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Change Log for Jimp 2

To do

• make the selection in the tree view reflect changes in selection from the opengl view
• delete measures when any of the atoms in their list are deleted (as long as there aren't too many measures, can this be brute force checked upon deleting atoms?)
• add move atoms code (and dialog)
  • move selected atoms/move all atoms (check-box)
  • translate atoms to a set position (default to origin)
  • translate atoms by a vector
  • rotate atoms by X, Y, or Z (or combination) and specify a center of rotation
  • set the rotation axis by performing a linear regression on selected atoms
  • set the center of rotation by averaging the positions on selected atoms
  • mirror the selection, changing its chirality (changing the sign of the Z-coordinates)
• smart selection dialog
• make more of the script functions undoable (load, setWorkarea, fenhall, moplot, uff)
• draw text when rendering with povray
• a bond should be renamed when one of its atoms is changed
• right clicking on a node in the hierarchy, should not deselect selected objects (reported: Edwin Webster)
• cannot "cut and paste" a node (reported: Edwin Webster)
• ability to reorder nodes (reported: Edwin Webster)
• sort reverse order (reported: Edwin Webster)
• selection mode: select only atoms, select only bonds, select both atoms and bonds, select only surfaces, select everything (reported: Edwin Webster)
• user can change the color and light settings (reported: Xiaoping Wang)
• Change scripting language to LUA
• More easily customized label text with checkboxes for common things to show
• changing properties of huge number of objects should be sped up -- dead slow for a protein
• add threading so that scripts don't hang the program if they take a long time or maybe add some way of canceling actions??
• there is still a bug in memory freeing and a couple of leaks. i really want a garbage collected language now

090 -> 091

• UFF will now only change the geometry of selected atoms if any atoms are selected
• selected atoms are drawn bigger so that they can be seen
• Made the Help->About dialog actually show.
• fixed bug loading jm2 files, value of fenhall_frag was read into v_radius instead and overwriting the radius. This made solid atoms seem to disappear when loaded or copied.
• add a “are you sure” to the C^Q quick key! (reported: Edwin Webster, same as below basically)
• Close confirmation if changes have not been saved (suggested: Shin)
• changed default colors and settings to be more like what people will commonly use. background is now while and things are drawn solid
• Show atom id in object name (suggested: Hong)
• removed #include "wx/msw/wx.rc" line from resource file, because it messed with debug build for msvc8
• fixed some memory bugs in parse.cpp and terrascript

089 -> 090

• removed old code for gradient based energy minimization step for UFF that didn't work and may have been causing problems and was clutter anyhow. Now, only simplex minimization is used.
• added atom ids, order of atoms from XYZ file is preserved
• atom label can be changed arbitrarily
• Jimp 2 now compiles and links on my linux test box, but it crashes immediately when run.
• cameras are not switched to automatically when changing workarea
• when opening a file, the molecule will be centered or use the first camera listed
• added maximizeFrame script function
• frame is maximized by default
• file dialog will recognize GJC files
• memory management may work now

088 -> 089

• as soon as a font is unused it is removed from the font cache. this reduces memory usage DRASTICALLY when fonts are scaled.
• bugfix: the default offset for an element should be 0. 0. 0. (instead of 0. 0.15 0., which is appropriate for bonds). (reported: Edwin Webster)
• bugfix: crashes when change 'Label:Offset' to just one number.
• bugfix: crashes when change 'Atom:Position' to just one number. (reported: Edwin Webster)
• added cameras
• MolRoot inherits from MolNode now instead of MolObj
• set the defualt atom color with setDefaultAtomColor()
• it is now possible to set the default properties of object types with setDefaultProperties()
• found a huge bug in the reference counting code -- jimp 2 will just leak like a sieve until I fix it
• added some save data that was missing (background color, label color for measures)
• offset for labels is now 2D instead of 3D (the 3rd parameter was mostly just clutter)
• labels may be rotated by any angle
• toggle to flip labels
• fixed bug with setting properties of a measure
• font size scales with zoom
• hidden/shown options in properties dialog
• now compiles on linux, but have not successfully linked yet

