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History of changes: new features and improvements, bugfixes

June 16th, 2017: Marvin JS 17.12.0

Bugfixes

  • In some cases, MolV2000 files containing aromatic heteroatom generated by Marvin JS could not be imported or pasted.
  • When the selection contained the reaction arrow and a merged agent, editor dropped error on opening context menu.
  • Undoing the last step, when a atom was merged to an atom of a merged agent group and the group was automatically ceased, resulted in the addition of bonds to the structure.

June 9th, 2017: Marvin JS 17.11.0

No changes.

June 8th, 2017: Marvin JS 17.10.0

Improvements

May 9th, 2017: Marvin JS 17.8.0

No changes.

May 5th, 2017: Marvin JS 17.7.0

No changes.

May 3rd, 2017: Marvin JS 17.6.0

Improvements

Bugfixes

  • In some cases partial clean resulted in structural changes in Marvin JS.
  • Importing RD file without specifying input format did nothing.

April 21st, 2017: Marvin JS 17.5.0

No changes.

April 3rd, 2017: Marvin JS 17.4.3

Bugfixes

  • In some cases after Auto mapping, Stereo labels did not show on the right atom.
  • In 3D mode, after pressing Add/Remove Explicit H for the third times resulted in an error.

February 27th, 2017: Marvin JS 17.2.27

Improvements

  • Merged agents in a reaction are preserved during import and export.

February 6th, 2017: Marvin JS 17.2.6

Improvements

  • Automatic lone pair calculation feature is added to Marvin JS Image Exporter. (See online example here.)
  • S-group export has been improved in Mol v2000 format.

January 30th, 2017: Marvin JS 17.1.30

Bugfixes

  • Marvin JS did not import Mol V2000 files with blank numeric field.

January 23rd, 2017: Marvin JS 17.1.23

Bugfixes

  • Exporting a molecule which contained two Abbreviated groups connected by a bond in Mol v2000 format, resulted invalid structure. Copy-pasting of this molecule in Mol v2000 threw an error message.
  • When merging Abbreviated groups, bonds, templates with 3D structures, the z-coordinates lost.
  • In some cases, undoing the expand action of the abbreviated groups could result in unwanted structural changes.

December 12, 2016: Marvin JS 16.12.12

No changes.

November 14th, 2016: Marvin JS 16.11.14

Improvement

If there is no electron flow arrow in a reaction, `electron` block is not written in the MRV file.

October 17, 2016: Marvin JS 16.10.17

No changes.

October 3rd, 2016: Marvin JS 16.10.3

Bugfixes

  • In some rare cases drawing with bond tool resulted invalid bond format in mrv source.

September 26th, 2016: Marvin JS 16.9.26

Improvements

  • SDF export in ctab format is available from Export dialog and also from API.

Bugfixes

  • Importing (or pasting) structures containing abbreviated groups with no attachment points caused an error.

September 12th, 2016: Marvin JS 16.9.12

Improvements

  • Cut/Copy/Paste actions are available via Context menus.
  • Reaction handling has been improved: client side reaction export has been introduced. (Documentation/Example)

Bugfixes

  • In Edge browser image download was not possible.

August 22nd, 2016: Marvin JS 16.8.22

No changes.

August 19th, 2016: Marvin JS 16.8.15

Improvements

  • Calculated stereo labels can be eliminated from the canvas by pressing the Calculate stereo button again.
  • Deleting structures is also possible by pressing Back-Space keyboard button.

Bugfixes

  • R-logic was set to default when the group definition was updated.
  • Minor fix in Export dialog.

July 4th, 2016: Marvin JS 16.7.4

Improvements

  • R-logic dialog has been introduced.

  • Mapping functionality has been added to the arrow tool tips.

Bugfixes

  • R-group definition could not be copied in MRV format.

June 6th, 2016: Marvin JS 16.6.6

No changes.

May 23rd, 2016: Marvin JS 16.5.23

Bugfixes

    • The molecule appeared to be smaller than expected, when the display property was set to be none, and structure was imported before the resize event of the iframe.

April 18th, 2016: Marvin JS 16.4.18

Bugfixes

  • The size of minus charge has been increased to make it more readable in OSX environment.

