chore(deps): update ketcher monorepo to v3.12.0 by renovate[bot] · Pull Request #1761 · InformaticsMatters/squonk2-data-manager-ui

renovate · 2026-01-13T12:22:30Z

ℹ️ Note

This PR body was truncated due to platform limits.

This PR contains the following updates:

Package	Change	Age	Adoption	Passing	Confidence
ketcher-core (source)	`3.2.0` → `3.12.0`
ketcher-react (source)	`3.2.0` → `3.12.0`
ketcher-standalone (source)	`3.2.0` → `3.12.0`

Release Notes

epam/ketcher (ketcher-core)

`v3.12.0`: Ketcher 3.12.0 March 4, 2026

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What's Changed

New features

#8777 – Change the logic for activation of 'Arrange as a Ring' tool and context menu item
#8781 – Change the logic for attachment points editing drop-down in the monomer creation wizard
#8857 – Monomer saving - presets in the monomer creation wizard
#8856 – Defining other monomer properties - presets in the monomer creation wizard
#8866 – Defining the preset - presets in the monomer creation wizard
#8851 – Highlighting presets in the monomer creation wizard
#8854 – Defining the preset - presets in the monomer creation wizard
#8849 – Entering the wizard - presets in the monomer creation wizard
#8852 – Additions to the structure - presets in the monomer creation wizard
#8850 – Add "Mark as a..." context menu option for Nucleotide (preset) in monomer creation wizard
#8008 – Implementation of Copolymer S-Group type

Bugfixes and improvements

#8437 – If no selection made, system doesn't define attachment points for monomer
#5701 – It is possible to connect all APs to same atom
#8800 – The hover on a selected atom differs in micro mode and in macro mode
#7797 – Underline colour for the base counter in the Calculate Properties window doesn't fit the requirement
#7789 – Fragment selection highlighting inconsistent between Micro and Macro modes
#7325 – Right-click copy option does not work for microstructures on macro canvas
#8837 – No bad valence indication on Macromolecules canvas
#8792 – Rename monomer symbol to monomer code in the monomer creation wizard.
#8898 – Selection ignored in Ketcher API calls
#7128 – Molecular formula letters are not on the same level
#8641 – Tooltip in popup Ketcher sequence mode appears beyond view area for sequences at the top
#4724 – After clicking the "Clear Canvas" button multiple times, a user has to click the "Undo" button multiple times to return the structure
#6071 – Change event does not trigger after switching to Micro mode
#6236 – Cycled aromatic bond looks wrong on Macro canvas
#7123 – Deleting one of multiple monomers does not trigger recalculation in Calculate Properties window
#5170 – Fixed "Process is not defined" error is displayed in console after Clearing Canvas in Macro Mode with the element with an attachment point and switching to Micro
#5125 – Fixed after copying and pasting, structure under cursor causes Uncaught TypeErrors in DevTool console when approaching the edges of canvas
#8205 – System shouldn't allow to upload monomers with no base IDT alias defined
#5656 – Bond properties are not implemented
#8954 – Undo/redo operations doesn't work for atoms, arrows and pluses after changing their positions in Macro mode
#7188 #7190 #7255 – Unknown peptide, sugar, unknown base and unknown phosphate looks like chems (in addition ketcher wrongly considers R3-R1 connection between unknown sugar and/or unknown base as side chain connection)
#9047 – Leaving group atom position is incorrect for nucleotides created in monomer wizard
#9032 – Flex mode icon is active after ketcher close and open again
#8965 – Migrate to Indigo v1.40.0 in-browser module
#8918 – Update the help document (3.11.)

Additional notes:

Ketcher 3.12.0 has been built and tested with Indigo version 1.40 (standalone and remote).

