Ketcher 2.5.0 (May 30, 2022)

Summary

We are happy to announce that new version 2.5.0 of Ketcher has been released.

Ketcher 2.5 release was focused on improving the user experience and design of the application along with delivery of other functions.
It has fresh and updated icons combined with renewed color scheme and new canvas zoom approach. Fullscreen ability can provide great sketcher experience even if Ketcher is embedded in the small frame. File operations flows and other functions have received an improved flows and renewed dialog windows. Access to the Extended table became much more easy and Template library will now combine ready-for-use templates along with set of predefined functional groups.

Please be aware Ketcher 2.5 has been tested with Indigo version 1.7.1 (standalone and remote).

The whole list of changes can be found below.

New features and improvements

• Ketcher redesign (see related issues for details)
• Full-screen mode support for Ketcher #1273
• use iframe embed standalone version ketcher init error #1235
• Implement miew viewer with miew-react #1188
• Extend ketcher API: Add possibility to run server functions #1172
• Arrow Tool: Elliptical Arrows #1045
• Text Tool: Add special symbols #1044
• Option to save as InChIKey #1334
• Enabling wildcard atom button in top-level UI #1409
• Support of custom headers #1628

Bugfixes

• Cannot deserialize input JSON if using Clean Up functionality on structure containing R-Groups #1391
• Via ketcher The size of mol displayed in the editor is inconsistent between calling ketcher.setMolecule(）and direct copy and paste #1322
• An error message is displayed when server functions are applied to an R-group member with invalid stereocenters. #1452
• Functional Group abbreviation context menu can't be opened without selecting FG #1386
• Invisible enhanced flag interferes with user selection #1332
• Strict mode warnings in console #1290
• Button group is not be presented if ketcher is in a drawer #1325
• Focus lost on second symbol while trying to enter atom label #1294
• Incorrect vertical scrollbar when saving in Daylight SMILES format #1307
• Sending structure to renderer in molfile format instead of ketcher format #1300
• Structure check modal window causes error when closed right after update #1291
• Incorrect horizontal scrollbars in Save Structure modal window #1292
• Templates with simple objects are incorrect after refreshing the page #1276
• Shift between pointer and atom #1272
• ketcher-react not working out of the box with create-react-app #1241
• Error on opening .txt file #1149
• Settings - Preview images of structures (Templates Library, FG Library) do not respect global display settings #900
• Clear Canvas hotkey not working on MacOS #397
• can not setMolecule in onInit #1174
• Stereomarks and stereoflag are not displayed for templates with stereocenters #1258
• Atom IDs are not shown when settings specify to display them #1231
• Extra scrollbar in Data S-Groups modal when Field name contains long string #1312
• Tool refers to unmounted canvas instance when new file is opened #1057
• Open, Save and Reset buttons in Settings window looks unclickable (grey) #1350
• Incorrect double click behavior in Custom Templates window #1364
• No waiting for server to respond between Structure Check checkboxes turning on/off #1367
• The floating windows don't close after clicking on the ESC button #1504
• Different merging of templates from template list and from template library #1587
• It's not possible to select parts of different structures using the 'Shift' key. #1552
• It's possible to create a custom template with a duplicate name #1553
• Incorrect rendering of Data S-Group when it is applied to part of the cyclic structure #1575
• List/Not List atoms are converted to 'L#' symbols after the replacement of atoms by the R-group label is undone #1530
• Cannot deserialize input JSON if using server functionalities on a structure containing Not List atoms #1603
• Wrong sign for specific types while ket-generation #1600
• Unable to save a reaction in server formats if text is present on the canvas #1444
• Elements should be hidden when the attribute hiddenControls is used #1601
• The valence of monovalent atoms is displayed incorrectly in the structure after the Copy/Paste actions #1531
• The structure with reaction is displayed incorrectly after applying the Layout #1617
• R-Group definition changes when server functions are applied #1487

Ketcher 2.4.2 (February 21, 2022)