087 -> 088

• added measure for angle between planes
• default position of labels is moved up
• torsion measure is correct for 0 degrees
• no longer depends on compatibility with wxWidgets 2.4 -- updated to 2.6
• compiles with unicode enabled, but doesn't work with foreign characters yet

086 -> 087

• changed location of msvc project files
• align labels to bonds for measures
• label text placement via offset

085 -> 086

• measure selected bond lengths added
• opening of multiple files at the same time added

084 -> 085

• documentation through Doxygen, and more descriptions added
• UFF now reports what contribution to the total energy each constraint type makes for the simplex minimizer

083 -> 084

• fixed some more issues with UFF
• add rotate selected atoms RMB+Drag+Ctrl

082 -> 083

• shift and select bonds does not allow addition of bonds (reported: Edwin Webster)
• adding a bond to an element will remove its typing
• changing an element will remove its typing
• redrawing over a bond that already exists will increase the bond order by one half
• calcBonding will use whole work area if one atom is selected
• addHydrogens added to calc bonding dialog
• thicken the selection line, because it really does not show up when using a projector (reported: Edwin Webster)

081 -> 082

• buttons for UFF have temporarily been placed in the CalcBonding dialog
• reduced file size by not saving unnecessary info
• saving and loading of UFF type
• UFF Type property in atoms dialog
• removed option of explicitely setting label text, because it was too confusing
• changed "open a file" to "save file as" in save as dialog (reported: Edwin Webster)
• fixed a sorting bug -- sorting by name was not done for atoms and bonds (reported: Edwin Webster)
• added a sleep function (suggested: Edwin Webster)
• fixed an issue with UFF (linear bonds)
• it is now possible to set the max number of cycles and if vander waals forces are considered
• if atoms have an invalid or no type, a type will be assigned to them when doing UFF instead of blowing up

080 -> 081

• fixed calcBonding to have no upper limit on bond length when using high bonding factors; the most efficient cube size is also calculated based on the factor
• fixed a bug with multiple identical bond creation in calcBonding()
• UFF energy minimization works
• atom typing mostly works

079 -> 080

• draw solid fractional bonds with cylinders for dashes instead of spheres
• probably fixed the problem with light outlines on the orbitals when using povray
• atom drawing with connecting to previously drawn atoms (update to below)
• atoms and bond centers must now be directly clicked on to select them
• atom drawing (not connecting to previous parts)

078 -> 079

• add "hide hydrogens" shortcut
• make a more intuitive way of changing the background color (a menu entry?)
• added menu entry for the properties dialog
• added ability to change the view radius of bonds and atoms in the properties menu and created some new naming properties for them
• add X,Y,Z coordinates (position) to the properties box
• added draw mode toggle to be Ctrl-D
• changed deselect to be Ctrl-Shift-D
• add status messages to the status bar to indicate the current mode of operation
• added a dotted line while drawing a measure

077 -> 078

• registry keys are opened as read-only, so no admin priveleges are needed any more
• a required dll, msvcr70.dll has been added to the windows installer

076 -> 077

• bug fixed with measurements attached to moving atoms
• bug fixed getChildrenR() and a couple of other functions that assumed that only nodes could have children
• fixed bug with measure not setting lighting to be false
• pos_with_moving() made part of general objects, surfaces now show being moved
• Ctrl-Shift-Alt select all atoms (only the atoms)
• draw measure indicators thicker when selected
• commented out the opengl view mouse actions that do not work
• MMB translates view
• MMB+Ctrl translates selected atoms
• added bond order to properties dialog
• separated the label options from the general options in the properties dialog

075 -> 076

• actionCreateNode no longer sets the workarea, but the script function returns the created node's id so that it can be set through the scripting language
• made the webpage part of the jimp 2 directory tree
• moved changes.html to website and got rid of openglview.html in place of the user guide being written for the website
• the documentation directory is no longer included in the installer
• added autorun.ts to the installer
• lots of work being done on the website (i guess that isn't directly a change to jimp 2, but whatever)
• was reading the wrong registry key

