2023-07-31 - Query box: labels are not truncated anymore 2023-05-07 - if the chain tool is selected, bonds can also be highlighted by mouse over - resetAtomMarks() (fix for issue #31) resetBondMarrks(), resetAtomMaps() - bug fix: issue #33: JSME set atom events not triggered when using keyboard to set atom type - improve rotation of molecule (shift drag) - IE6/IE7 supports removed from permutations (GWT user-agents) - bug fix: show chain length in info during chain build - bug fix: bond centers are now recomputed after atom move action (mouse over -> no bond highlight) 2022-09-26 - Renaming of "star" option to "circle" or "marker" in the example HTML files 2022-09-03 - https fix for the JSME_chemical_resolver_demo.html - bug fix: noShowdragandDropIconindepictmode (github issue # 24) - bug fix: deprecation warnings in Firefox (github issue # 23) - bug fix: Delete molecule using Delete key caused error (github issue #25) - bug fix bondhighlight (github issue #27) - new atom inspector function: set atomic charge 2022-02-26 - background color palette changed: yellow color more saturated, additional light green color - new option: disable gui zoom (github issue #17) - bug fix: AfterPaste event was not working (github issue #22) - bug fix: marked atom in template (github issue #20) 2021-07-13 - improved example file JSME_test.html - sulfonylmethanediamine SMILES generation bug fix - improved JavaDoc 2021-06-10 - Undo stack stores the state of the editor during editor initialization - Possibility to set default format for copy/cut and D&D - Chiral flag status shown in the info bar - Avoid browser window automatic scroll when the mouse pointer moves on the editor - bug fix: setTemplate() 2021-05-10 - sub and superscript text style for the number of hydrogens and charges 2021-04-05 - bug fix: JME output for fragments, no more coordinate overlap - bug fix: recompute 2D coordinates: problem with explicit hydrogens - new option: guiAtomColor (customization of JSME look) - the depict example page has been extended - new example JSME_access_internal_data.html - new example JSME_alternative_look.html - new methods: getAtom(), getBond() and getMolecule() - replaced all setAfterStructureModifiedCallback() from the examples because of deprecation - setBondAdditionalData bug fix (wrong event name reported) - improved readability of atom labels when a background colored circle is shown (additional text stroke) - custom background coloring is now independent from atom numbering and atom marker 2021-01-31 - new option showAtomMapNumberWithBackgroundColor 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