Releases: epam/ketcher
Releases · epam/ketcher
Ketcher 3.0.3 March 5, 2025
v3.0.2
Ketcher 3.0.1 February 20, 2025
What's Changed
Bugfixes and improvements
- #6546 - Macro structure duplicated on canvas when using ketcher.getMolfile() and pasting
Ketcher 3.0 February 17, 2025
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
Ketcher v2.28.0 February 17, 2025
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
Ketcher v2.27.0 January 13, 2025
What's Changed
This release includes several bug fixes and new features. Please be aware Ketcher 2.27.0 has been tested with Indigo version 1.26.0 (standalone and remote).
New features
- #5354 – Apply new hash spacing setting to canvas
- #5579 – Introduce Hand tool for macromolecules mode
- #5590 – Zoom in macromolecules mode should be in relation to the top left corner of the structures
- #5403 – Introduce hydrogen bonds in macromolecules mode
- #5600 – Zoom in automatically upon import of small sequences
- #5637 – Display hydrogen in atom label for molecules in macromolecules mode
- #5556 – Allow import and export of sequences with three letter amino acid codes
- #5640 – Multiple monomers expansion in micro molecules mode
- #5187 – Introduce new amino-acid colors
- #6174 – Update indigo to 1.26.0 in browser module
Bugfixes and improvements
- #5370 – System should remember the canvas mode on Molecules/Macromolecules mode switch (do not switch to Sequernce by default)
- #5372 – Toggling between Flex and Sequence modes causes loosing layout info
- #5564 – Search of ambiguous monomers doesn't work
- #4475 – Numbers on top of letters are not centered
- #4936 – Applying Enhanced Stereochemistry to monomers causes its disappear from the canvas (and exception in console)
- #4941 – System shows Edit S-Group option for every bond of molecule if it has attachment point
- #5181 – getKet duplicates items when macro molecules are use
- #5398 – Elliptic arrow icons order is wrong at arrow toolbar
- #5935 – Unable to establish hydrogen bond connection if monomer has no free attachment points
- #5941 – Hydrogen bonds remain in place on monomer delete
- #5940 – Copy/paste operation works wrong (copy only two hydrogen bonds and drops others)
- #5933 – Error message is wrong if user tries to establish hydrogen bond if it is already exist
- #5967 – System should not change monomer position after switching from Molecules to Macromolecules - Sequence
- #5972 – Export to three letter amino acid codes cause convert error
- #5969 – Load from file having only micro structures on macro canvas causes unnecessary zoom up to 200% and shift molecule to top left angle
- #5970 – Unable to connect monomer to molecule in snake mode
- #5949 – Delete of micro molecules bonds works wrong (or doesn't work)
- #5910 – Fix closest sgroup detection to allow focusing on entities within expanded monomer's bounding box
Ketcher v2.26.0 November 20, 2024
What's Changed
This release includes several bug fixes and new features. Please be aware Ketcher 2.26.0 has been tested with Indigo version 1.25.0 (standalone and remote).
New features
- #5400 – Expand macromolecules in micro mode
- #5359 – Display molecules in macro mode: basic structures with atoms and bonds
- #5325 – Change natural analogue of monomers
- #5324 – Change symbols of monomers
- #5323 – Change names of monomers
- #5195 – Some content problems in monomer library
- #5111 – Change structure of monomers
- #4984 – Highlight atoms and bonds
- #4965 – View only mode
- #4986 – Ctrl+move copy
- #1838 – Create custom top toolbar buttons
- #5156 – Add new option in settings acs style
- #5154 – Change "Double bond width" setting
- #5175 – Allow entering values in settings with the precision of one decimal place
- #4982 – Choose both directions of wedged/hashed bonds from right-clicking the bond
- #5435 – Change bond length for ACS styles settings
- #5351 – Change the default size of a plus and the arrows
- #5945 – Update indigo to 1.25.0 in browser module
Bugfixes and improvements
- #5430 – Fix ESLint error in selectClearCanvasTool function
- #4983 – Settings for the "attachment point tool" don't update with changed pixel settings
- #4757 – Incorrect stereo-label placement for (E) and (Z)
- #5536 – White screen is displayed after change direction of wedge bond
- #5296 – Save Support for RDF Format
- #5615 – Overlapping UI elements in Query Properties right-click menu
- #4394 – In the Sequence mode, the tooltip “Start new sequence” is shown outside of the canvas
- #5651 – The reaction can't save to MDL RXN V3000 (returns RXN V2000 instead)
