chore(deps): update ketcher monorepo to v3.17.0

[renovate]

This PR contains the following updates:

Package	Change	Age	Adoption	Passing	Confidence
ketcher-core (source)	3.12.0 → 3.17.0
ketcher-react (source)	3.12.0 → 3.17.0
ketcher-standalone (source)	3.12.0 → 3.17.0

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Release Notes

epam/ketcher (ketcher-core)

v3.17.0: Ketcher 3.17.0 July 13, 2026

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What's Changed

New features

• #​8855 – Add preset-specific error messages in monomer creation wizard
• #​8922 – Add Edit Instance prefill for monomer creation wizard
• #​9456 – Add BILN format and monomer alias support
• #​6784 – Home and End keys support in Sequence mode

Bugfixes and improvements

• #​8779 – Allow moving selected S-groups and monomers in molecules mode
• #​9779 – Add an additional amino acid (E*) and assign it and D* a new modification type
• #​9757 – App crashes while editing sequence containing particular ambiguous monomers
• #​7726 – Bond thickness is less than others on monomer preview
• #​8006 – LGAs label numerals are not subscripted
• #​9820 – Adding bond to atom could ended with wrong bond angle if user slightly moved mouse during click
• #​9692 – RNA Builder: Impossible to specify the phosphate position before any preset components are added
• #​9990 – Undo has no effect on bond type changes
• #​9738 – Swap stereo labels and stereo atoms when bond is flipped
• #​8251 – Monomer should be selected on the canvas after creation
• #​9489 – Nucleotide presets: Creating preset with the same component codes replaces properties of the existing preset
• #​7546 – Canvas does not reset scroll position after using “Clear canvas” - added monomers appear offset
• #​9751 – RNA Builder: Missing "Switch to right/left" tooltips when hovering over the phosphate position picker options
• #​9731 – Rotation tool: Rotation center of partially selected structure changes color when hovering over
• #​9383 – Rotation tool: After moving the rotation center the rotation handle is not set to the starting position and rotation circle does not cross the dashed line
• #​8181 – It is possible to define preset (group) name more than 200 symbols
• #​6273 – Thick foreground bonds do not work if the atoms are not carbons
• #​9837 – Correct the warning message for unusual base leaving group
• #​8199 – System allow to upload monomer that has IDT alises that is longer than allowed (it shouldn't!)
• #​4309 – Delete and Backspace hotkeys deletes elements under mouse cursor (hover), but not selected ones
• #​8198 – It is possible to add monomer with HELM alias is too long
• #​5849 – Expanded monomer inconsistent behaviour
• #​8600 – Single Up bond between two monomers painted wrong
• #​4093 – Keep loading indicator visible until paste completes
• #​9349 – Stereo group labels are overlapped
• #​5468 – Multi-Tailed Arrow can't be selected if Structure Selection Tool is used and clicking on tails or head
• #​8778 – Only show the possible monomer properties in the attributes panel in the monomer creation wizard
• #​8173 – IDT alias could be longer than 10 symbols without slashes
• #​10134 – Update the help document (3.16.)
• #​9991 – Remove "Highlight" checkbox from monomer creation wizard
• #​10054 – Nucleotide preset: R-group labels disappear when switching component tabs
• #​9299 – Fixes on new lexical library
• #​10102 – Type combobox is empty if S-Group Properties` dialog opened for Copolymer s-group for edit
• #​7940 – Export to HELM of monomer with attached micromolecule should cause warning message: The molecule will be exported using inline SMILES, and on load will appear as a CHEM monomer
• #​10260 – Warning message for unusual base leaving group incorrectly refers to "hydroxyl" instead of "hydrogen"
• #​10146 – Migrate to Indigo v1.45.0 in-browser module

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Additional notes:

• Ketcher 3.17.0 has been built and tested with Indigo version 1.45 (standalone and remote).

v3.16.0: Ketcher 3.16.0 July 13, 2026

Compare Source

What's Changed

New features

• #​8996 – Show attachment points in the attributes panel when defining presets
• #​9310 – Library and autochain support for presets with 5' phosphates