`v3.11.0`: Ketcher 3.11.0 March 4, 2026

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What's Changed

New features

#8248 – Define nucleotide presets using the monomer creation wizard (POC)
#8254 – Allow for stereo bonds up and down to be a bond between AA and LGA
#8383 – Introduce library searching using HELM aliases, AxoLabs aliases, and modification types
#7915 – Enable flipping of all expanded monomers in a structure
#8363 – Include 'Arrange as a Ring' button for Flex mode

Bugfixes and improvements

#8386 – Update the help document (3.10.)
#8739 – Migrate to Indigo v1.39.0-rc.1 in-browser module
#4188 – Choosing wedged/hashed bond direction doesn't work from right-clicking context menu
#7148 – Number of selected elements in context menu is wrong for sense/antisense chain
#7735 – System shows inner circles of aromatized benzene rings from collapsed monomers on Molecules canvas
#6855 – Labels for empty ambiguous monomer categories are present in the library
#7244 – File format name for Sequence is cut off in Save Structure modal dropdown
#5578 – Peptide section for ambiguous monomers should have "Ambiguous Amino Acids" name
#5580 – Order of sections for ambiguous bases is wrong - Ambiguous Bases should come first
#5927 – Font size and label position should be corrected at "Open structure" dialog
#7995 – Unable to create more than one attachment point per atom
#8395 – "Attachment points are set
#5481 – Ambiguous CHEM shown wrong at Sequence mode
#5799 – S-Group properties window should be disabled for monomers
#7385 – Cannot delete and copy microstructures via right-click context menu in macromolecule canvas
#4772 – Fix Platinum valence
#8403 – There is no way to remove HELM alias
#7506 – Tooltip is shown in wrong place for ambigous monomers in popup mode
#8461 – Function calls should not pass extra arguments
#6737 – 5NitInd unsplit nucleotide should be shown as X symbol instead of @ one
#8459 – Getters and setters should access the expected fields
#5361 – getInChIKey returns just the InChI string as JSON
#5751 – Establishing connection between ambiguous CHEMs works wrong
#5214 – The tooltip does not appear below the cursor when hovering over the “plus” button and stripe
#6725 – Ambiguous sugars (alternatives and mixed) in sequence shown as % symbol instead of @ symbol
#4891 – When using the “ketcher.setMode(mode)” method, the icon of the "Type mode" drop-down does not change
#8554 – System losts AxoLabs alias while save it KET
#8556 – System losts Modification types values while save it KET
#7372 – "Ghost image" doesn't satisfy the UX design
#6731 – Ambiguous phosphates (alternatives and mixed) in sequence shown as % symbol instead of @ symbol
#8584 – Tooltip for attachment points appears too far from attachment point
#8397 – Context menu remains visible after creating cyclic structure via right-click menu
#7776 – In Macro mode clicking on Selection tool icon does not open dropdown menu as in Micro mode
#4645 – In the “Modify RNA Builder” mode, when hovering over the buttons “Yes” and “Cancel” in the “Update Sequence” window, tooltips are displayed
#7610 – R-groups are not shown if to Open from file as New project
#7559 – Charge tools doesn't work for "star" atoms
#7022 – Dropdown for units (Da/kDa/MDa) is not aligned in width with the selector button
#5677 – Preview for chain of CHEMs works wrong in sequence mode
#5664 – Selection circle is different on micro and macro mode
#5469 – Preview tooltips for monomers loaded from HELM with inline smiles are wrong
#7956 – Presence of R32 group in molecule makes impossible to create monomer from it
#5534 – Ambiguous monomer tooltip content doesn't sorted properly in case of equal quantities
#5382 – System shouln't allow user to load empty mol file - Add to Canvas should be disabled
#7689 – No tooltip shown and invalid attachments allowed when adding monomers consecutively without moving mouse from arrow button
#5567 – System losts height data during copy/paste operation
#7191 – Change 3SS6 monomer type to Phosphate
#8726 – Name should not be mandatory any more, Symbol value should be used instead if user left it empty
#8723 – User should be able to type ambiguous monomers symbols in edit sequence mode (current sequence type should be taken in to account)
#6730 – System doesn't unite ambiguous bases (alternatives and mixed) into one @ symbol
#8721 – Create a monomer button remain selected (colored) after user done with monomer creation (creation wizard got closed)
#8720 – Library update event is triggered after API usage
#7578 – Undo/Redo restores partial selection after cancelling monomer creation
#8752 – All types of ambiguous monomers alone represented on sequence canvas as @ symbol should be represented
#7519 – In case of multiple R1 or R2 groups second R1/R2 groups should be assigned to the smallest available Rn (n>2) if available
#5922 – Non-polar amino acid (with W as natural analog) should have shade of green but currently it is violet
#5445 – Labels for ambiguous monomers at Bond Preview tooltip are wrong
#7189 – Unknown unsplit nucleotide looks like chem
#8846 – Unable to create more than one nucleotide monomer - system throws exception
#8845 – Creation nucleortide preset causes som bonds to disappear
#8847 – Former molecule selection causes invalid attachment point creation in Monomer creation wizard

Additional notes:

Ketcher 3.11.0 has been built and tested with Indigo version 1.39 (standalone and remote).

