)
NEW CMD Allow specifying whether to generate script for arrayed dataset. It can be tricky to figure out if indirect dims are actually frequency dims, so this allows specifying that last dim is not a frequency dim and shouldn't have processing commands added in genScript
BUG GUI When closing chart remove its crosshair lines from plotContent Also, add moveTo that takes single axis data
BUG CMD Sweep was getting set incorrectly when reading vector from dataset.
IMPROVE GUI Import Python os module into console interpreter
IMPROVE GUI Scale window ppm (when making proportional windows) by nuclei g ratio
NEW GUI Can now disable crosshairs by clicking on icons in the crosshair ppm text windows in status bar.
IMPROVE GUI When minimizing borders of spectrum charts, now adjust chart sizes to be proportional to ppm range of the window (with some scaling by what nucleus is in use)
BUG GUI Align spectra wasn't picking correct peak regions.
BUG GUI When window is very small just draw a single tick/label at center
BUG GUI Minimize axes and grid/horiz/vert layout wasn't working properly
IMPROVE GUI Use getPercentile in auto scaling so that lvl doesn't get set too low.
IMPROVE GUI Reference gui updates. Fix C- to - F temperature conversion. Can now prompt for reference at crosshair position. H2O PPM mode inserts water ppm in script (rather than word H2O) C to F conversion was missing 0.15 (273.0 instead of 273.15)
BUG GUI Fix hitting (selecting) 1D peak label boxes
NEW CMD Add new SpinSystem code
BUG CMD Fix adjusting sw when vector not size of dataset
NEW GUI Add pop-up menus for peak, integrals and regions for 1D analysis.
IMPROVE CMD Add norm field to dataset to store dataset normalization value. Normalization used to translate integrals into number of atoms, for example
BUG GUI Fix drawing of integrals and add display of integral text value.
BUG GUI Get interactive adjustment of 1D regions working.
BUG GUI Get clipping for GUI display of peaklists working properly
NEW CMD When processing is complete on all dimensions set nFreqDim field to the number of processed dimensions. This is useful for pseudo 2D files
BUG GUI Drawing 1D vectors of pseudo-2D failed when display region smaller than 2nd dim
BUG GUI Scrolling in y-axis was backwards (after update to new axes code)
IMPROVE GUI Change Baseline drawing to be flat line at 0.0
IMPROVE GUI Add ability to populate the scanner table from an arrayed dataset
NEW GUI Add measure sdev and s/n
BUG GUI Fix spectrum axis syncing
IMPROVE GUI Increase preferred wdith of spectrum attributes window so its all visible
IMPROVE GUI Stop using popOverMode for spectrum attributes. A little flaky and hard to resize window
IMPROVE GUI Add separate Open FIDs and Open Datasets and Recent FIDS and Datasets menu
BUG CMD Fixes for setting coupling values, including fixes to removing extra peaks
IMPROVE GUI Add TextField to Integer Range displays in operation details
IMPROVE GUI New contouring algorithm using the marching squares algorithm. This generates continouse curves rather than a separate line segments.
NEW GUI SVG export now exports all the spectra charts in canvas. Used to just export the active one
NEW GUI Create new plotting that does spectra on a single canvas