New features and improvements

• Add highlighting API to ketcher object #1242

Bugfixes

• Impossible to paste a structure on the canvas after clicking the 'Paste' button #1267
• On change subscription in Editor #1261

Ketcher 2.4.1 (January 13, 2022)

Bugfixes

• Exception if insert a molecule past the Ketcher #1175
• Cannot Install 'ketcher-react' or 'ketcher-standalone' Using NPM #1182
• can not setMolecule in onInit #1174

Ketcher 2.4.0 (December 30, 2021)

Summary

We are happy to announce that new version 2.4.0 of Ketcher has been released.

New features and improvements

• Add an error handler to inform a user about the server problems #555
• Implement support of Functional Groups #692
• Use Internal format to communicate with Indigo side #571
• Getting static files from ketcher-react package itself #857
• It should be impossible to add attachment point(s) to an atom with R-Group Label and vice versa #513
• 'Save As' Window - Rename 'Graph Format' to 'Ket Format' #837
• Redesign Error window #898
• Add warning message when saving structure with QUERY in Smiles format #712
• New design of modal windows #894
• 'Custom Templates' button isn't highlighted in black color when the user chouse Template to add on canvas #880
• Scrolling the left toolbar programmatically #779
• Update Ketcher API to allow to download structure in any formats #737
• Hiding buttons on the left menu #713
• Add global error handling #726
• Transform dialogs global css styles into css modules #277
• Styles are not component based #699
• Add the ability to turn off the auto fade of AND/OR stereo labels #689
• Make decomposition of arrow tool #696
• Add additional arrow types #697
• Implement resizing of arrows #698
• Decomposition of Copy button #707
• Copy drawing to the clipboard as an image #691
• Text Tool: Add Font Size #703
• When a user creates two connected double/triple bonds they should appear at a 180 degree angle #526
• Atom/Bond property should be applied for all selected objects #156
• onChange property on the ketcher-react #645

