chore(deps): update dependency ketcher-core to v3.8.0

[renovate]

This PR contains the following updates:

Package	Change	Age	Adoption	Passing	Confidence
ketcher-core (source)	3.2.0 -> 3.8.0

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Release Notes

epam/ketcher (ketcher-core)

v3.8.0

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v3.7.0: Ketcher 3.7.0 September 19, 2025

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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

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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

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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

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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

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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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What's Changed

Bugfixes and improvements

• #​7568 - Unable to use Ketcher in the most basic of Vite projects

v3.4.0: Ketcher 3.4.0 June 20, 2025

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What's Changed

New features

• #​6832 – Update the help document 3.3
• #​6625 – Support of expanded monomer option
• #​6271 – Support for CIP stereo labels in macromolecules mode
• #​5727 – Add "Calculate Properties" for macromolecules
• #​5797 – Highlighting attachment point of expanded monomers on hover in micromolecules mode
• #​7237 – Migrate to Indigo v1.32.0 in-browser module

Bugfixes and improvements

• #​4838 – Incorrect structure for Phe-L-Phenylalanine in template library
• #​5497 – Refactor (SnakeModePolymerBondRenderer): Create and use SVGPathDAttributeUtil
• #​6288 – Incorrect numbering in sequence
• #​6871 – Connection points become visible and broken if user switch window focus from one app to another and back
• #​6870 – Enter key adds undeletable preset to preset section
• #​4476 – Tooltips in sequence mode not disappear after right-click on letters
• #​6762 – System shows natural analog monomer as modified if source mol file contains only 3-letters natural analog name
• #​6791 – Change activation area of the New sequence button
• #​6788 – Reduce "Add new sequence" control width
• #​7008 – Support of expanded monomer options doesn't work if monomer loaded from file/clipboard
• #​7007 – Rotation doesn't work for expanded monomers on Molecules mode
• #​5791 – It is possible to expand unknown nucleotide on micromolecules canvas
• #​5789 – It is possible to expand ambiguous monomers on micromolecules canvas
• #​7014 – No tooltip displayed for the “Calculate Properties” button in main toolbar
• #​7019 – Data in “Calculate Properties” window disappears after switching browser tabs, selection remains
• #​7030 – Missing Celsius symbol (°C) in “Melting temperature” label
• #​7039 – App crashes when adding Ambiguous Amino Acids to peptide sequence with open Calculate Properties window
• #​7015 – Alt+C / Option+C hotkey does not open the “Calculate Properties” window
• #​7033 – calculateMacroProperties API is called immediately on sequence selection, even when Calculate Properties window is closed
• #​7018 – Unable to clear monomer selection after switching browser tabs
• #​7026 – Calculate properties for peptides are missing in case of mixed peptide and RNA/DNA chain
• #​7017 – “Calculate Properties” shows wrong behavior when sequence is connected to microstructure
• #​7062 – Rotation is incorrect upon exporting transformed monomer to SVG or PNG
• #​7074 – Formula in "Calculate Properties" window is not updated when selecting monomers with connected microstructure
• #​7034 – Unipositive ions default value is shown in nM instead of mM for double-stranded sequence selection
• #​7085 – Ketcher does not send bond type to Indigo if connection is different from R2–R1, causing missing data in "Calculate Properties"
• #​7027 – Incorrect highlight (missing fill) for leaving-group atoms
• #​7028 – Turquoise monomer outline has incorrect gap for attachment points and blue outline too thin
• #​7096 – Clearing canvas while "Calculate Properties" window is open causes console errors
• #​6974 – System removes monomers from Molecules mode canvas is switched from Macro mode (bonds remain!) if ketcher in embedded mode (custom style iframe)
• #​7118 – Cannot edit concentration values of unipositive ions and oligonucleotides in Calculate Properties
• #​7249 – Input fields for ion concentration and oligonucleotides become inactive after clearing or entering zero
• #​7266 – Oligonucleotides input field becomes unresponsive after entering zero