`v3.10.0`: Ketcher 3.10.0 February 27, 2026

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What's Changed

New features

#7500 – Update the monomer preview
#7633 – Allow for setting of modification type in the monomer creation wizard
#7932 – Add warning messages to the monomer creation wizard in case of unusual leaving group atoms
#7928 – Allow for setting of HELM alias in the monomer creation wizard
#8200 – Add parameter to Editor to disable saving new monomers to local storage
#8281 – Adjust subscription to library update event of Ketcher API
#7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard
#7970 – Include 'Create cyclic structure' option in the context menu for Flex mode

Bugfixes and improvements

#8602 – Migrate to Indigo v1.38.0 in-browser module
#7971 – Update the help document (3.9.)
#7887 – Molecule rotation causes error in console: Uncaught TypeError: Cannot read properties of undefined (reading 'pp')
#4467 – Ket label should be renamed to Ket Format
#7746 – System replace few spaces in monomer name to one space on monomer preview
#7421 – "Ghost image" of CHEM is white (different from "ghost image" of other monomer types)
#7740 – System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard
#3742 – Wrong tooltip for "minimize window" button (shows "expand window")
#7373 – "Grabbing hand" mouse cursor is absent on grabbing monomers from the library
#5570 – PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label
#8294 – Do allow to collapse s-groups (superatom type) without name
#7936 – Add tooltips to some attachment points in the monomer creation wizard
#7997 – For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled
#8328 – Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically)
#8377 – Add data-topology and data-reacting-center attributes for bonds
#7553 – Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode
#5520 – Percentages for mixed bases ain't sorted from biggest to smallest in tooltip
#8414 – System should throw The following string cannot be interpreted as an AxoLabs string. error if symbols without brackets cannot be interpreted
#8039 – Ketcher doesn't send input_format parameter to Indigo in case of AxoLab load request
#8418 – All monomers from SDF loaded via updateMonomersLibrary appear in Base group instead of their correct classes
#8404 – No documentation for libraryUpdate event subscription
#8463 – Batch monomer import aborts on a single invalid entry and does not indicate which record failed Standalone mode
#8599 – Correct the stereo-bonds of sugars

Additional notes:

Ketcher 3.10.0 has been built and tested with Indigo version 1.38 (standalone and remote).

`v3.9.0`: Ketcher 3.9.0 February 27, 2026

Compare Source

What's Changed

New features

#7690 – Allow for modification of the structure in the monomer creation wizard
#7730 – Continuation of attachment points editing in the monomer creation wizard
#7748 – AxoLabs format support
#7674 – Add ability to update monomers library API in SDF format
#7560 – Improving snake layout logic to include small molecules
#7709 – Update the help document (3.8.)
#8270 – Migrate to Indigo v1.37.0 in-browser module