April 7th, 2016: Marvin JS 16.4.4

Bugfixes

  • Lone pairs were lost, during copying as mrv, if these were next to an abbreviated group.

March 30th, 2016: Marvin JS 16.3.28

Improvements

  • New options has been introduced in Abbreviated group context menu: "Expand and Clean" and "Ungroup and Clean"

  • For longer processes, loading bar has been added.

  • Zoom mode `autoshrink`works for svg image generation as well.

Bugfixes

  • Partial clean moved all the structures in the middle of the Canvas.

February 29th, 2016: Marvin JS 16.2.29

Bugfixes

  • Marvin JS could import molecule files containing the same atom for the starting and ending point of a bond.

February 22th, 2016: Marvin JS 16.2.22

No changes.

February 8th, 2016: Marvin JS 16.2.8

Improvements

  • Integrate Marvin JS with Structure Checker example has been added.

Bugfixes

  • Hidden iframe was initialized with minimum zoom level.
  • Import failed on some files, exported from Marvin Sketch, which contained r-group and electron flow arrow.

  • Some reaction files from Marvin Sketch, containing abbreviations and electron flow arrow, could not been opened.
  • Extra MElectronContainer items appeared in the source on clipboard copy, when lone pair calculation was disabled.
  • In Internet Explorer 9 in some cases keystrokes did not work.

January 11th, 2016: Marvin JS 16.1.11.1

Improvements

  • rb* and s* atom query properties are available from Atom query properties dialog.
  • SRU polymers accept any lowercase letters except " c " and " f ".

Bugfixes

  • The subscripted numbers in abbreviated group labels' display has been improved in Internet Explorer 9 and 10.
  • R-group attachment was partially out of frame after zoom all action.
  • R-group attachment covered the atom indices the canvas.
  • R-group definition highlight could be out of the canvas after zoom all action.

January 4th, 2016: Marvin JS 16.1.4

No changes.

December 14th, 2015: Marvin JS 15.12.14

Improvements

  • The list of abbreviations has been extended, revised and synchronized with MarvinSketch.
  • Abbreviated group rendering takes the bond position into account.

Bugfixes

  • The attachment point of certain abbreviated groups was not exported to MRV format.
  • Atom and Template toolbar buttons were missing in Internet Explorer 9 browser. 
  • In some cases atom indexes was rendered out of the picture and these were also out of the frame in the canvas after Zoom to fit action.
  • In Internet Explorer 9 browser, selecting an abbreviation from a long list could move the editor out from the iframe.

December 7th, 2015: Marvin JS 15.12.7

Improvements

  • Image export in SVG format has been implemented. See an online example here.

Known issues

  • Atom and Template toolbar buttons are missing in Internet Explorer 9 browser. 

November 23rd, 2015: Marvin JS 15.11.23

No changes.

November 16th, 2015: Marvin JS 15.11.16

Improvements

  • Radical and lone pair buttons are swapped, when the editor loads with disabled automatic lone pair calculation. (Adding lone pair button is the default in this case.)

 

Bugfixes

  • When zoom level reached the minimum zoom value,the zoom buttons became inactive.

November 2nd, 2015: Marvin JS 15.11.2

Features

  • Unique id has been introduced to atoms and bonds in Marvin JS. This property is automatically generated by the editor, and it is available via calling exportStructure() function with the hasUID option.
  • Highlight can be added to structures by unique ID or index.
  • Atom Value property is preserved by Marvin JS during import and export.

Bugfixes

  • Painting failed on certain query structures.

September 5th, 2015: Marvin JS 15.10.5

Features

  • Lone-pair alignment has been improved.

September 28th, 2015: Marvin JS 15.9.28

No changes.

September 21th, 2015: Marvin JS 15.9.21

Features

  • Minimum zoom value has been changed to 10%.
  • Charge sign has been increased to be more visible.

Bugfixes

  • Deprecated util.js overwrote window.Promise object.

July 20th, 2015: Marvin JS 15.7.20

Bugfixes

  • From version 15.6.15 in the Atom properties Advanced tab Substitution was indicated by (r) instead of (s).

July 13th, 2015: Marvin JS 15.7.13

No changes.

June 29th, 2015: Marvin JS 15.6.29

No changes.

