v3.1.0: Ketcher 3.1.0 March 27, 2025

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What's Changed

New features

• #​6167 – Long bonds for linearly displayed circular structures
• #​5942 – Update the representation of sense and antisense chains in sequence mode (1/2)
• #​5995 – Synchronize the library tab with typing type switcher in sequence mode
• #​6222 – New chain tool behavior
• #​6246 – Import indigo with EXPORT_ES6 & USE_ES6_IMPORT_META options
• #​6417 – Update Indigo to 1.29.0 in browser module

Bugfixes and improvements

• #​6164 – Changing any parameter at Settings cause Undo/Redo work wrong (or delete undo history)
• #​6166 – Color schema for Favorites tab at RNA Library is wrong for Peptides
• #​6088 – Disable create antisense strand option if antisense-less base present in chain selection
• #​5696 – Adding Attachment point to microstructure already connected to monomer - causes problems
• #​6201 – Circular hydrogen bond connection between three (or more) chains, those hydrogen bonds isn't considered as side chain connection for layout purposes
• #​6195 – Nucleotide wrongly become antisense oriented if have hydrogen connection to sugar
• #​6194 – Unknown monomer and CHEM overlap to each other if both are the side chain for same chain
• #​6422 – Long bond appears behind monomers when using attachment points
• #​6084 – System doesn't allow select ambiguous monomers from the library
• #​6085 – Changing of ambiguous base via RNA Builder on Sequence mode causes sequence corruption
• #​6098 – Adding second chain with antisense chain to the canvas cause layout problem
• #​6446 – System shouldn't merge two antisense chains if separator monomer got deleted
• #​6447 – System doesn't split chain pair on two if - symbol deleted
• #​6460 – Troubles with switching to Edit mode if - symbol present in sequence
• #​5780 – Connection points appear visually disconnected when moving monomers in Flex and Snake mode
• #​6462 – Adding peptide between RNA and - symbol breaks sense/antisense chain
• #​6456 – Long bond appears behind the structure after Copy-Paste in Flex Mode
• #​6471 – Removing peptide from sense/antisense chain cause unnecessary phosphate removal
• #​5780 – Connection points appear visually disconnected when moving monomers in Flex and Snake mode
• #​6493 – Undo of deleted bond on sequence mode causes "ghost" monomer appearance on the canvas
• #​6505 – Hotkey CTRL+ALT+P does not switch library to Peptides
• #​6628 – Add export of ketcher-standalone esm module as cjs
• #​6159 – Aromatizing doesn't work for Pyridone and Pyrone (molecules from Template library)
• #​6588 – Peptide sequence not pasting directly on canvas
• #​6661 – Adjust ketcher-standalone entrypoints to work for all builders

Additional notes:

• Ketcher 3.1.0 has been built and tested with Indigo version 1.29 (standalone and remote).

v3.0.3: Ketcher 3.0.3 March 5, 2025

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What's Changed

Bugfixes and improvements

• #​6563 - Incorrect bond length and angle for some natural monomers

v3.0.2: Ketcher 3.0.2 February 26, 2025

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What's Changed

Bugfixes and improvements

• #​6557 - Modified phosphates shift away from main structure during expand in Micro Mode
• #​6556 - Expanded macromolecules in Micro Mode causes unintended merging
• #​6563 - Incorrect bond length and angle for some monomers

v3.0.1: Ketcher 3.0.1 February 20, 2025

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What's Changed

Bugfixes and improvements

• #​6546 - Macro structure duplicated on canvas when using ketcher.getMolfile() and pasting

v3.0.0: Ketcher 3.0 February 17, 2025

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What's Changed

🎉 We’re excited to introduce Ketcher 3.0, featuring the newly available Macromolecules mode!

This mode enables users to work with monomers and RNA presets, combine them into polymer chains, create antisense chains, import/export of different formats (HELM, SCSR/MOL V3000, Sequence, FASTA, IDT, Ket). More information provided in User manual for Macromolecules mode

Along with this major enhancement, we've included various improvements and bug fixes to enhance performance and usability.

New features

• #​6034 – Make macromolecules switcher enabled by default
• #​6029 – Enter flex mode when macromolecules mode was not entered in before and there is a drawing on canvas
• #​6027 – Support for single atom properties in macromolecules mode
• #​6028 – Support all remaining types of bonds from small molecules mode in macro molecules mode
• #​6227 – Update indigo to 1.28.0 in browser module