Bugfixes and improvements

• #​6603 – Replace AJV with jsonschema in runtime to allow Ketcher work in CSP-strict environment
• #​6094 – It is possible to create antisense even if it is not allowed (when base has extra bond out of r1-r3 to sugar)
• #​8977 – No focus inside modal confirmation of type changing in monomer creation wizard
• #​6093 – Phosphate in antisense chain converted wrong
• #​7781 – Inconsistency in fragment selection hover behavior between Micro and Macro modes
• #​7204 – Long names and short names of 3D Templates in the Structure Library are swapped and short names are missed
• #​7278 – N-methylation option is missing even if monomer in selection is eligible for it
• #​5110 – Aromatize the molecules after drawing
• #​7083 – Delete operation on Sequence mode causes hanging bonds and undeletable monomers
• #​5480 – Ambiguous monomer tooltip covered
• #​5934 – Error message is wrong if user tries to establish hydrogen bond if it is already has single one
• #​5740 – Establishing connection between ambiguous phosphate and sugar works wrong
• #​6090 – Antisense creating doesn't work if ambiguous phosphate present in the chain selection
• #​4247 – When pressing the “Open from file” button, the full-screen mode closes
• #​9291 – Slow build problem (part 2): reduce circular imports with static-import rollback, mode initialization fixes, and lockfile reset
• #​9139 – Incorrect structure while press UNDO aftrer Create Monomer action on the Molecules Mode
• #​9730 – Rotation tool: Rotation-angle label overlaps 0° label in Macro mode
• #​8332 – cursor flickers between grabbing and pointing hand while dragging a monomer across the cards
• #​5543 – Styles from macromolecules mode break global styles
• #​9559 – S-Group: Subtype drop-down menu for Copolymer contains an extra option
• #​3951 – Aromatizing causes NULL in export to MDL Molfile V2000 format file
• #​9709 – It is not correct to have 5' indicator on an antisense chain.
• #​6314 – Export to Sequence (3-letter code) and export to IDT doesn't throws an error if user tries to save micromolecule structures
• #​8715 – File format dropdown height should be equal to File name edit box
• #​6091 – Antisense creating doesn't work if ambiguous sugar present in the chain selection
• #​6053 – D peptide with asterik is marked as modified
• #​9458 – Add validation for monomer name to ensure valid characters are used
• #​7745 – Preview tooltip doesn't appear on the canvas if monomer name too long
• #​6907 – Memory leaks for ketcher when it is opened inside modal
• #​8389 – Hanging bonds after sequence edit operation
• #​7574 – IDT code is missing from preview tooltip on sequence canvas
• #​7514 – IDT codes list is wrong for all presets
• #​7827 – Some bond types shouldn't be allowed in Create monomer wizard
• #​6234 – Thick foreground bond looks wrong on Macro canvas
• #​9817 – Double call of context menu for symbol on sequence canvas causes different menu to appear
• #​9622 – Update the help document (3.15.)
• #​9138 – Update the appearance of the monomer creation wizard
• #​9491 – Monomer Creation Wizard: Creating a Nucleotide (preset) allows empty mandatory field natural analogue
• #​8203 – System allow to define position IDT aliases with slashes inside
• #​8958 – Bond element stays after clear canvas is clicked in Macromolecules canvas
• #​8637 – Molecule structure chages made in monomer creation wizard doesn't appear at molecules canvas after monomer creation
• #​9887 – Copy paste does not work in Safari
• #​10123 – Migrate to Indigo v1.44.0 in-browser module

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Additional notes:

• Ketcher 3.16.0 has been built and tested with Indigo version 1.44 (standalone and remote).

v3.15.0: Ketcher 3.15.0 June 10, 2026

Compare Source

What's Changed

New features

• #​9118 – Update KET and SDF format to include information about preset phosphate position
• #​9129 – Allow 5' position of the phosphate in the monomer creation wizard
• #​9310 – Expand RNA Builder presets to support 5' phosphates using preset connections