Bugfixes

• Error message Convert error! IndigoException: inchi-wrapper: Indigo-InChI: InChI generation failed: Empty structure Code: 2. InChi for empty canvas #1058
• IndigoException: element: can not calculate valence on C, charge 0, connectivity 6 #995
• Reaction arrow and plus are removed after Clean Up action #1131
• Generate structure from InChI String - Incorrect structure rendering in Remote mode #824
• Calculated Values tool: When calculating reaction, there is different behavior in different modes #650
• When saving file in InChi format atom's alias is taken as query #656
• Server functions do not work with structures with dative/hydrogen bonds #668
• Atom is not changed if change in Label Edit window #1102
• 'generateImageAsync' method does not work in Remote mode #371
• Stereocenter labels color gradient does not work in Firefox #1163
• (E) and (Z) stereo labels appear so far from stereobonds after calculate cip action #1158
• It is impossible to change arrow when the arrow selected by selection tool #1151
• Benzene ring loses circle when exporting #838
• ket file with no nodes cannot be deserialized #1137
• Convert error! Cannot read properties of undefined (reading 'slice') on opening file in Extended Smiles format and Daylight Smiles format #1143
• S-Group: incorrect rendering when using structures from Template pallete and different options from S-Group Properties window #797
• 'Calculated Values' works incorrect for selected structure #1112
• Cannot read properties of undefined (reading 'struct') error if connect two (or more) Cyclopentadiene(T) and click Aromatize #984
• Aromatic structure changes to not aromatic if try to connect with other structure #1093
• It is not possible to rotate R-group member if it was opened from file #1074
• Convert error if Load file as fragment and Ctrl+V #1052
• Redo action does not work for R-Group members if Cut->Paste->Undo->Redo #1054
• Structure shouldn't flipped when a part structure is selected #1029
• Error when apply 3D to empty canvas #1003
• Incorrect bond rendering on Benzene ring after dearomatize #1005
• Copy/Cut and Paste don't work with Plus #1036
• Error message when trying to calculate values of the structures with the hydrogen and dative bonds #540
• Copy/Past actions dont work for simple objects #1030
• Copy/Cut/Paste for any Arrow. If copy any arrow and past- Arrow Open Angle always pasted #1038
• Bond Tool - Double/ Triple bonds: When a user changing chain structure Double/ Triple bound should appear at a 180-degree angle #834
• Atom Generics (except A) and Special nodes are replaced with R# after saving in Daylight Smile format. #39
• Disable "Copy" button if nothing selected on the canvas #990
• Incorrect double bonds building #986
• Error message when try to open file with extension other than Custom files #962
• Not possible to expand Shape figure if it is selected #947
• Dependency installation failure #926
• Custom Templates - Templates duplicated when user saving templates with the same name #889
• Add possibility to hide elements by passing query parameter #862
• 'S-Group Properties' window - 'Absolute' radio button checked in all case #866
• S-Group tool - 'S-Group Properties' symbols are not clickable #850
• Hotkeys aren't working without previously clicking on canvas or any buttons #813
• Simple Objects - Shape Line: Wrong 'Shape Line' color when clicking on icon #786
• Simple Objects - Shape Rectangle: The error appears when drawing a rectangle of small height #787
• If User create simple molecule on canvas when it is minimum zoom value - molecule have increased distance between atoms. #180
• Stereo flag is overlapped with a structure #602
• Open from file window - File formats are duplicated #839
• Recognize molecule - Ketcher is broken when clicking the 'Recognize molecule' button #820
• If a structure with double bond(s) is the first structure created on the canvas the double bond is rendered incorrectly #517
• Save to Templates - Errors are appear when trying to save to templates structure with reaction arrow #821
• Save to Templates - The structure isn't displayed correctly in the 'Template edit' window when saving structure with Simple Objects #822
• Can not open InChi AuxInfo file in Standalone mode #667
• 'Template Edit' window: There is no 'Atom Id: xx, Bond Id: yy' text under the template image after changing Atom/Bond ID #807
• Template Library: there is no limit for input symbols when editing structure name or add new template in library #799
• Structure with NOT[] atom does not open #641
• Not all atom properties are shown if an Alias was set #674
• Stereo doesn't update after two bonds merge #684
• The gradient stays for mixed (&) stereomarks when 'Bonds Only' is selected in 'Color stereogenic centers' #677
• When selecting several structures with Segment Selection Tool they are not moving together #628
• Copy image fails in remote mode #1007
• Standalone mode. Error on saving chain structure with connected Double Cis/Trans Bond #1010
• Layout action do not work with structures with dative/hydrogen bonds #669

Ketcher 2.3.3 (November 17, 2021)

Summary

The main goal of release 2.3.3 is adding CDXML files support to standalone version and fixing some critical issues.

New features and improvements

• Support CDXML #920

Bugfixes

• Undo works incorrect, errors in console #955
• Application hangs after undo action applying to S-Group type changes #975
• Aromatize tool does not work for aromatic structures #973
• Unhandled Rejection (TypeError): Cannot read properties of undefined (reading 'pp') #859

Ketcher 2.3.2 (October 5, 2021)

Bugfixes

• Setting initial molecule #806

Ketcher 2.3.1 (August 30, 2021)

Summary

The main goal of release 2.3.1 was to stabilize the release v2.3.0.

New features and improvements

• 'R-Group Label Tool' and 'Shape Eclipse' buttons should not be expanded #719

Bugfixes

• Structure with some S-groups cannot be opened #723

Ketcher 2.3.0 (July 22, 2021)

Summary

We are glad to announce that a new stable version of Ketcher 2.3.0 is released.
The main features implemented in scope of this release are support of enhanced stereochemistry, ability to save structure as an image file, text tool, and support of multiple reaction arrows.