Bugfixes and improvements

#7572 – "Create a monomer" option is missing in right-click menu when selection meets conditions
#7443 – Save to SDF button is missed on Salts and Solvents tab in Structure Library dialog
#7359 – Stereochemistry dialog crashes Ketcher if only one stereo bond on the canvas
#7697 – IDT alias of CHEM 5TAMRA is displayed wrong
#7919 – Change the symbol of CHEM Cy5.5 dye
#5417 – IDT aliases not shown at preview tooltip at Monomer Library
#5202 – Update visuals in Right-click context menu
#7395 – Line between Paste option and Create RNA antisense strand option is missing in the context menu
#7364 – Gap between icon and Delete label is twice bigger than it should be in Molecules mode
#7327 – Missing separator line above "Delete" in context menu
#7256 – Ketcher losts aliasHELM property for unknown monomers that makes export to HELM incorrect
#7912 – Errors in console in dev mode "Cannot update a component"
#7770 – Pressing Right Scroll Arrow button of top menu cause exception to console
#7700 – System allow to delete monomers leaving connected bonds on the canvas
#7934 – Export to SVG Documets works wrong for unsplite nucleotides with dash symbole (-) in alias
#7649 – Undo/redo works wrong for monomer reposition corrected by snapping
#7783 – Microstructure disappears from canvas in Sequence mode when adding new sequence row
#7918 – Change the IDT alias format in the library file and adjust the logic for IDT aliases on preview
#7581 – Undo/Redo buttons become inactive and canvas Up, Bottom, Left and Right toolbars remain active inside Monomer Wizard
#7893 – System shouldn't allow to create monomers for selection with aromatic bonds to non-selected part
#7923 – Undo after deleting RNA preset connected to benzene ring leaves undeletable artifacts in Flex, Snake, and Sequence modes
#7914 – Microstructure not removed properly with Redo, duplicates on repeated Undo/Redo in Sequence mode
#7978 – Create monomer process changes atom of not related part of the molecule
#7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine)
#8000 – Monomer Wizard allows creation of monomer with Functional Group
#8002 – No validation message shown for minimal monomer structure in Monomer Wizard
#8005 – Changing name for attachment points works wrong
#8040 – R2 attachment point is missing for vinU monomer
#8041 – System loads invdC monomer as unresolved monomer from AxoLabs
#8067 – Do not save added or updated monomer in local storage
#8068 – Unable to update monomer library via API on Remote Ketcher – input format error
#8070 – Existing Presets in the library disappear after adding new preset via API
#8123 – HELM (and IDT) alias collision is possible after library update
#8296 – Create Monomer tool can not be hidden by toolbar buttons config

Additional notes:

Ketcher 3.9.0 has been built and tested with Indigo version 1.37 (standalone and remote).

`v3.8.0`: Ketcher 3.8.0 October 17, 2025

Compare Source

What's Changed

New features

#6287 – Expanding the snap functionality to monomer groups inside of a structure
#7441 – Allow for modification of the attachment points in the monomer creation wizard
#6657 – Bump react to ^19.0.0 in ketcher-react package
#6358 – Add lasso selection/fragment selection tool in macromolecules mode
#7554 – Correct existing and add new structures to the library with appropriate IDT codes
#7221 – Change the colour of nucleobases
#7384 – Create documentation for hiding toolbar buttons
#7505 – Update the help document (3.7.)
#7760 – Migrate to Indigo v1.36.0 in-browser module

Bugfixes and improvements

#7222 – Incorrect leaving group atoms for expanded monomers
#6993 – Atoms and "monomer to atom bonds" are not removed when all other bonds are removed from atom
#7619 – Pressing ? key at Text Editor form while creation text label opens Macromolecules help link
#7525 – Specify a target origin for this message. vulnerability
#6747 – Unnecessary leaving groups (R-groups) appear upon "Removing Abbreviation" of expanded monomer when an attachment point is occupied
#7571 – Ctrl+M does not open monomer creation wizard when selection meets conditions