074 -> 075

• added copy, cut, and paste
• fixed a center view bug with the root node
• added ctrl-n to make a new node
• upon creating a node the workarea is set to it
• moved position of new node in popup menu

073 -> 074

• added new properties to save and load (labels and measurement)
• pdb file loader now works on old style format
• automatically center the view after loading a file
• added printf style formatting to measurements
• will load files given in command line (doble clicking to open a file now works)
• name of the app says if it was compiled in debug mode

072 -> 073

• added measurement tool/object (distances, angles, and dihedrals)

071 -> 072

• added script function setPerspectiveMode
• changed help message
• can toggle labels
• label drawing defaults to false now
• in fenhall dialog 4- is interpreted as -4 for the charge
• fenhall results are written to a file and to the script dialog as comments
• use the registry key to load files from the right location and save them to the right location (autorun.ts, log.ts)

070 -> 071

• setting label fonts works
• can change label color
• rendering of text is now depth sorted
• only true type fonts can be selected (selecting others caused a crash sometimes)
• stuff about file loading

069 -> 070

• can now set the label of atoms
• changing atom type works properly now

068 -> 069

• fixed an issue with drawing labels when not centered at the origin
• all objects now have label properties
• fixed an issue with grab screen
• moving things is at correct scale now for orthographic
• center view now uses a bounding box instead of average positions
• center view now changes the zoom level as well as focus
• povray lines now look right for orthographic

067 -> 068

• grab screen works for orthographic
• grab screen dialog can get size of the current view times a factor
• povray works for orthographic
• povray dialog can get size of the current view times a factor
• fixed a slight visual glitch in bond drawing
• made offset bond parts always draw with rounded caps
• fixed an issue with font drawing where transparent font was occluding solid
• basic atom labels are working
• grab screen with jumbo sizes automatically scale the resolution of the font to be crisp

066 -> 067

• font drawing works
• orthographic projection mostly works

065 -> 066

• resizing window updates view
• grab screen now works perfectly

064 -> 065

• fixed cube inport/export to work with multiple orbitals
• fixed cube and xyz import to not crash on calcBonding.. it didn't before and doesn't any more?
• fenhall fragment analysis works
• using the default image viewer to show povray images now works correctly
• the povray function has been improved
• fixed a crashing bug with negative coordinates in calcBonding

063 -> 064

• fixed misalignment of text for calcbonding dialog
• made pov-ray dialog (povray doesn't want to work though. stupid program)
• it has become apparent that the rendering engine must be untied from opengl so that it can work with povray as well
• the general rendering and opengl specific parts have been separated
• both opengl and povray can now render through the same system

062 -> 063

• load cube files
• save cube files
• change the behavior of calc bonding
• automatically calc bonding when loading files that don't store bonding info (.xyz, .cube)
• changed the way exec works so that if it is called while running the new command will be stored in a queue and run when it is finished execing

061 -> 062

• added minimal property dialog for atoms and stub for bonds
• added fragment analysis, but it has not been checked if it works, but it compiles :-)

060 -> 061

• completely and totally fixed bug with undoing and then calculating again the bonding
• order is not messed with when moving and deleting objects
• when adding objects, atoms and bonds are put at the end, everything else is put at the top
• added some properties to field (save and load also)
• moplot is now awesome

059 -> 060

• Set default save format to jm2
• fixed exec() on a file that doesn't exist to not give a strange error
• fixed bug with undoing and then calculating again the bonding (kinda)

058 -> 059

• right click in opengl view for menu with properties dialog
• change in selection updates properties dialog
• file format selection in opening and saving
• extensions are verified in saving dialog
• jm2 loading will directly attach root objects now, converting them to nodes
• root nodes can now have any object as a child
• automatically create surfaces in moplot dialog
• added resolution to name of moplot fields
• calculate multiple moplot fields at the same time
• dotted drawing for fractional bonds in solid drawing mode
• show selection of solid bonds
• fixed selectAll() to select all in workarea. not the whole hierarchy. oops
• natural sorting of numbers in names
• fixed zoom bug
• calcbonding dialog box