- #5597 – New rendering for highlight
- #5561 – Set a new name for the button acs style
- #5672 – Multiple duplicate items
- #5205 – Edit Connection points dialog can cause invalid connection between monomers
- #5709 – Unable to load variant sugar from HELM - system throws an error: Convert error! {}
- #5710 – Unable to load variant phosphate from HELM - system throws an error: Convert error! {}
- #5711 – Unable to load variant CHEM from HELM - system throws an error: Convert error! {}
- #5621 – O and U sumbols are not supported in sequence mode
- #5612 – The file size is the same when saved to png
- #5634 – ketcher.getMolfile() stopped working for macro canvas with peptides
- #5649 – Default values for bond settings (at least for bond) got corrupted and become wrong after ver 2.26 version installed
- #4316 – In the Sequence and Flex mode the nucleotide preview is closely adjacent to the left edge of the screen
- #5557 – Bond/monomer tooltip preview placed wrong in on edge cases
- #5097 – Selection frame is displayed improperly for overlapped images
- #5148 – Image changes the layer to top after scaling actions
- #5581 – If switch to View Only Mode with Fragment Selection you cannot change or select another selection mode
- #5657 – Clear canvas doesn't work for micro structures on macro mode
- #5679 – Unable to establish connection between micro structure and macro ones
- #5401 – Side-chain connections are not displayed in Snake mode
- #5662 – Fix inability to select Erase tool after monomer expansion
- #5612 – The file size is the same when saved to png
- #5686 – Bonds between micro and macro structures couldn't be selected and deleted
- #5659 – Moving of selected microstructures on macro canvas works wrong
- #5665 – Show remove abbreviation dialog when trying to erase expanded monomer
- #5725 – Cursor position is incorrect when editing sequence in Macro mode
- #5800 – Application crashes with white screen in Macro mode when loading local storage data from a previous version
- #5758 – Highlight only bonds when selected bonds + atoms
- #5703 – Added tooltip for image resolution option
- #5673 – Micro structures connected to polymer chains are not shown on Sequence mode canvas
- #5650 – The reaction with catalysts is displayed incorrect with ACS style setting and after layout
- #5761 – Fix minimal distances for mult-tail validation in KET format
- #5413 – Can't add specific SVG image to Canvas in Mozilla Firefox
- #5434 – Document creation and behaviour of custom buttons
- #5776 – Add API Method getRdf for retrieving RDF representation of structures
- #5786 – Uncaught TypeError is in console when trying to move tail of Multi-Tailed Arrow added from KET with small size between tails
- #5753 – Issue with moving of tail of Multi-Tailed arrow with several tails when user needs to move the tail close to another one
- #5679 – Unable to establish connection between micro structure and macro ones
- #5848 – Unable to establish connection between micro structure and sugar or phosphate (and partially - unresolved monomer)
- #5703 – The picture is incorrect when image resolution high and bond thickness changing
- #5685 – The diagonal bond in the molecule is displayed incorrect with ACS style
- #5674 – Inconsistent behavior of copy-paste and cut-paste operations with macromolecule abbreviations
- #5658 – Incorrect selection behavior when using Selection tool on Macromolecule abbreviations
- #5699 – After bulk deletion of monomer abbreviations, Undo returns expanded monomers
- #5836 – R-Group fragment labels font size doesn't defined by Sub Font size property at Settings
- #5834 – S-Group (Data type) Field value label font size uses Settings - Font size property value instead of Sub font size one
- #5833 – Importing functional groups (e.g. Boc, Bn, CF3) ignores drawing settings (e.g. ACS style)
- #5809 – System opens wrong context menu for monomers on micro canvas if clicked on atom or bond
- #5887 – After save and load a MOL V3000 file in macro and micro mode, bond connections are changed, and the microstructures are shifted
- #5814 – On Remote environment, the reaction/molecule can't be saved to V3000 formats (returns V2000 instead): MOL, RXN, SDF, RDF
- #5886 – Loading a KET file in macro mode, bond connections are preserved but microstructures are shifted
Ketcher v2.25.0 October 10, 2024
What's Changed
This release includes several bug fixes and new features. Please be aware Ketcher 2.25.0 has been tested with Indigo version 1.24.0 (standalone and remote).