#7683 – Remove Add attachment point functionality
#7578 – Undo/Redo restores partial selection after cancelling monomer creation
#7509 – Export to SVG doesn't work in Ketcher mode
#7788 – Tooltip and restriction not triggered when selecting monomer without R2 in Macro mode
#7794 – Selection remains on original structure after creating Antisense RNA/DNA and cannot be cleared by canvas click
#7782 – In Macro mode selection tool resets to Rectangle when switching between Flex, Snake, and Sequence modes
#7791 – Highlight is not secured for clicked r label in monomer creation wizard
#7152 – Copy keyboard shortcut works wrong for text content
#7837 – Unable to create monomer if molecule loaded from KET
#7846 – Connection between created monomer and the rest of molecule got lost after monomer creation
#7814 – Connection point enumeration is wrong if they are already enumerated form range [3-8]
#7688 – Attached groups are lost when saving and reopening monomer created via Monomer Wizard in KET format
#7828 – Unable to assign atom as a leaving group event if it is eligable
#7806 – Problematic points are not highlighted in red when validation is failed
#7877 – Ketcher losts attachment point name on loading s-group from mol v3000
#7786 – In Snake mode after Undo bonds remain on canvas and cause console errors
#7777 – Incorrect shortcut displayed for selection tools in Macro mode
#7854 – Ketcher api doesn't work in proper order
#7785 – Clicking toolbar buttons resets selection tool from Lasso/Fragment to Rectangle
#7784 – In Sequence mode selection tool resets to Rectangle when entering or exiting sequence edit mode
#7782 – In Macro mode selection tool resets to Rectangle when switching between Flex, Snake, and Sequence modes
#7850 – System doesn't add the leaving group atom (a hydrogen) by default at the end of the bond connecting the attachment atom and the non-selected part of the structure
#7807 – Selection of cyclic molecule causes application crash: Uncaught ReferenceError: process is not defined
#7817 – Connection point enumeration is wrong R-groups outside [1-8] range
#7838 – The leaving group atom (a hydrogen) is not added by default at the end of the bond
#7821 – Connection point enumeration is wrong R-groups outside [3-8] range
#7813 – System should not allow to create monomer if atom with many R-groups in the selection
#7815 – System changes right connection point (R2) to left one (R1) if no R1 group defined
#7816 – System swaps left connection point (R2) and right connection point (R1) if R2 group was created early that R1
#7606 – Pasting text into Symbol or Name fields in Monomer Wizard triggers unrelated "Convert error"
#7801 – Incorrect edit dialog behaviour when right-clicking on attachment atom
#7798 – Atom label is not correct in attributes panel for leaving atoms different from hydrogen
#7807 – Selection of cyclic molecule causes application crash: Uncaught ReferenceError: process is not defined
#7804 – Incorrect atom label upon monomer saving when removing automatically assigned attachment point via R-group
#7788 – Tooltip and restriction not triggered when selecting monomer without R2 in Macro mode
#7794 – Selection remains on original structure after creating Antisense RNA/DNA and cannot be cleared by canvas click
#7782 – In Macro mode selection tool resets to Rectangle when switching between Flex, Snake, and Sequence modes
#7791 – Highlight is not secured for clicked r label in monomer creation wizard
#7152 – Copy keyboard shortcut works wrong for text content
#7837 – Unable to create monomer if molecule loaded from KET
#7846 – Connection between created monomer and the rest of molecule got lost after monomer creation
#7814 – Connection point enumeration is wrong if they are already enumerated form range [3-8]
#7688 – Attached groups are lost when saving and reopening monomer created via Monomer Wizard in KET format
#7828 – Unable to assign atom as a leaving group event if it is eligable
#7806 – Problematic points are not highlighted in red when validation is failed
#7877 – Ketcher losts attachment point name on loading s-group from mol v3000

