2020-12-26
- migration of help.html file to https://jsme-editor.github.io/help.html
2020-12-20
- bug fix: deletion of an unwanted used to compute a WindowPanel size (mosaic library bug)
- new example page: JSME_inchi_direct_interactive.html
- JSME event "seAtom": atom number removed from the event.action field
JSME-2020-11-22"
- atom inspector (number option on, right mouse click on atom) set atom map bug fix
- atom numbering:: typing 0 allows to reset next clicked atom (bug fix)
JSME-2020-09-24:
- new option: markNothing
JSME-2020-09-05
- improved examples pages JSME_atom_highlight_demo.html
JSME-2020-06-30:
- setBackGroundColorPalette bug fix
JSME-2020-06-26
- new option: markerMenu
- new method: setMarkerMenuBackGroundColorPalette
- bug fix: toggle depict to edit, centering of molecule was needed
- R group number input bug fix
JSME-2020-06-14
- internal bond scaling bug fixed
- new test page: JSME_Rgroups.html
- R group R9 bug fix
- numeric keypad numbers bug fixed
JSME-2020-06-11
- new mouse over information for some JSME functions
- MOLfile input with aromatic bond type 4, conversion to single and double bond
- import RXN and SMIRKS works (see test_depict_patent_reactions_smirks.html)
- RXN input: bug fix: detection of agents was not working
- improved detection of reaction role
- in marker mode, the color index can be set with the keyboard like atom maps
- methods setStarColor and setMarkerColor have been replaced by activateMarkerColor
- documentation update: hydrogens, nohydrogens - display / hide implicit hydrogens on heteroatom labels (default is hydrogens). Implicit hydrogens are calculated only if the valence state option is switched on
- R group works again
JSME-2020-05-3
- jsmeEvent: additional variable atomBackgroundColorIndex
- colored background atom labels have rounded corners
- bug fix: SMILES output of atom with color marking had no atom map
- new active marker system: accept MOL and JME input with atom map as input
- the default color palette has been changed
- JME output format available in I/O menu
- atom highlight is not disabled anymore if bond stereo action is selected
- carbon chain bug fix: wrong charge on closing atom
- carbon chain event does not trigger addBond event for each bond addition anymore
- do not split fragments in depict mode (cross atom issue)
- HTML examples cleanup
- Additional HTML example and test pages
JSME-2020-04-19
- new active marker system - preliminary
- generic input fires an event for MOL, RXN and JSME inputs
JSME-2020-04-13
- bug fix: hydrogen handling options have no effect
- bug fix: nocanonize was not working
- reaction arrow can be moved
- molecule popup menu: compute 2D coordinates of the selected molecule
JSME-2020-04-08
- new method: setMenuXShortcuts()
- 3 bug fixes related to valence sate during template addition
- improved chemical format detector (SMARTS, CSRML)
- compute 2D coordinates if input molecule has none or is 3D
- improvement and HTML code reformatting of the example files
- JME string parser bug fix: handling of charges
- improved atom map display (smaller font, better placement)
- new options:
markerIconColor, markAtomOnly, markBondOnly, pseudoMark
- setMarkerColor() method replaces setStarColor()
- background color highlighting new functionalities: getNumberOfColorsForBackGroundPalette, getBackGroundColorPalette, setBackGroundColorPalette
- bond colored background shape is rectangular
- new API method: getMultiSDFstack
- new JSME event: readMultiSDF
- new methods: g(s)etAtomAdditionalData, g(s)etBondAdditionalData
- new methods: hasMarkedAtom(), hasMolecule()
- new test pages:
- JSME_template_cysteine_lesson.html
- JSME_custom_x_shortcuts.html
TODO: provide in the dev doc the list of all events
JSME-2019-05-11
- bug fix for option valenceState
JSME-2019-05-05
- new atom shortcut: *,g
JSME-2019-04-22