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Additional notes:

• Ketcher 3.4.0 has been built and tested with Indigo version 1.32 (standalone and remote).

v3.3.0: Ketcher 3.3.0 June 20, 2025

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What's Changed

New features

• #​6508 – Update the logic for recognizing sense and antisense chains
• #​6435 – Do not retain snake mode layout when passing though snake mode
• #​6519 – Implement the library redesign and modify the RNA builder behavior
• #​6620 – Add salts to the "Salts and Solvents" tab in the monomer library
• #​6472 – Add "Copy", "Paste", and "Delete" to the r-click drop down menu in sequence mode
• #​5999 – Added "Create Antisense Strand" icon on the toolbar
• #​6317 – Introducing the snap to distance functionality for monomers connected via bonds
• #​6612 – Update the help documentation (3.2)
• #​6987 – Migrate to Indigo v1.31.0 in-browser module

Bugfixes and improvements

• #​6293 – Remove base monomer border after selection
• #​6573 – Incorrect bond length and angle for non-natural monomers in the library
• #​6695 – Unable to create antisense RNA/DNA chain in case of multiple сhain selection (if not eligible for antisense chain selected)
• #​6573 – Incorrect bond length and angle for non-natural monomers in the library
• #​6842 – Single click on already selected monomer cause monomer sticks to mouse cursor and snapping elements appear on the canvas forever
• #​6813 – Click on monomer selection area causes an exception Uncaught TypeError: Cannot read properties of undefined (reading 'drawingEntity')
• #​6774 – Modified bases selected via RNA Builder revert to natural analogs in all modes
• #​6495 – System replaces A base with always RNA N base (alternatives of A,C,G,U) even if user selected DNA N base (alternatives of A,C,G,T)
• #​6716 – Cursor can escape to the void after same actions and broke canvas
• #​6671 – Removing dash should turn aligned nucleotide to nucleoside
• #​6541 – Undo of clear canvas operation causes molecules bonds overlap atom labels
• #​6712 – Adding RNA/DNA before empty space in sense sequence causes exception and broken canvas
• #​6776 – Phosphate does not appear immediately when added via keyboard in SYNC mode
• #​6780 – Phosphate always added to sense strand in non-SYNC mode when targeting antisense strand
• #​6781 – Phosphates added via keyboard in SYNC mode are not reverted by Undo and cause console errors on hover
• #​6779 – Unable to add phosphate to antisense strand in SYNC mode via keyboard
• #​6775 – Adding monomer to first from the left position of antisense chain works wrong and causes exception: Uncaught TypeError: Cannot read properties of undefined (reading 'chain')
• #​6863 – Horizontal/Vertical snap to distance doesn't work for hydrogen bonds
• #​6814 – System should turn nucleotide to nucleoside on sequence break by Enter
• #​6783 – Incorrect cursor jumps after phosphate insertion in middle or at end of sequence
• #​6824 – Unable to delete multiple sequences at once via right-click menu in Sequence mode
• #​6705 – Antisense complement is not skipped when terminal monomer lacks an attachment point (R1/R2), causing incorrect structure on canvas
• #​6833 – Tooltips on monomer cards in all sections instantly disappear on hover in popup Ketcher
• #​6830 – RNA Builder section do not highlight corresponding monomer in library on first click
• #​6828 – Star icon for Favorites tab in monomer library is too small compared to design specification
• #​6831 – Last row of monomers in Sugars, Bases, and Phosphates sections is not visible in popup Ketcher
• #​6834 – Clicking on base card in RNA Builder does not scroll to selected base if multiple bases from the same section are selected
• #​6816 – Incorrect hotkeys are displayed and triggered for RNA and DNA Antisense strand creation

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Additional notes:

• Ketcher 3.3.0 has been built and tested with Indigo version 1.31 (standalone and remote).

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