New features and improvements

• Stereo Flags shouldn't appear for structures without correct stereocenters #418

• It's impossible to open Ketcher with already entered molecule #601

• Add a warning when saving a reaction equilibrium arrow in a format that does not support it #543

• Add possibility to replace api path while App is building by passing additional argument #507

• Add multiple arrow support for the same canvas #145

• SETTINGS for the STEREO FLAGS and STEREO MARKS #60

• SAVE and OPEN STRUCTURE with STEREO MARKS #64

• Set PUBLIC_URL as './' by default #508

• Add possibility to add plain text on canvas #144

• Colors for the STEREO FLAGS and STEREO MARKS #62

• Implement "Create Stereo Marks" window #417

• Add support for hydrogen bonds #72

• Representation of Stereo Flags #57

• Stereocenter should disappear after replacing the stereobond with the dative bond or the double cis/trans bond #554

• Implement "Enhanced Stereochemistry" window #527

• Chiral flag should be removed when all Up/Down stereobonds are removed #61

• User can change the text of the four Stereo flags #518

• Rename the "Do not show the Stereo flags" setting and change the default value #556

• Rendering only feature #107

• Add possibility to save structure as image #437

• Unclear/inconsistent handling of absolute/relative stereochemistry #290

• Label Display At Stereogenic Centers for the STEREO FLAGS and STEREO MARKS #63

• Extend Text tool by bold, italic, subscript and superscript support #339

• Move dative/hydrogen bond tools to a separate block in the 'Bond' tool menu #538

• Add the ability to save information about the coordinates of the Stereo flags in * .ket #559

• Update position of stereo flag while structure is moved #167

Bugfixes

• Adding a stereo flag when opening the structure #632

• Incorrect template addition #676

• The descriptor overlaps the structure after Layout #219

• Layout action does not work on the distorted S-group members #671

• No alert error message when trying to open incorrect InChi string #657

• "Undo" after template merging does not work correctly #670

• Stereo-label doesn't update after stereoBond flipping #661

• Left toolbar is not visible in Firefox #612

• Redo does not work for simple object "Shape line" after moving its dots #635

• IE: Save as *.svg file does not work #627

• Atom is not underlined in red after adding to the template #636

• Application crashes after saving a template #652

• The incorrect structure when marks "Load as fragment" #633

• IE: The structure does not open #624

• The application doesn't work after "Undo" #615

• When marks "Load as fragment and copy to the Clipboard" structure don't save to clipboard #634

• Modal windows don't close when pressing the esc button #626

• The structure with R-Group is not visible #621

• Multiple arrows are saved as a reaction in Daylight Smiles format #590

• Ketcher build does not work on Linux #505

• Rotation angle doesn't display after I change its value #380

• 'Calculated values' - The data in 'Elemental analysis' field is displayed incorrectly #445

• Calculated values: old values blink before displaying new once #389

• 'Add text' - The initially created text object remains selected after adding the second one #464

• 'Add text' - It's not obvious how to reduce the "Text editor" window when a scroll is present in it #473

• 'Add text'- Impossible to edit a single letter text object #470

• 'Add text' - Double scroll appears when a long text is entered into the "Text editor" window #467

• 'Save Structure' and 'Structure Check' windows are enlarged when trying to save/check a big molecule #454

• It is possible to save a structure in incorrect format when network connection is slow #456

• The error occurs when trying to undo the delete action for a structure with stereo bonds #485

• Blank page appears after trying to save a reaction with an R-Group member #488

• A part of S-group brackets is enlarged after Cut - Undo actions #448

• 'Add text'- 'Cut'/'Copy' buttons become enabled when a text object is added to the canvas #472

• Incorrect rendering of Stereo Flags in reactions #58

• Console error after delete - undo/redo actions with a structure with stereobonds #573

• "Help" module doesn't display correctly in IE11 #572

• Incorrect stereo flag calculation #579

• Browser crash when copy and paste a sgroup structure #592

• Stereo labels after pasting display incorrectly #194

• The Stereo labels and Attached Data keep their positions after the Flip action #201