- new option: valenceState
JSME-2019-01-30
- doc.html cleanup
- setUserInterfaceBackgroundColor() bug fix
JSME-2019-01-19
- new initialization parameter: guicolor
- new method: setUserInterfaceBackgroundColor()
JSME-2018-11-18
- new copy option: Copy as raw SVG
JSME-2018-11-10
- new option: star1
- bond highlight is disabled if an atom only action is selected (e.g. set atomic charge)
- atom highlight is disabled if a bond only action is selected (e.g. set bond stereo)
JSME 2018-10-28
- improved documentation: new parameter section
- two new parameter: atombgsize and bondbgsize
JSME 2018-10-21
- bug fix: when importing or pasting a structure with atom map number, the numbers are not displayed if the editor is in star mode, instead the atom with an atom map are displayed with a blue background color
- bug fix: when two atoms are very close, it was impossible to select the bond between the two atoms
JSME 2018-10-15
- delete method to disable the functional group menu enableFGMenu()
- new option: fgmenu / nofgmenu
- bug fix: atom marking using the star option
- pasting a SMILES with one or more leading or trailing blank will be accepted and corrected
JSME 2018-10-07
- new method to disable the functional group menu enableFGMenu()
- new method: setBondBackgroundColors()
- additional HTML example page that shows an alternative way to use templates (see JSME_template_aminoacids.html)
- change default background color for GUI elements
JSME 2018-06-03
- atom and bond highlight mouse leave events are fired before mouse enter events
JSME 2018-06-01
- improved atom background highlight with mutliple color mixing (see JSME_atom_highlight_demo.html)
- JSMEevent includes atoms of selected bonds and atom and bond indices of the molecular fragments
- additional HTML example page that shows how to use the built in InChi computation (see JSME_inchi_direct.html)
JSME 2017-11-15
- default string width and font height are provided when the font size computation fails
JSME 2017-11-14
- improved font cache - invalid values are not stored in the cache anymore, fix a display bug when the applet is hidden in a iframe
- new API method: clearFontCache
- API method repaint() always repaint the whole applet, even the parts that has not been changed
JSME 2017-08-23
- changed showInfo() method - the custom message is not erased by a menu click
- improved full screen function
- direction of mouse wheel zoom reversed (use same convention as other web applications)
JSME 2017-08-08
- SMILES generation stereo bug fix
- Chemical format detector accepts invalid "M END" with only one space
JSME 2017-07-09
- Copy&paste windows: clicking outside the window closes it
- Popup windows have the maximum Z index
- Full screen functionality and icon
JSME 2017-06-18
- improved visual feedback for group deletion
- improved visual feedback for atom moving (bond highlight not shown anymore)
- copy/paste windows can be closed by pressing the ESC key
- RXN export agents (non standard format)
- RXN export format new option: merge reaction component
- when a reaction role is changed, an event is generated
- setting atom maps for reactions is easier with mouse clicks
- bug fix: applet resize will keep the reaction components around the reaction arrow
- bug fix: paste a reaction when the molecular area scale is different than 1
- bug fix: if the molecular area scale is different than 1, the reaction role of the reaction components were not correctly reported
- bug fix: error message for a non supported input file format showed the enum number instead of the enum name
- preliminary implementation of full screen icon (still disabled by default)
- java code refactoring
JSME-2017-05-22
- context menu can be disabled (new option)
- SMILES export: No more EZ stereo for double bonds in ring size <= 7