Bugfixes and improvements

• #​9358 – Rotation tool: A dashed bounding box disappears when the focus is moved outside of the browser window
• #​9368 – Rotation tool: Rotation handle does not change its view (color and icon) when rotation mode is activated
• #​5568 – The "magnet angle" is too large; drawing arrows ±15° of n·90° is impossible; to forbid one third of possible angles is too much.
• #​9377 – Right-click on monomer should not only open context menu but select monomer if it was right-clicked
• #​9374 – Rotation tool: Current rotation angle is not displayed at starting position in Macro mode
• #​9379 – Arrange as a Ring option in context menu should be visible only on Flex mode (Macromolecules canvas)
• #​9384 – The layout mode dropdown is overlapped
• #​9382 – Rotation tool: It is possible to move the rotation center when part of structure is selected
• #​9105 – The monomer is moved after pressing the "Submit" button for any type of monomer
• #​7240 – ABS label becomes detached from the structure after horizontal or vertical flip
• #​9407 – Labels for monomer natural analog category is missing if filter applied in Ketcher popup mode
• #​9060 – Search using some AxoLabs aliases fails
• #​9420 – System don't show Fullscreen/window mode in correct state if user switches mode being in fullscreen mode
• #​9102 – Incorrect selection a part of structure for phosphate when moving mouse from top to bottom
• #​8799 – Changing Implicit H count properties thru Atom properties dialog works wrong
• #​9143 – System removes bond between monomers if user removes abbreviation from them on molecules canvas
• #​9132 – The “Mark as a…” option is displayed after switching to another type in the Attributes panel
• #​8937 – Disable molecules/macromolecules switcher and settings when the monomer creation wizard is active
• #​9474 – AxoLabs alias is missing from library preset card preview tooltip and symbol preview tooltip on sequence canvas
• #​9141 – System removes atoms that holds unoccopied leaving groups if user removes abbreviation from monomer on molecules canvas
• #​9130 – It is not possible to save only the sugar and phosphate in the Nucleotide (preset) type
• #​6772 – SYNC mode button is absent if sense/antisense chain pasted from clipboard
• #​7021 – Monomer layout inside r-group box become corrupted if user grabs and moves bond between monomers
• #​6476 – Unable to paste using Ctrl+V chain from clipboard after clear canvas action
• #​9140 – The Structure selection after moving the entire Structure is incorrect.
• #​9460 – Implicit H count value doesn't change number of attached hydrogens if applied to canbon (C)
• #​9198 – Expand monomer on molecules canvas works wrong if monomer consists of one atom and one leaving group - shows empty structure
• #​9542 – Update the hint for preset components defining in the monomer creation wizard
• #​8960 – Number associated with symbol is visible
• #​8402 – Scrollbar appears unnecessarily in “Create Monomer” attributes panel after selecting Type, and disappears when expanding Aliases
• #​4248 – The “File format” drop-down does not open in the “Save Structure” window in the full-screen mode
• #​9590 – Fix vite server config error and remove warnings
• #​8394 – HELM (and IDT) alias collision should log error in console
• #​6616 – Hydrogen bond layouted in flex style on snake mode
• #​4675 – It is impossible to cut a structure from a canvas using Ctrl+X
• #​9455 – Nucleotide presets: Unable to create preset after adding and removing simple extensions – console error
• #​9123 – Monomers disappearing when expanding/collapsing in Molecules Mode after moving in Macromolecules Mode
• #​5198 – Added a darker hover state for selected sequence items in Sequence Layout Mode.
• #​6239 – Aromatic bond is mirrored if used as inside one on Macro canvas
• #​8818 – Add/Remove explicit hydrogens operation inside create monomer wizard causes exception: process is not defined
• #​7141 – System shows molecular mass and molecular formula even if few chains on the canvas
• #​4694 – Add Hotkeys in Macro Mode Similar to Micro Mode
• #​8142 – System allow to load monomers with invalid HELM aliases
• #​6851 – Bond to C10H20 superatom rendered wrong if loaded from CDXML
• #​9617 – Correct the LGA of meK and meE amino-acids
• #​9336 – Update the help document (3.14.)
• #​9645 – Migrate to Indigo v1.43.0 in-browser module
• #​9774 – Change the structure and the name of Gly-ol amino-acid
• #​9828 – Copy functionality is broken on Chrome

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Additional notes:

• Ketcher 3.15.0 has been built and tested with Indigo version 1.43 (standalone and remote).

v3.14.0: Ketcher 3.14.0 June 10, 2026

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What's Changed

New features

• #​8352 – Introducing rotation of monomers in Macromolecules mode
• #​6917 – Support for enhanced stereochemistry markings in macromolecules mode

Bugfixes and improvements

• #​9113 – The Copolymer S-Group type should not be displayed unless there are at least two structural repeating units (SRUs) in selection
• #​9108 – Incorrect valence for nitrogen
• #​9126 – Some keyboard shortcuts don't work on Macromolecules canvas
• #​8187 – It is possible to create preset with empty name
• #​8896 – Unable to load KET file in Molecules mode
• #​9328 – Migrate to Indigo v1.42.0 in-browser module
• #​9327 – Update the help document (3.13.)

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Additional notes:

• Ketcher 3.14.0 has been built and tested with Indigo version 1.42 (standalone and remote).

v3.13.0: Ketcher 3.13.0 June 10, 2026

Compare Source

What's Changed

New features

• #​8948 – Add fragment selection tool and rename structure selection tooltip

Bugfixes and improvements

• #​8245 – Small molecules positioning rule is not respected when connected to multiple monomers in different chains
• #​7927 – Monomer area selection works wrong if user uses mouse wheel to scroll down
• #​7729 – “Field value” textbox is active in “S-Group Properties” modal when “Context” field is empty
• #​7899 – CIP labels got rendered under the bond after atom selection and move
• #​8981 – Stereo bonds between monomers become single bonds if monomer collapsed
• #​8986 – ketcher-standalone memory leak
• #​8980 – System shows bad valence for atoms that attached to bonds that connects monomers
• #​8987 – Labels for monomer natural analog category is missing if filter applied
• #​7153 – Molecule from expanded monomer disappears on switching to Macromolecules mode
• #​9065 – System shows natural analog category for phosphates
• #​9078 – Update the help document (3.12.)
• #​9084 – Ketcher saves incorrect attachment points configuration for new nucleotides

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Additional notes:

• Ketcher 3.13.0 has been built and tested with Indigo version 1.41 (standalone and remote).

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