• Stereo Flag is not highlighted #604

• Vertical/Horizontal flip hot keys don't work correctly #524

• Error message when copying structure #606

• Blank page and a console error appear while saving #514

• Simple objects - An error in console after the 'Undo' action #511

• 'Add text'- 'Cut'/'Copy' buttons are disabled when a text object is added to the canvas #522

• Error message when trying to open *.ket files with stereochemistry features #532

• 3D Viewer - The light mode doesn't work #531

• Stereo flags are confused with stereo marks in *.ket files #544

• Unable to paste the text objects after cut/copy #551

• The periodic table opens when a text object is selected with the Lasso/Rectangle/Fragment selection tools #549

• Stereo label (E) saves in .smi file #208

• Wrong modal window, a blank page and an error in console after trying to add the Attachment points/R-sites to a structure #499

Ketcher 2.2.1 (April 22, 2021)

Summary

The main goal of release 2.2.1 was to stabilize the release v2.2.0. The whole list of critical issues that were fixed is provided below.

Bugfixes

• Blank page appears after trying to save a reaction with an R-Group member #488

• The error occurs when trying to undo the delete action for a structure with stereo bonds #485

Ketcher 2.2.0 (April 15, 2021)

Summary

We are glad to announce that a new stable version of Ketcher 2.2.0 is released. The main goal of current release was adding support of standalone mode. The list of changes related to this functionality can be found here.

New features and improvements

• Get Molfile in v3000 format #21

• Track if origin file was changed #246

• Add save to MDL molfile v3000 support #190

• Transform global css selectors into css classes #278

• Split Ketcher into Core and Presentations modules #196

• Extend editor API to generate png files based on structure #240

• Fire custom event on structure change #54

• Add delete button for user templates #160

• Add ketcherWindow.ketcher.getSmilesExt() method #266

• Add possibility to hide buttons on control panel #244

• Add bonds information for ket format in DAT s-groups #280

• Add indicator to inform users about execution of 'heavy' operations #255

• Ketcher API: Add possibility to save RXN files #296

• Add ellipse simple object #85

• 'Font' field should be disabled untill list will be loaded #321

• Modal window displaying in Ketcher instance format #325

• Simple Objects selection and resizing mechanism #315

• Add ability to download image in several formats #373

• Allow select simple object by several points in selection area #367

Bugfixes

• If structure contains SRU-Group User can't click 'Calculated Values' button - nothing happens after clicking. #215

• Stereo labels appears on not stereo structure after 'Aromatize' action. #206

• User can create incorrect Multiple S-Group but can't save and warning message doesn't appears. #175

• Calculated Values displays some values from last calculation #279

• Remove process.env.PUBLIC_URL from ketcher-react #282

• Fonts drop-down list can't be opened when User opens settings for the second time #320

• User can't copy/cut and paste part of structure or structure with SRU-polymer S-Group. #177

• When User draw circle without height - Ketcher becomes disabled. #317

• Error after Undo/Redo actions when User has edited S-Group #311

• Unable to calculate values for selected structure #361

• S-Group brackets place in incorrect place on structure with double bonds and sprouted single bonds #269

• Calculated values for reaction: missing last bracket for chemical formula #364

• The structures with atoms with valences rendering incorrectly after saving #46

• Different structure between ketcher.setMolecule() and ketcher.ui.load() #386

• Templates in template library are shifted down when Ketcher have less than 855px width #338

• Display Settings: 'Show hydrogen labels' triggers error #391

• 'Calculated values' fields are editable #388

• Incorrect behavior of Ketcher after deleting of a part of R-Group member #419

• In Template Library scroll bar jumps up and down when it is centered #184

• Incorrect behavior of Ketcher after deleting of a part of S-Group member #433

• 'Any Atom' tool incorrect behavior when selected with hotkey or typed in from keyboard #368

• 'Custom Templates' - User templates are shown without the images in the right pane of the 'Template library' #431