June 22nd, 2015: Marvin JS 15.6.22

New features and improvements

  • API
    • Automatic lone pair calculation can be turned off from API.
  • Edit
    • Radical electrons and Lone pairs can be assigned to atoms manually.

Bugfixes

  • More abbreviated groups in a structure made Marvin JS responding slowly.

June 15th, 2015: Marvin JS 15.6.15

New features and improvements

  • Keyboard shortcuts
    • Atom query properties dialog can be opened from the Query atoms combo box on the Atoms toolbar or by the "." hotkey.
    • Abbreviations can be handled more easily:
      • For "Space" key Abbreviated group dialog opens.
      • Abbreviated groups dialog can be closed by pressing the "Enter" button repeatedly.
      • Pressing the "Shift" key expands the abbreviation on the tip of the mouse cursor.
    • Rotation of the templates (during merge on a bond) can be achieved by the "Shift" keyboard button instead of "Space".

Bugfixes

    • Mol V2000 format copied from Chem Draw couldn't been pasted into Marvin JS.

June 1st, 2015: Marvin JS 15.6.1

No changes.

May 25th, 2015: Marvin JS 15.5.25

New features and improvements

  • GUI
    • More frequently used atoms (such as S, F, Cl, Br, I) has been introduced to the Atoms Toolbar.
    • Abbreviated group dialog has been renewed: the search function is improved.
    • New icon has been added to Reaxys Group Generics tool.

May 18th, 2015: Marvin JS 15.5.18

No changes.

May 11th, 2015: Marvin JS 15.5.11

No changes.

May 4th, 2015: Marvin JS 15.5.4

New features and improvements

  • GUI
    • Rich text editor has been introduced in Marvin JS.

Bugfixes

  • When colored boxes was imported into Marvin JS, the color settings changed.
  • Sometimes MarvinJSUtil.getEditor function wasn't resolved with sketcher instance.

April 20th, 2015: Marvin JS 15.4.20

No changes.

April 13th, 2015: Marvin JS 15.4.13

No changes.

April 6th, 2015: Marvin JS 15.4.6

New features and improvements

March 30th, 2015: Marvin JS 15.3.30

No changes.

 March 23rd, 2015: Marvin JS 15.3.23

New features and improvements

  • Atom and bond coloring is displayed and can be imported from MRV file. This information is preserved during exporting MRV files or generating pictures.

March 16th, 2015: Marvin JS 15.3.16

Bugfixes

  • Export did not work under Internet Explorer.

March 9th, 2015: Marvin JS 15.3.9

New features and improvements

  • GUI
    • Repeating Group tool has been developed. With this tool polymers containing repeating units and link nodes also can be created and edited.
    • Group Generics panel has been introduced to Marvin JS.
    • The Atom Toolbar has been changed: a few elements have been eliminated, the (Reaxys) Group Generics  have been added.

February 23rd, 2015: MarvinJS 15.2.23

No changes.

February 16th, 2015: MarvinJS 15.2.16

No changes.

February 9th, 2015: Marvin JS 15.2.9

No changes.

February 2nd, 2015: Marvin JS 15.2.2

New features and improvements

  • GUI
    • Selection menu has been impoved: Duplicate feature has been introduced; it can be find in Selection context menu.

January 19th, 2015: Marvin JS 15.1.19

No changes.

January 12th, 2015: Marvin JS 15.1.12

New features and improvements

  • GUI

    • New arrow type: Equilibrium arrow  has been introduced.
    • Position variation bond  (variable point of attachment) has been introduced.
    • Advanced Panel's logic has been changed to the Basic Panel's logic in Atom properties menu.

January 5th, 2015: Marvin JS 15.1.5

No changes.

December 15th, 2014: Marvin JS 14.12.15

No changes.

December 8th, 2014: Marvin JS 14.12.8

New features and improvements

  • GUI

    • The icon of the Reaction tool has been updated.

  • API
    • External css resources has been wrapped into the JavaScript code to reduce the size of the downloaded resources.

 Bugfixes

  • GUI
    • Atom properties and Bond properties dialog windows could not been closed by clicking next to them.

December 1st, 2014: Marvin JS 14.12.1

No changes.