- Hydrogen count is exported for some metals for MOL (v2000+v3000) and JME formats, and imported for MOL (V2000) and JME formats
JSME-2017-05-07
- Coordination bond shown in SMILES as ~ (canonization is disabled)
JSME-2017-04-01
- First support for coordination bonds
JSME-2017-03-21
- new system clipboard handling
- support for wiggle and crossed stereo bonds
JSME-2017-02-26
- improved URL for searching InChI Key (google verbatim search)
- bug fix: popup menu positions when the GUI is scaled
- bug fix: getMolecularAreaScale() generated an infinite loop
- bug fix: no error were reported when the V3000 parser fails
- bug fix: setAtomMolecularAreaFontSize() was not working
- bug fix: set or unset antialising did not update the drawings
- improved template example page
JSME-2017-02-20
- bug fix: chiral flag was not saved in the undo state
- bug fix: ChemicalFormatDetector trimmed MOL first line if it is empty
- improved template example page
JSME-2017-02-08
- bug fix: SDF buffer navigation messages were not shown
- HOME and END keys can be used to navigate the SDF buffer in addition to page up and page down keys
JSME-2017-02-06
- bug fix: structure change event recorded after setting the chiral flag
- bug fix: NEW button shown as disabled after structure change
- new feature: when NEW button is on, the pasted or dropped structure is added to the molecular drawing area
JSME-2017-01-22
- bug fix: in depict mode, DnD arrow size does not vary with zoom level
- DnD arrow in depict mode is smaller
- new event types for reading SMILES, SMIRKS, RXN, JME string
- new event field: origin (GUI, INIT, DROP, or API)
- new API method:readGenericMolecularInput()
- import MOL in V3000 format accepted (extended stereo collections are ignored)
- exported SVG contains an embedded MOL in V3000 format, this SVG can be pasted/imported back in JSME
- bug fix: depict mode automatic scaling and resizing
- bug fix: zooming in and out for reactions
- new internal class: ChemicalFormatDetector
- JME internal code cleanup
JSME-2016-12-06
- new API methods: getMolecularAreaScale(), setMolecularAreaScale(), getMenuScale(), setMenuScale()
- depict mode: structure can be moved around
- multiple button after setting R option : GUI bug fixed
JSME-2016-11-13
- improved documentation (options useoclidcode, toggle, InchiResult)
- Search InChIKey can be customized by using a custom base URL or a custom callback function
- Search InChIKey menu entry renamed
- Inchi export disabled for IE < 9
JSME-2016-11-05
- option parser code rewrite
- bug fix Export SVG for IE < 9
JSME-2016-11-01
- Export SVG for molecules using the OpenChemLib SVG depictor
JSME-2016-10-30
- bug fix: parsing of chemical input for IE
- bug fix: stereo cumulenes smiles generation
- bug fix: EZ stereo bond in rings enabled (smiles generation)
- Export InChI, InChiKey and auxinfo
- Search google with InChiKey
JSME-2016-10-19
- bug fix: getMolecularAreaGraphicsString
- bug fix: slow down of FireFox SVG display
JSME-2016-10-17
- bug fix: Cursor does not become a text edit cursor over SVG text
- the right border uses a separate graphics, which fixes several bugs
- bug fix: readMolfile sends JS event after repaint() of the applet
JSME-2016-10-09
- useOclIDCode new option: preliminary implementation
JSME-2016-10-06
- delete hydrogens popup menu entry
- bug fix: removehs fixed
- bug fix: infinite loop when setAfterStructureModifiedCallback uses getMolecularAreaGraphicsString()
JSME-2016-10-02
- clipboard window improved for long lines text
JSME-2016-09-25
- display sp carbon in cumulene bond
JSME-2016-09-18
- bug fix: H+, H-
- undo shows empty state
- depict bug fix
- internal change for event reporting
JSME-2016-09-11
- bug fix: cumulene and autoez option
- getMolecularAreaGraphicsString function refreshes the drawing before yielding the SVG. Also, it does not show the touched atom or bond.