New features
- #4884 – Implement basic preview display for monomer bonds
- #4554 – Support ambiguous monomers in Ketcher (flex mode)
- #5186 – Add ambiguous monomers to the library and allow their addition to the canvas
- #4556 – Support of ambiguous monomers in sequence view
- #4557 – Support of ambiguous monomers in small molecules mode
- #4872 – New approach and UI for switching between types in sequence mode
- #4555 – Preview for ambiguous monomers
- #5224 – Implement basic preview in connection modal for ambiguous monomer
- #4861 – Introducing multi-tail arrows
- #4985 – Support retrosynthetic arrows
- #4853 – Search monomer in library by IDT
- #4926 – Add IDT alias to chem monomer
- #5244 – Add CHEMs to the library
- #5264 – Add amino acids to the library
- #5152 – Add new settings for ACS style
- #5560 – Update Indigo to 1.24.0 in browser module
Bugfixes and improvements
- #5200 – The users choice is not saved in the settings but is recalculated in px
- #4658 – Some bonds remain selected on export to SVG in Snake mode
- #5201 – it is not possible to enter a value when selecting cm inch pt manually in the settings
- #5454 – Export of variant monomers to Sequence/FASTA doesn't work for presets
- #5425 – Undo-Redo operations over ambiguous monomer causes broken canvas
- #5464 – Undo operation removes ambiguous monomer from the canvas but keep in the KET file export
- #5209 – Cancel of Edit Connection points dialog cause existed connection points eliminated
- #5453 – Circle with monomer number should be few pixels down
- #5427 – Preview tooltip for mixture ambiguous monomer shows wrong percentages
- #5466 – HELM inline SMILES monomer canvas color is wrong
- #5470 – Export of different mixed and alternatives peptides (with different proportions and percents) works wrong
- #5313 – Creation preset without phosphate causes R3-less sugars disabled in the library
- #5447 – Added fixed precision class, updated multi-tail calculations with fixed precision usage
- #5368 – An error appears in the Console, when dragging a bond between any monomers
- #4212 – Limit size of structures in preview
- #5473 – Export of different mixed and alternatives RNAs (with different proportions and percents) works wrong
- #5465 – Export of different mixed monomers (with different ratios) works wrong
- #5512 – System saves mixture ambiguous monomers as alternatives ambiguous monomers
- #5519 – Alias labels for mixed bases loaded from IDT are wrong
- #5521 – Sugar color is wrong if loaded from HELM with inline SMILES
- #5545 – After uploading a multi-character monomer in HELM format, abbreviations in sequence mode are cluttered together
Ketcher v2.24.0 September 10, 2024
What's Changed
This release includes several bug fixes and new features. Please be aware Ketcher 2.24.0 has been tested with Indigo version 1.23.0 (standalone and remote).
New features
- #4878 – Add/Replace monomer in sequence mode from library
- #4880 – Adjust previews – add APs, show IDT aliases for previews in sequence mode, increase debounce time
- #4888 – Enable editing sequences by click between symbols
- #4887 – Starting new sequences with "Plus" icon on canvas
- #4780 – Remove monomers from the library (Peptides and CHEMs)
- #5167 – Change natural analogue of monomers Peptides and CHEMs)
- #4787 – Change structure of monomers (Peptides and CHEMs)
- #5166 – Change symbols of monomers (Peptides and CHEMs)
- #4781 – Change names of monomers (Peptides and CHEMs)
- #4905 – Open Edit Connection Points dialog via right click on bond
- #4911 – Insert image from ket to canvas
- #4897 – Insert image to canvas via "Add image" tool, Select, Move and Scale the image
- #4981 – Support for SSR
- #4979 – Support for Strict mode
- #5190 – Include Indigo without render module into ketcher-standalone build process
- #5284 – Update Indigo to 1.23.0 in browser module
Bugfixes and improvements
- #4763 – It is possible to create forbidden RNA preset
- #4962 – Bond tool and Erase tool buttons have to be disabled in Sequence mode (since they are not applicable)
- #4659 – Export result SVG contains some labels that are selectable
- #4108 – There are no tooltips when hovering over each of the sequence modes
- #4806 – It is allowed to change bond type between micro and macro
- #4936 – Applying Enhanced Stereochemistry to monomers causes its disappear from the canvas (and exception in console)
- #5090 – The favorites icon overlaps unsplit nucleotide names in the RNA and favorites tab
- #4947 – Distance between unresolved monomer and preview tooltip is too large and it has no IDT alias