Additional notes:

Ketcher 3.8.0 has been built and tested with Indigo version 1.36 (standalone and remote).

`v3.7.0`: Ketcher 3.7.0 September 19, 2025

Compare Source

What's Changed

New features

#6552 – Create a monomer from a selected part of the structure
#6785 – Support aliases from HELM
#3253 – Introduce the arrow button on library cards for easy monomer/preset addition to canvas
#7430 – Adjust sgroup hover rendering to remove overlapping parts
#6150 – Add the star atom to the special nodes section of the extended table
#7535 – Add api for switching between macromolecules and molecules modes
#7660 – Migrate to Indigo v1.35.0 in-browser module

Bugfixes and improvements

#7377 – Update the help document (3.6.)
#7351 – Profiling and optimization for many monomers on molecules canvas
#6270 – Add "About" (i) and "Help" (?) buttons to the main toolbar in macromolecules mode
#7222 – Incorrect leaving group atoms for expanded monomers
#7168 – Opening the 3D Templates section in Structure Library causes multiple errors in the DevTools console
#7252 – Integrate with SonarQube
#7273 – System loads micro-macro connected structure on snake canvas and created understandable bond
#7283 – Context menu is wrong if clicked on top of sequence
#7205 – Layout shift when changing mode from sequence to flex and back upon first macromolecules mode initialization
#7245 – Missing tooltip for standalone input field in ruler control
#7440 – Area selection doesn't work till bond/atom reposition
#7381 – Create documentation for 'change' event subscription
#7152 – Copy keyboard shortcut works wrong for text content
#7423 – It is possible to drag monomer from library and drop it to sequence canvas
#7512 – Library doesn't fit view port in Sequence mode in Popup mode
#7513 – "Ghost image" doesn't positioned below mouse cursor if dragged from Library to canvas in popup mode
#7531 – Arrow icon appears in Sequence mode, violating requirement for Snake and Flex modes only
#7538 – Unable to add ambiguous monomers via arrow button - no preview and errors in console
#7539 – No tooltip shown and invalid attachment allowed when adding a monomer without R1 to selected monomer with free R2
#7548 – Tooltip not shown and addition allowed when multiple monomers with free R2 are selected
#7551 – Monomer drag-n-drop from Library to the canvas doesn't work for peptides it they were clicked on Sequence canvas
#7562 – Tooltip overlaps monomers when hovering over arrow button on monomer card
#7575 – Monomer creation wizard opens despite selection being connected via non simple bond
#7576 – Create monomer wizard is available for structures containing S-groups, R-groups, or extended table atoms
#7577 – "Create a monomer" button becomes active for disconnected structures
#7563 – Selection after chain/monomer addition (autochain improvement)
#7580 – Zoom actions in Monomer Wizard throw errors in the console
#7601 – Wizard allows editing atoms and bonds via right-click menu without showing an error
#7604 – Name, Symbol, Natural analogue input fields are not highlighted when left empty and Submit is clicked in Monomer Wizard
#7606 – Pasting text into Symbol or Name fields in Monomer Wizard triggers unrelated "Convert error"
#7607 – Missing S-group name in KET after saving a monomer via the wizard
#7609 – Symbol uniqueness validation is missing in Monomer Wizard (no error, no highlight)
#7612 – Natural analogue is not cleared when monomer type changes
#7614 – After creating a monomer via wizard, switching to macro mode shows two separate entities instead of one
#7615 – Phantom structure remains on canvas after closing wizard and is visible in exported files
#7620 – Creating a monomer from a partial benzene selection causes console errors and no hover highlight on created region
#7624 – Created Sugars and Phosphates via wizard are not added to Macro library
#7625 – No validation against existing monomers - newly created monomer with duplicate name overwrites the existing one in the library
#7627 – Selection tools stop working after creating first monomer via wizard when many structures are on canvas
#7629 – API does not implement library change subscription
#7684 – Only selected atoms connected with bonds should be taken into account on monomer creation
#7714 – System shouldn't allow to create monomer for selected structure that have any non-simple single bonds to non-selected parts of the structure
#7692 – System shouldn't allow to create monomer for molecules with R-Groups attachment points
#7691 – System shouldn't allow to create monomer for molecules with R-Groups
#7725 – Hand tool and Area Selection Tool buttons close Monomer creation wizard if pressed
#7722 – Connection preview does not follow cursor and AP to AP connection is not possible
#6581 – Monomer placement offset from cursor when Ketcher runs in a popup with increased browser zoom

Additional notes:

Ketcher 3.7.0 has been built and tested with Indigo version 1.35 (standalone and remote).

`v3.6.0`: Ketcher 3.6.0 September 17, 2025

Compare Source

What's Changed

New features

#6404 – Drag and drop for the library elements in macromolecules mode
#7164 – Introduce marking of nucleotide components
#7125 – Support for reaction arrows and reaction pluses in macromolecules mode
#7132 – Update and add icons to right-click drop-down menus in all modes
#7347 – Migrate to Indigo v1.34.0 in-browser module

Bugfixes and improvements

#7231 – Update the help document (3.5)
#7073 – Unable to create hydrogen bond: Uncaught RangeError: Maximum call stack size exceeded
#7178 – The tooltip appears behind the context menu options
#7187 – IDT code shown wrong for SS3 chem
#6410 – Incorrect bond attachment to micro molecules in Macro Mode
#7277 – Cannot open multiple instance of Ketcher in one window
#6986 – Context menu appears on both canvas in molecules mode for several Ketcher instances on same page
#7207 – Rectangular input field should be wide enough to fit any (at least 4) digit number
#7117 – Chemical elements disappear when attempting to Expand the Structure in Micro mode after selecting one in Macro mode
#7170 – Monomer tooltip appears and remain in place even if mouse cursor moved away
#7209 – The ruler is limited to 190 divisions
#7365 – Console errors appear when using actions on structures with nucleotide component marking
#7386 – Delete operation causes exception: Uncaught (in promise) Error: Minified Redux error
#7432 – Security: form-data uses unsafe random function in form-data for choosing boundary
#7371 – Mouse cursor doesn't positioned at the top left corner of preset

Additional notes:

Ketcher 3.6.0 has been built and tested with Indigo version 1.34 (standalone and remote).