JSME-2016-09-05
- small bug fixesm reading mutipart mol
- readMolfile sends JS event after repaint() of the applet
JSME-2016-09-04
- small bug fixes
JSME-2016-08-21
- R number can be changed by selecting the R atom and typing a number on the keyboard
- the */- button allows changing charge of metals with only two major oxidation states
- X atom charge parsing bug fix for Ca2+
- New keyboard shortcut for changing atomic charge '+' (works only for the Java applet)
JSME-2016-08-01
- bug fix add new part was not working correctly if the pasted structure is multipart
- autoez bug fix , autoez is on by default
JSME-2016-06-19
- new options: showdraganddropsymbolindepictmode and noshowdraganddropsymbolindepictmode
- new options: addnewpart and noaddnewpart
- bug fix add new part was not supported for JME string input
- split and merge new behavior
- mutipart option is on by default
JSME-2016-05-16
- bug fix: depict was not scaled anymore
- MDL chiral flag reading was generating an exception if no digit character were present
- New JSME initialization:
JSME-2016-04-27
- disable SVG text selection with global CSS
- Bug fix: bond addition with keyboard on selected atom
- atom mapping option in the context popup menu is shown only in reaction or number or autonumber mode
JSME-2016-04-19
- atom mapping option in the context popup menu is shown only in reaction mode
- bug fix
- Setting the chiral flag shows a message in the info area
JSME-2016-04-17
- dialog box to set atom map available with the context menu
- autonumbering of atom maps of a molecule using the context menu
- read and write chiral flag for both V2000 and V3000
- set MDL chiral flag with the context menu
- in multipart, activate closest fragment by a mouse click
- in multipart, move the fragment that is the closest to the mouse pointer coordinates
- in multipart paste, keep the original coordinates of the fragments
- mouse wheel for zooming in and out (does not work correctly for reactions)
- allow zooming option (zoom, nozoom)
- openchemlib for SMILES input
- SMIRKS input using openchemlib for SMILES input
- use openchemlib option
- highlight in red molecule to be deleted
- highlight in blue molecule to be copied (in reaction mode)
- various bug fixes
- refactoring of bond code
JSME-2016-02-16
- Bug fix for multipart copy
- Reaction copy and structure delete highlight (still buggy)
- NCI website demo: example: http->https
JSME-2016-02-01
- Bug fix for multipart and reaction (delete, add , undo stack)
JSME-2015-12-06
- Bug fix bond rubberbanding
JSME-2015-11-22
- Refactoring of JME code: bond creation bug fix
JSME-2015-11-15
- Refactoring of JME code
JSME-2015-11-04
- Tool chain bug fix
- Applet resizes automatically when the browser window resizes
JSME-2015-11-01
- Empty mol return a valid MOL with 0 atoms and bonds
- After importing a reaction with atom mapping, the numbering atom tool will use the largest atom map + 1
- Refactoring of JME code
JSME-2015-10-04:
- Bug fix: clicking on NEW and 123 does not generate structure change events
- Disable logging of null events
- Changing atom type using the keyboard while the cursor is over an atom does not change the atom type menu selection
- Using the ring keyboard shortcuts while the cursor is over an atom or a bond does not change the menu
JSME-2015-06-25
- depictAction bug fix
JSME-2015-06-20
- new generic callback
- atom clicked and bond clicked callback
JSME-2015-06-14
- New button for I/O
- Updated smaller icon for drag and drop
JSME-2015-05-28
- fixed broken links in doc.html
JSME-2015-05-14
- bug fix: read JSME string with more than 10 marked atoms
- replaced the star by a circle
- jsa,css bug fix
JSME-2015-05-07
- depict mode:leave 16 px for the DnD icon to avoid overlap
JSME 2015-05-03
- bug fix: autonumber was not working anymore after array optimization (123)
- remove linker name (e.g xsiframe) from the name of the distribution
- Microsoft Edge compatibility test performed: Window clipboard is not supported anymore