November 24th, 2014: Marvin JS 14.11.24

New features and improvements

  • GUI

    • In Atom properties dialog window "trash and checkbox" icons, next to the input fields, has been changed to a padlock to make the settings easier.
    • OK button appears on Periodic Table dialog, when "Atom list"/"NOT list" selection is active.
  • API
    • Access has been changed for some files: editor.css, editor_ie9.css files have been moved to gui/css folder; js/promise-0.1.1.min.js file has been moved to gui/lib folder.

November 17th, 2014: Marvin JS 14.11.17

Bugfixes

  • API

    • Invoking the setDisplaySettings function reset the toolbar layout.

November 10th, 2014: Marvin JS 14.11.10.

Bugfixes

  • When long pressing on an atom, not the appropriate context menu appeared in iPad.

  • When the atom properties context menu appeared on the right side of the editor, the editor widget shifted to left in IE9.

  • Electron flow arrow could not be drawn from an atom which had been already a part of another incipient bond.
  • Some mrv files could not be imported if the `lone pair visibility` was turned off.

November 3rd, 2014: Marvin JS 14.11.3

New features and improvements

  • Import/Export
    • The import of structures with coordinate bond has been introduced.

October 27th, 2014: Marvin JS 14.10.27

No changes.

October 20th, 2014: Marvin JS 14.10.20

New features and improvements

  • API change: exportStructure (format, options) can be invoked with PNG and JPG formats.

October 13th, 2014: Marvin JS 14.10.13

New features and improvements

  • New function has been given to set the copy format (MRV or MDL MOL) via API. 

Bugfixes

  • When the canvas size was zero in width and/or height, error has occurred in Internet Explorer 9.
  • Expanded abbreviated groups couldn't been contracted.

October 6th, 2014: Marvin JS 14.10.6

New features and improvements

  • Examples
  • Image export examples have been refreshed to avoid potential CSS conflict. 

Bugfixes

  • Import/Export
    • Image scaling was incorrect, it resulted for example that atom label were out of frame in case of image export.
    • Import failed on certain ChemDraw generated MDL MOL (V2000) files in which bond rows where shorter than expected.
  • GUI
    • In Internet Explorer 9 Periodic Table exceeded the canvas size in iframe.

September 29th, 2014: Marvin JS 14.9.29

Bugfixes

  • GUI
    • A tooltip of a template was mistyped. (It has been changed to "Pyrrole".)

September 22th, 2014: Marvin JS 14.9.22

New features and improvements

  • Import/Export
    •  In IOS browsers, image download and molecule export have been resolved. The download button has been removed in cases when download is not possible.

Bugfixes

  • API
    • Return value of getSupportedFormats() was undefined.

September 15th, 2014: Marvin JS 14.9.15

New features and improvements

  • API
    • "Undo" and "Redo" events can be observed via on ("undo", callback) and on ("redo", callback) functions.

Bugfixes

  • Editing
    • In some cases selection with "Freehand Selection" tool was not accurate.

September 8th, 2014: Marvin JS 14.9.8

New features and improvements

  • Editing
    • Atom query properties has been introduced.

September 1st, 2014: Marvin JS 14.9.1

New features and improvements

  • Import/Export
    • In Internet Explorer 9 and OSX Safari browsers, image download and export by web service have been resolved. The download button has been removed in cases when download is not possible (MDL MOL file, MRV).
    • If the source contains implicit hydrogen, it is imported and displayed on the MarvinJS canvas.
  • Editing
    • R-group labels can be drawn by "r" keyboard shortcut or they can be placed on the canvas by selecting the Smart R-group tool and then clicking on the clear canvas.
  • Example
    • A code example is given to show how the buttons which refer to web services can be removed from the General Toolbar.

Bugfixes

  • Browser-dependent issues
    • In Internet Explorer 9, clicking the Export button didn't result in the export dialog opening.

    • Internet Explorer 9, the canvas "blinking" problem has been resolved.
    • In Internet Explorer, the "s" keyboard shortcut did not make the sulfur atom active in the application.
    • In Internet Explorer 10 and 11, file formats related to web services could not be downloaded.
  • API
    • Clean 3D URL could not be set separately from Clean 2D URL.
  • Editing
    • Changing the bond type in the abbreviated group by the drawing tool did not make the abbreviated group ungrouped.
    • If there was only one element which was selected by the Smart R-group tool, an additional R-group connected to that element during the selection.
  • Display
    • Vertical alignment of the atom labels was fixed.
    • The Erase tool highlight issue has been fixed.
    • When zooming on the reaction arrow, delete-mark magnifying resulted a big circle.
  • GUI
    • The dialog windows (Import/Export, Atom properties, Bond properties) could not be closed by the ESC keyboard button.