`v3.5.0`: Ketcher 3.5.0 August 26, 2025

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What's Changed

New features

#6738 – Ability to change the number of monomers in a line
#5208 – Allow modifying amino acids on canvas
#6995 – Smart positioning of CIP stereo labels for atoms
#6852 – Improve the hydrophobicity graph in the "Calculate Properties" window
#6589 – API lacks support for 3 letter code sequence export in macro mode
#7070 – Include the removed versions of some 3D templates in the templates library in addition to the corrected ones
#7224 – Migrate to Indigo v1.33.0 in-browser module

Bugfixes and improvements

#7094 – Update the help document (3.4.)
#6294 – Hiding toolbar buttons doesn't also hide disable the corresponding keyboard shortcut
#6930 – Replace File comparison (for MOL files ONLY!) operations with valid helper function - verifyFileExport
#7032 – Ketcher allows to make changes in sequence while being in nucleotide modification mode
#5971 – Inconsistent selection sensitivity when highlighting sequences
#7023 – Hydrophobicity section is missing tooltip icon and description
#6834 – Clicking on base card in RNA Builder does not scroll to selected base if multiple bases from the same section are selected
#7031 – Layout shift when entering symbol in sequence mode upon first macromolecules mode initialization
#6958 – Monomers positions are not preserved when pasting macromolecule in MOL format
#7200 – App crashes after modifying amino acids and switching to Micro mode
#7203 – N-methylation is shown as available for Hyp even though it shouldn't be
#7142 – Monomer selection without bonds should work the same as with bonds
#7251 – Incorrect tooltips for properties and logic for the hydrophobicity graph in the "Calculate properties" window
#7130 – Incorrect calculation when part of a microstructure is selected - full structure is sent to Indigo
#7150 – Molecule mass should be calculated for partial selected micromolecule (ketcher part)
#7202 – Incorrect order of amino acid modification options in context menu
#7281 – App crashes when closing Ketcher
#6985 – Structure appears on incorrect canvas in molecules mode for several ketcher instances on same page
#7288 – Monomers shifts out of visible area when adjusting layout with ruler in sequence edit mode
#7318 – Bonds are overlapped by CIP labels when moving the structure or when the structure has small bond angles

Additional notes:

Ketcher 3.5.0 has been built and tested with Indigo version 1.33 (standalone and remote).

`v3.4.1`: Ketcher 3.4.1 August 8, 2025

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chore(deps): update ketcher monorepo to v3.12.0

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chore(deps): update ketcher monorepo to v3.12.0#1761

chore(deps): update ketcher monorepo to v3.12.0#1761
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renovate Bot commented Jan 13, 2026 •

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renovate Bot commented Jan 13, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Release Notes

v3.12.0: Ketcher 3.12.0 March 4, 2026

What's Changed

New features

Bugfixes and improvements

Additional notes:

v3.11.0: Ketcher 3.11.0 March 4, 2026

What's Changed

New features

Bugfixes and improvements

Additional notes:

v3.10.0: Ketcher 3.10.0 February 27, 2026

What's Changed

New features

Bugfixes and improvements

Additional notes:

v3.9.0: Ketcher 3.9.0 February 27, 2026

What's Changed

New features

Bugfixes and improvements

Additional notes:

v3.8.0: Ketcher 3.8.0 October 17, 2025

What's Changed

New features

Bugfixes and improvements

Additional notes:

v3.7.0: Ketcher 3.7.0 September 19, 2025

What's Changed

New features

Bugfixes and improvements

Additional notes:

v3.6.0: Ketcher 3.6.0 September 17, 2025

What's Changed

New features

Bugfixes and improvements

Additional notes:

v3.5.0: Ketcher 3.5.0 August 26, 2025

What's Changed

New features

Bugfixes and improvements

Additional notes:

v3.4.1: Ketcher 3.4.1 August 8, 2025

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renovate Bot commented Jan 13, 2026 •

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`v3.12.0`: Ketcher 3.12.0 March 4, 2026

`v3.11.0`: Ketcher 3.11.0 March 4, 2026

`v3.10.0`: Ketcher 3.10.0 February 27, 2026

`v3.9.0`: Ketcher 3.9.0 February 27, 2026

`v3.8.0`: Ketcher 3.8.0 October 17, 2025

`v3.7.0`: Ketcher 3.7.0 September 19, 2025

`v3.6.0`: Ketcher 3.6.0 September 17, 2025

`v3.5.0`: Ketcher 3.5.0 August 26, 2025

`v3.4.1`: Ketcher 3.4.1 August 8, 2025