Bugfixes and improvements

• #​5978 – Entire element bounding box should be clickable, not only black dots
• #​6127 – Hover mouse over ambiguous monomer on Micromolecules canvas causes app crash
• #​5476 – Copy/Cut and Paste using Ctrl+C/X and Ctrl+V doesn't work for static elements in Mozilla Firefox
• #​5317 – Some side chain bonds are not shown in Sequence mode for bases, CHEMs, phosphates and sugars
• #​5796 – Indigo functions doesn't work if monomer on micro canvas - system throws an error: Error: Cannot deserialize input JSON.
• #​5032 – Selection of monomers should disappear when the user moves the cursor
• #​5139 – After pressing the Clear Canvas button in sequence-editing view, the Enter button does not start a new sequence but erases it
• #​5231 – Canvas should remain in edit mode if we insert monomer from the library
• #​5795 – Undo operation doesn't work for monomer at micro mode if it was deleted - system throws exception in console
• #​6112 – System opens "intellisence"-like dropdown control in unnecessary case
• #​5663 – Movement of microstructures on Sequence mode doesn't work
• #​4533 – After inserting a nucleotide in the Text-editing mode, the cursor blinks in the wrong place
• #​6026 – Bond length is different for monomers loaded from HELM and from the library
• #​4723 – When pressing Enter, a user can create new sequences in the “Modify RNA Builder” mode
• #​6022 – Side chain attachment point shown in wrong place in Snake mode
• #​5341 – Replacing all monomers (or part of them) in edit mode - works wrong - system cuts sequence on two
• #​5670 – Structural distortion occurs during multi expand and multi collapse of macromolecule abbreviations in micro mode
• #​6021 – Connection between molecule and monomer does not affect an amount of implicit hydrogens
• #​5115 – Switching from Sequence mode to Flex mode and back shifts visible area of canvas beyond visible frame.
• #​4526 – In the Text-editing mode, the canvas is not moved to make the newly added sequence visible
• #​6240 – Export to 3-letter sequence doesn't work
• #​6235 – Incorrect representation of hydrogens for alias charge valence and radical properties in macro mode
• #​6034 – Combine two editors in ketcher-react package in order to make macro switcher enabled by default
• #​6247 – Update the help document
• #​3627 – Ketcher requires unsafe-eval in order to run, which contradicts content security policy best practices
• #​6344 - Excessive scroll appears in macromolecules mode in canvas if Ketcher is inside dialog window
• #​6291 - Super G and Super T monomers do not load from a saved RXN V3000 file
• #​6370 - Inconsistent zoom behavior when inserting a molecule via setMolecule and Paste from Clipboard/Open from File
• #​6375 - Ketcher renders editor twice in dev mode
• #​6379 - Ketcher does not respond if switch to macromolecules, close popup with ketcher and open again
• #​6411 - Ketcher structure copy-paste in KET instead of MOL
• #​6196 - Ambiguous DNA bases (N, D, H, W) wrongly converted to DNA bases on antisense creation
• #​6106 - Two sense chain to one antisense connection render
• #​6272 - Cursor position after adding preset in sequence mode causes an incorrect sequence formation
• #​6132 - System should not re-layout canvas in case of antisense creation

Additional notes:

• Ketcher 3.0 has been built and tested with Indigo version 1.28 (standalone and remote).
• How to hide Macromolecules mode

v2.28.0: Ketcher v2.28.0 February 17, 2025

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What's Changed

This release includes several bug fixes and new features. Please be aware Ketcher 2.28.0 has been tested with Indigo version 1.27.0 (standalone and remote).

New features

• #​5678 - Introduce creating antisense chains
• #​5925 - Layout for antisense chains in sequence mode
• #​5712 - Update snake layout logic taking into account hydrogen bonds
• #​5990 - Extend Ketcher API to allow updating monomers library
• #​5630 - Mark all modified monomers on canvas (flex and snake modes)
• #​5629 - Mark modified amino acids on canvas in sequence mode
• #​5854 - Add "Copy to Clipboard" to the export window
• #​5618 - Ketcher doesn't trigger change event in macromolecule mode
• #​5515 - Add ketcher calculate values API
• #​6008 - Update indigo to 1.27.0 in browser module

Bugfixes and improvements

• #​5873 - Export to ket (and getKET function) change incrementally internal IDs every call
• #​5270 - Warning should not displayed for importing CDXML, base64 CDX
• #​5351 - Inform User to Apply Layout after Settings Adjustment
• #​5931 - Copy/Cut-Paste functionality not working for microstructures in Macro mode
• #​5982 - Label shift problem for ambiguous monomers
• #​5954 - The reaction with catalysts is displayed incorrect with ACS style setting and after layout
• #​4352 - Gap between button and drop-down list of Macro modes
• #​5855 - System reset micromolecule canvas settings to default if switched to Macro mode and back
• #​5974 - Paste to canvas recogniton logic should be changed
• #​3813 - Page auto jump to top when ketcher editor inited
• #​5988 - Exception when modifying a functional group after adding a Ketcher editor subscription
• #​6068 - Same chain configuration imported by different HELM layouted differently (anyway - both are wrong)
• #​6089 - Antisense creation doesn't work for the chain if not eligable base present in other chain presented in selection
• #​6061 - RNA chain remain flipped after hydrogen bond removal
• #​6067 - Two chains connected by H-bond arranged wrong if third bond present on the canvas
• #​6070 - System doesn't flip chain if connected to monomer but not to base
• #​6074 - System doesn't flip chain if connected to monomer but not to base (2)
• #​6080 - System doesn't flip chain if connected to monomer but not to base (3)
• #​6075 - In case of multipal H-bonds system should arrange antisence chain to first base of bottom chain
• #​6076 - Two-to-one base H-bond connection layouted wrong
• #​6077 - H-bond is not alligned to Snake mode view in some cases
• #​6081 - Smaller chain should be at the bottom
• #​6087 - Antisense layout is wrong for any ambiguouse base from the library
• #​6097 - System creates antisense chain only for top chain if many of chains selected
• #​6102 - System keeps antisense base layout and enumeration even after chain stops being antisense (and vice versa)
• #​6105 - Layout works wrong if bases of the same chain connected by H-bonds
• #​6086 - Unable to create antisense chains for ambiguous monomers from the library
• #​6107 - Create Antisense Strand doesn't work in some cases
• #​6096 - Antisense creation works wrong in case of partial selection
• #​6109 - Antisense of layout doesn't work on flex mode after load
• #​6083 - Creation of antisense chain causes monomer re-arrangement on the flex canvas
• #​6115 - Lets get back to U (instead of T) for the complementary base of A
• #​6129 - Undo operation creates unremovable bonds on the canvas (clear canvas doesn't help)
• #​6161 - Stereo flags are displayed despite enabling 'Ignore chiral flag' in MOL V2000 files
• #​6185 – Make SGroups expandable while placed within a chain