    • If MarvinJS was embedded, the right side of the component could not be seen on iPad.

August 25th, 2014: Marvin JS 14.8.25

New features and improvements

  • Display
    • Atom map numbers are displayed in square brackets.

Bugfixes

  • Performance
    • Placing a pseudo atom on the canvas made the Marvin JS slower.

August 18th, 2014: Marvin JS 14.8.18

Bugfixes

  • Editing
    • In Atom Properties "Alias" function could not be turned off.
  • Display

    •  The application tended to freeze in "Couple of editors" example opened by Internet Explorer Browser.

August 11th, 2014: Marvin JS 14.8.11

No changes.

August 4th, 2014: Marvin JS 14.8.4

Bugfixes

  • Display
    • Spacefill and Ball&stick display was not the expected color in Internet Explorer.

    • Reaction in R-group definition caused some problems in the display of the structures on the canvas.

July 28th, 2014: Marvin JS 14.7.28

New features and improvements

  • Editing
    • Auto Map button has been introduced. (This feature is only available with Standardizer licence.)

Bugfixes

  • Display
    • Valence error visibility could not be set from API.

July 21th, 2014: Marvin JS 14.7.21

New features and improvements

  • Editing
    • New reaction tool has been introduced. (Inserting reaction operator, drawing arrows, creating atom maps on the same atoms with one tool.)

Bugfixes

  • Import/Export
    • Unsuccessful molfile import, in case of the missing optional data, has been fixed. (Forum)
  • Editing
    • Minor highlight fixes has been made.
    • Confusion with inserting an atom and Zoom all functions has been resolved. (Inserting atom by pressing Enter option has been cancelled.)

July 14th, 2014: Marvin JS 14.7.14

New features and improvements

  • Display
    • Atom map visibility can be set from API or GUI.

Bugfixes

  • Editing
    • Markush structure attachment point clipboard issues has been fixed.

    • Atom list/NOT list refreshing issue after autoclosing window has been resolved.

July 7th, 2014: Marvin JS 14.7.7

New features and improvements

  • Marvin JS GUI
    • New, user-friendly R-group drawing tool has been developed.(video)
    • Autoclose property of dialog windows has been introduced.
  • Data transfer
    • File drag and drop has been introduced.
    • Files can be opened from the file system of the user's computer.
  • Display
    • New display options have been introduced (Stick, Ball and Stick, Spacefill).
    • Electron flow arrow feedback has been removed

  • Properties
    • Bond topology (in ringin chain) has been introduced, it is available from bond context menu.
    • Reacting Center  (centernot centerchangemake and changemake or breakoptions have been added.
  • Editing
    • The behavior of Electron flow arrow tool has changed. From now the incipient bond is the first state to choose.
    • Basic 3D options are available such as 3D clean (server side), 3D rotation, fogeffect.
    • New graphical objects have been introduced (rectangleellipse). Arrows can be connected to the boxes. Connected objects could be moved together.
    • Adding/removing explicit hydrogens - server side- functionality has been introduced.
    • New homology groups have been added.

  • Toolbars
    • There is an option to add custom templates from server side. 
    • Benzene template has been rotated. 
    • Naphtalene template has been removed from the Templates toolbar.

Bugfixes

  • Display
    • Only the half of the canvas could be seen on iPAD if Marvin JS was embeded.
  • Editing

  • While "Drawing" function was on, Atom properties pop-up menu didn't showed up, instead of that Edit context menu was displayed.
  • Abbreviated group's default drop-down list couldn't be opened after the creation without moving the mouse pointer.
  • Import/Export
    • Mol file opening error, in cases when it contains missing zeros, has been resolved. Forum

July 8th, 2014: Marvin JS 6.3.2

No changes.

June 11th, 2014: Marvin JS 6.3.1

Bugfixes

  • Marvin JS GUI
    • "Cut", "Copy" and "Paste" buttons have been restored to the General Toolbar.