JSME 2015-03-19
- Fixed many bugs in the depict mode in order to allow to switch back and forth between depict and edit mode
- new methods isDepictMode(), addMouseOutHandler()
JSME 2015-03-01
- Enable touch events on a ChromeBook
- JavaScript Bootstrap library compatibility fix (computation of character height)
- R4 to R9 smiles generation fix
JSME 2015-02-25
- R4 to R9
JSME 2015-02-09
- bug fix for SMILES generation of pyrrole [nH], H was missing
JSME 2015-01-28
- Ctr V shortcut fixed
JSME 2015-01-22
- file out browse button
- V3000 export
- bug fix: missing event record for closing a bond on an atom
JSME 2014-12-24
- bug fix: missing event record for paste
JSME 2014-12-20
- reenable older event callback
JSME 2014-12-07
- missing event record for more keyboard events, improve undo/redo record event
JSME 2014-12-04
- missing event record for set atom type with keyboard
JSME_2014-11-19:
- BUG: copy SDF of a multipart: invalid ISO
- array JavaScript optimization
- Record an event during add chain for each bond
JSME_2014-10-16
- template bug fix
JSME_2014-10-13
- Bug fix: JSME in a hidden DIV would not be visible
JSME_2014-09-21
- Drag and Drop enabled on IE6 to IE9 (does not work with files)
- Template 1st implementation
- Missing new lines in doc.html
JSME_2014-08-26
- incorrect atom mapping read from RXN when numbering option is set - fixed
- export SMIRKS with "a" did not works with atom mapping - fixed
JSME_2014-07-14
- Paste behavior changed: if current status is multipart or reaction, then the new structure will be added and will be the selected structure
- new linker (xsiframe) for CDT testing
JSME_2014-06-28
- Paste behavior changed: if current status is multipart or reaction, then the new structure will be added
- remove H bug fix
- bug fix: structure underneath the menu region: highlight must dissapear
JSME_2014-05-20
- new resize method
JSME_2014-03-30
- bond marking allowed
- bug fix: paste of a multipart structure with isotopic atom
JSME_2014-03-12
- setAction, depictaction
JSME_2014-02-20
- Font size can be changed with setAtomMolecularAreaFontSize
JSME_2014-02-03
- bug fix: date in exported MOL
- new callback setAfterStructureModifiedCallback
JSME_2014-01-27
- isotopic atoms implementation
- star marker: the MOL generation now set the atom map for each marked atom
JSME_2014-01-05
- smaller initial download size by about 25 %
- scaling picture: further improved for very small depiction
- high precision 2D coordinates
JSME_2013-11-06
- removehsc new
- scaling picture: improved for very small depiction
JSME_2013-10-27:
- initialization error will not open an alert but write a message to the console instead
JSME_2013-10-13:
- small refactoring inside the JME code
- bug fix in doc.html
JSME_2013-10-09:
- callback function setNotifyStructuralChangeJSfunction does not need the nocanonize function anymore
JSME_2013-10-03:
- bug fix:D&D icon disappears after resizing JSME
- bug fix: resizing JSME, avoid multiple SVG/VML generation after each resize
- improved setNotifyAtomHighLightChangeJSfunction
- two more example pages about JSME resize
- depict mode takes the callback function notifyAtomHighLightJSfunction
- after clearing the canvas, the undo stack is not deleted anymore
JSME_2013-09-29:
- bug fix in index.html
JSME_2013-09-28:
- More simple installation examples
- index.html file
- improved doc.html file
- star option documented
JSME_2013-09-19:
- New methods: addClickHandler(), addMouseOverHandler()
JSME_2013-09-17:
- New methods: getOffsetSize(), getOffsetWidth(), getOffsetHeight(), setWidth(), setHeight(), isVisible(), setVisible()
- improved javadoc API
JSME_2013-09-15:
- new utility function: Utils.runAfterBrowserEventLoopReturns
- setSize() method
- call back function argument for replaceAllAppletsByJSME
- JME: cache font and font metrics for the drawing area useful for many depictions
- scaling picture bug fix: the 2px padding around the atom labels was not scaled
JSME_2013-09-08:
- Easy migration JME->JSME