057 -> 058

• Added Select all, deselect, hide selection, invert selection
• delete will now deselect the recently deleted nodes.
• message dialogs indicating how fenhall calculation finished
• automatically set directory for moplot after fenhall calculation
• profile.txt is no longer created
• added command echo setting
• on startup, run "autorun.ts"

056 -> 057

• exec() in terrascript now works
• fixed recursive sorting
• fixed moplot surface drawing

055 -> 056

• Loading and saving of native file format works
• Fixed name being reset sometimes when canceling editing of a label
• fixed to not select hidden atoms
• fixed to not center the view based on hidden atoms
• multiresolution moplot surfaces

054 -> 055

• Drag n drop reparenting now works properly.
• changed how type is shown through getProperties so that it can be used in saving files
• getProperties node specific stuff removed along with some useless info
• beta version of jm2 format saving (no loader yet)

053 -> 054

• propfield can make surfaces
• setSelection() behavior changed
• renaming of objects in the tree now mostly works. other things will have the name change sometimes, but refreshing the view makes them what they were originally
• drag and drop kinda sorta works

052 -> 053

• property changing fixed
• selection doesn't mess up drawing of surfaces in wireframe mode
• fenhall bug fixed (multiple runs giving different results)
• can now sort and sort recursively the nodes in the tree
• selection drawing bug in surfaces fixed
• surfaces now default to being drawn solid

051 -> 052

• transparency can now be set (but it won't draw right)
• surfaces can be drawn solid or wireframe

050 -> 051

• finished framework for dialog (changes can not yet be undone)
• made first changable option - v_solid
• fixed cap drawing of solid bonds
• changed background color to being stored in the workarea node in v_color
• changed vect.h to return refs to T in operator[]
• changed color behavior of atoms and bonds
• properties dialog can now change colors, but some more work is still needed on the feature

049 -> 050

• added properties dialog menu item to popup tree menu
• fixed layout problems of fenhall dialog
• created some of the basic framework for the properties dialog

048 -> 049

• changed determination of visibility of objects in tree and viewopengl and molobj. the visibility is now precalculated beforehand in a correct way. before a recursion was done on each drawing, so this should be faster as well as more correct.
• added arrayFromVars() builtin to terrascript
• changed drawing in viewopengl to draw root instead of messing with trying to reduce the number of things to try to draw
• changed shortcut key for script dialog from Ctrl-P to Ctrl-L to prevent confusing users with printing
• fixed refreshing of treeview to expand everything as needed
• changed behavior of tsVariable getInt and getFloat to return the first element in an array if it is an array

047 -> 048

• fixed separator in tree popup dialog
• added toggle hidden to tree popup dialog
• added toggle shown to tree popup dialog

046 -> 047

• all objects can now have children, and have a filter on types of children allowed
• constructor of MolObj makes more sense now
• changed all throw statements to throw_joe function to assist debugging
• iso surfaces are created as children of the field that made them
• iso surfaces have default color values based on the sign of the iso level

045 -> 046

• load file returns the object created
• automatically set workarea to molecule when it is loaded through the file menu
• converted change log into html
• resized script dialog
• changed centerView() to center on selected, else center on all in workarea
• changed calcBonding() to work on selected, else work on all in workarea
• confirmed and modified all existing scripts to run (select_lone_oxygen.ts has odd crashes)
• gave moplot field a better default name
• gave iso surfaces a better default name
• modified script crash recovery behavior (who knows if it will work though)

044 -> 045

• moplot crash fixed
• moplot orbital selection now works (passed in through function call)
• moplot dialog slightly prettier
• changed "vector<MolObj*> workarea" to "MolObj* workarea". Having multiple things in the workarea is too confusing. All molecule - wide operations such as fenhall or moplot will operate on the workarea. If nothing is selected for operations that need a selection everything in the workarea will be considered selected, such as calculate bonding. To view all of the objects, select the root as being the workarea.

043 -> 044

• Changed sizer behavior in MoplotDialog
• Changed default focus for ScriptDialog
• Change ScriptDialog log to uneditable, and different color
• Created installer using NSIS (untested)

042 -> 043

• Made solution compile with new version 2.6.0 of wxWidgets
• Fixed some issues with fenhall dialog