May 15th, 2014: Marvin JS 6.3.0

New features and improvements

  • Marvin JS GUI
    • Marvin JS now calculates the lone pairs of atoms automatically. The visibility of lone pairs can be turned on and off in the View settings dialog.
  • Editing
    • Chemical reactions can be drawn, edited, imported and exported in Marvin JS using either straight arrows or resonance arrows. 
    • Single and double electron flow arrows can drawn, edited and imported/exported in MRV format in Marvin JS. 
    • "Monovalent" radical electrons can be added to atoms using the Atom properties dialog.
    • Mapping numbers can be added to atoms using the Atom properties dialog.
  • Import/Export
    • Structuress containing single step reactions can be exported as reaction files from server side in the following file fromats: MRV, RXN, SMILES, CXSMILES, SMARTS, CXSMARTS, CML, RXN V3000, SDF, CSSDF, CDX, SKC.
      Structures containing more than one or multistep reactions can be exported from client side. The arrows and "+" signs in the reactions will be exported as graphical objects in this case. 
    • During MOL file import, Marvin JS normalizes the coordinates and uses consistent scaling irrespectively of the content of the MOL file.
    • During MRV export, fragments inside R-group definitions are exported as separate molecules.

Bugfixes

  • Marvin JS GUI
    • On Mac OS X, simulating a right-click by using Ctrl + left-click on a selected atom did not contain the elements of the Selection popup menu. Forum
  • Editing
    • Removing more than one atom alias in one step could not be undone.
    • Adding crossing bonds to an abbreviated group could not be undone after the group had been expanded.

December 2nd, 2013: Marvin for JavaScript 6.2.0

New features and improvements

  • Editing

    • R-group definitions can be created and edited in Marvin for JavaScript. Documentation
    • R-group attachment points can be defined on atoms.
    • R-group attachment points are automatically numbered.
  • Marvin for JavaScript Menus
    • "Bonds" pop-up menu has been removed.
    • "Delete" option has been removed from the pop-up menus.
    • Drop-down lists behind pop-up menus can be reached with long-press.
  • Clipboard Handling
    • Copy and paste from and to Marvin for JavaScript in MDL Molfile V2000 format using the Ctrl+C and Ctrl+V keyboard shortcuts respectively.
    • Pasting structures into Marvin for JavaScript is possible in MRV format using the Ctrl+V keyboard shortcut.
  • Import/Export
    • Import and export of SMARTS and ChemAxon Extended SMARTS files has become possible when the relevant webservice is available.
  • Touchscreen Devices
    • Icons on toolbars have been enlarged.
    • Pop-up menus can be opened by long-press on the canvas.
    • Extra button for reaching pop-up menu elements have been removed from the toolbar.

November 29th, 2013: Marvin for JavaScript 6.1.4

No changes.

October 31st, 2013: Marvin for JavaScript 6.1.3

No changes.

October 17th, 2013: Marvin for JavaScript 6.1.2

No changes.

October 11th, 2013: Marvin for JavaScript 6.1.1

Non-public version

September 10th, 2013: Marvin for JavaScript 6.1.0

New features and improvements

  • Marvin for JavaScript Toolbar
    • "More" button has been introduced on the toolbars.
  • Editing
    • Pre-defined homology groups are available from the Atom properties dialog. Documentation
    • Atoms, bonds, and selection can be erased with the Delete button of the keyboard.
    • Atoms can be changed with an atom shortcut while the bond tool is active and vice versa: bonds can be modified with a bond shortcut while an atom tool is active.
  • Touchscreen Devices

    • Pop-up menu elements are available through toolbar buttons on touchscreen devices.

August 27th, 2013: Marvin for JavaScript 6.0.5

No changes.

August 6th, 2013: Marvin for JavaScript 6.0.4

No changes.

July 23rd, 2013: Marvin for JavaScript 6.0.3

No changes.

June 25th, 2013: Marvin for JavaScript 6.0.2

No changes.

June 21st, 2013: Marvin for JavaScript 6.0.1

Bugfixes

  • Zooming problem in case of two fingers's zooming has been resolved.
  • Unnecessary console log reference has been removed from code.
  • Merging and rotation feedback in Chrome browser has been fixed.

 

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