- #4957 – Disabled query features in extended table not disabled in right-click menu
- #5126 – The error appears in the Console, when connecting two unsplit nucleotides in Snake mode
- #4069 – Right-click context menu protrudes beyond edges of the Ketcher workspace
- #4806 – It is allowed to change bond type between micro and macro
- #5196 – An error appears in the Console when opening any section in the RNA tab
- #5242 – Replace phosphate at the end with peptide causes cycled polymer
- #5184 – Fix unresolved monomers bond establishing issue
- #4935 – Enumeration is missing for cycled unsplit nucleotides after load from file (KET/MOL doesn't matter)
- #5255 – Fix adding new monomers to canvas in sequence mode while editing RNA in builder
- #5245 – Replacement of peptide at the end of sequence on preset w/out base works wrong
- #5228 – System insert monomer from the library to the canvas even if it shouldn't (and error message is wrong)
- #5300 – Attempt to insert improper monomer from the library to the sequence causes wrong error
- #5301 – New preset creation process interferes with monomer replacement on the sequence mode
Ketcher v2.23.0 September 10, 2024
What's Changed
This release includes several bug fixes and new features. Please be aware Ketcher 2.23.0 has been tested with Indigo version 1.22.0 (standalone and remote).
New features
- #4852 – UX support for HELM import/export
- #4846 – Make Sequence view default in Macromolecules mode
- #4431 – Implement support of unresolved IDT monomers
- #4382 – Implement support of unsplit nucleotides
- #3532 – Displaying side chain connections in snake-like mode
- #4856 – Add new CHEM monomers to the library
- #2654 – Improve WASM loading performance
- #5083 – Update indigo to 1.22.0 in browser module
Bugfixes and improvements
- #4660 – Zero charge shows explicit 0 instead of blank after using A+/A- Tools
- #4801 – Cut operation for attachment points makes canvas inaccessible/unoperational and delete entire molecule
- #4636 – In the Sequence mode, when selecting elements on the canvas, the total number of elements is not displayed in the Right-click menu
- #4686 – After moving the structure in the Macro mode, in the Micro mode the S-group value is displayed separately from the structure
- #4823 – In sequence mode, each press adds two characters and when deleted, also removes two
- #4793 – Context menu for attachment point labels should contain only Delete option
- #4784 – Attachment point enumeration logic works wrong
- #4786 – Keyboard shortcut stops working after adding/removing attachment point
- #4607 – Inconsistent display of a separate phosphate in the sequence representation in the Sequence mode
- #4782 – It is possible to attach bond to attachment point label
- #4791 – System saves selection states of attachment point labels to KET file (it should not)
- #4837 – Library filter does not reset when switching between Micro and Macro mode
- #4833 – Support rendering multiple Ketcher editors on a page without an iframe
- #4773 – It is impossible to apply R-group to atom with attachment point attached
- #4927 – Able to change attachment point label to an atom if it is selected first
- #4925 – Unable to change atom to another if molecule has attachment point
- #4929 – System allow to change atoms inside S-group without removing abbreviation
- #4930 – Fix missing IDT aliases and label positioning for unsplit nucleotides
- #4889 – After using "Clear Canvas" in the Sequence mode and entering new sequence, extra structures are shown in Flex and Snake modes
- #4924 – RNA Preset without Base causes constant crash after switching to Macromolecules mode
- #4977 – System doesn't show side chain bonds if chain loaded directly to Snake-mode canvas
- #4997 – The second of three horizontal bond overlaps backbone connection line
- #4975 – Connection is displayed at the bottom of the row, if drag a horizontal side-chain connection between the extreme nucleotides of a row
- #5035 – Bonds in the snake chain are displayed differently after saving in ket format
- #5034 – When dragging the side chain connections between CHEM, all these connections pass exclusively from the left, and not the shortest path
- #4881 – When switching from Sequence mode to Flex mode, RNA abbreviations remain
- #4995 – The bottom horizontal bonds does not shift if there is an overlap
- #5074 – Switching from Sequence mode to Snake mode and back shifts visible area of canvas beyond visible frame. Forever.
- #5121 – Copy does not work in the firefox browser
- #5335 - The application crashes when selecting Enhanced Stereochemistry from the right-click menu