- new documentation file: doc.html - still incomplete
- new option: paste/nopaste to disable pasting MOL into the applet
- query mode disabled by default
- aromaticity SMARTS query bug fix
JSME_2013-08-04:
-xbutton, noxbutton options work
JSME_2013-06-29:
- For IE11, the clipboard management had to be adapted because of the unconventional user agent in IE11 (=Firefox)
- Android and iPad do not show the drag out button because dragging out does not work on these systems
- bug fix: undo & redo was not working for atom atom mapping
- Note: the number of GWT permutations has increased to 30
JSME_2013-06-09:
- atom move atom button is optional (turned off by default)
- improved JSME_chemical_resolver_demo.html page
JSME_2013-05-30:
- move atom button
- java application exits when its window is closed, no more END button
- new simpler HTML demo page
JSME_2013-05-01:
- bug fix: IE has no console unless the debugger window is open
- deleting explicit hydrogens when importing a structure from chemical resolver (demo page)
JSME_2013-04-09:
- Custom paste menu and custom paste operation
- non GPL licensed image for the drag and drop icon
- local antialias for VML
- line width for the molecular area
- JavaDoc of the API
- clear function added
JSME_2013-04-01:
- bug fix in JSObject
JSME_2013-03-30 :
- Drag out of MOL/RXN and drop onto another applet or on to a file system window to save the file
- DnD demo page
- No more alert window if the function jsmeOnLoad is not defined - instead provides a message to the console
- clear SDF stack as well when clicking on the clear icon
- stereo bond cancel bug fix (bug shows up visible with undo/redo)
- interactive atom marking demo page
- multiple instances of the editor in the same HTML page work
JSME_2013-03-24 :
- Drag and drop of files onto the applet
JSME_2013-03-21 :
- undo bug fix
- showInfo function
JSME_2013-03-19 :
- antialias is on by default for SVG and off for VML
- new help page
- first public release
JSME_2013-03-18 :
- spiro button
- triple bond in menu is improved - looks better with browser with poor antialias
JSME_2013-03-16 :
- rename JavaScriptApplet to JSApplet to avoid trademark problems with JavaScript
- disable molecule scaling for IOS
- removes blue marking about atoms and bonds after click enabled unless touch device
JSME_2013-03-14 :
- increased touch radius for atoms and bonds - much better usability on iPad
JSME_2013-03-13 : not for redistribution
- first DIV shield - still bugs
- rubber banding box was not saved in the undo stack - fixed
JSME_2013-03-12 : not for redistribution
- Rollback of all the Smiles changes, no more example of NotifyStructuralChangeJSfunction provided
- improved rotation&scaling on iPad. Scaling is still buggy
JSME_2013-03-11 : not for redistribution
- Smiles generation changes the atom ordering of the atoms in the editor, which is a problem for the NotifyStructuralChangeJSfunction. Fixed.
JSME_2013-03-10 : not for redistribution
- Scaling of the molecule implemented for touch devices - still buggy. Problem with rotation, does not work on Android
- NotifyStructuralChangeJSfunction - problem with smiles generation
JSME_2013-03-07
- Marked atoms are not displayed anymore with a blue square after touch/mouse up
- Touch device: rotation bug fixed (random jump move at the end of the rotation)
- bug fix for CSS distribution
JSME_2013-03-04
- Touch device: rotation works on iPad
JSME_2013-03-03
- Touch device: touch and hold will show the copy&paste popup menu
- Touch device: mouse events of drawing area were replaced by touch events in order to have a faster response on the iPad
- Touch device: structure can be moved. It is smooth on a iPad 4, slow on a Samsung Note
- Touch device: bond angle can be changed, multichain works
- CSS pollution: all global CSS definitions were removed from all the included CSS files from GWT and gwt-mosaic
- CSS global protection: better protection against global CSS definitions from the host page
Known bug: scaling and bond length rubber banding