chore(deps): update dependency ketcher-react to v2.25.0 - autoclosed

[renovate]

This PR contains the following updates:

Package	Change	Age	Adoption	Passing	Confidence
ketcher-react (source)	2.18.0 -> 2.25.0

---

Release Notes

epam/ketcher (ketcher-react)

v2.25.0: Ketcher v2.25.0 October 10, 2024

Compare Source

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

v2.24.0: Ketcher v2.24.0 September 10, 2024

Compare Source

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

v2.23.0: Ketcher v2.23.0 September 10, 2024

Compare Source

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

v2.22.0: Ketcher v2.22.0 September 3, 2024

Compare Source

What's Changed

This release includes several bug fixes and new features. Please be aware Ketcher 2.22.0 has been tested with Indigo version 1.21.0 (standalone and remote).

New features

• #​3934 – Support selection entity selection flag in KET format
• #​4307 – Migrate Monomer library from MOL V2K to KET format
• #​4388 – Allow Nucleoside of sequence edit in RNA builder
• #​4427 – Store custom presets in browser local cache by
• #​4495 – UI support for IDT import/export
• #​4530 – Convert Rx connection points created in molecules mode into chem attachment points in macromolecules mode
• #​4531 – Allow moving and connecting "small" structures in macro mode
• #​4539 – Export macromolecules canvas as svg image
• #​4692 – Cursors should be copied from small mode
• #​4697 – Highlight connection point (change mouse cursor) on mouse hover
• #​4311 – Send monomer library from Ketcher to Indigo upon monomers import/export
• #​4530 – Add ability to define attachment points for molecules
• #​4380 – Display IDT aliases in monomer library
• #​4701 – Unify toolbars with small molecules mode
• #​4530 – Add ability to define attachment points for molecules fixes
• #​5391 – Migrate to Indigo 1.21.0 in-browser module

Bugfixes and improvements

• #​3943 – System allow to create atoms with Charge value out or range
• #​3501 – 3d mol files appear as 2D in Miew
• #​4349 – Selection does not work in sequence editing with Shift+Up/Down arrow combination
• #​4508 – In the Text-editing mode, when selecting nucleotides linked through phosphates R2-R2, an error appears in the Console
• #​4340 – When adding new nucleotides to the beginning of a row, the order of the chains changes in the Sequence mode
• #​4470 – Any click on toolbar buttons should cause cancel of "Modify in RNA builder" process
• #​4479 – Quick double paste operation from clipboard leads to invalid entities on canvas
• #​4488 – System doesn't allow duplicate same preset twice
• #​4501 – The system allows you to paste on canvas while modifying nucleotides in the RNA builder
• #​4640 – Presets saved to local storage appear on canvas after switching Macro/Micro modes
• #​4615 – Implement sorting for RNA builder components
• #​4543 – The cleared object is not returned by the Undo button in the Macromolecules mode.
• #​4590 – RNA Structure is broken while we Copy from Macro and Paste to Micro canvas.
• #​4509 – In the Text-editing mode, when inserting a fragment after pressing Ctrl+V twice, the cursor is moved to another row
• #​3816 – Added validations and monomer Item disablement
• #​4575 – New Sequences are created while we add cyclic to middle of sequence.
• #​4693 – Incorrect bond alignment to tBu S-group
• #​4730 – System doubles number of pasted monomers after switching from flex to sequence
• #​4734 – Monomers from macro mode are not erased by Erase tool in micro mode
• #​4690 – Undo problem while layout is changed on the Snack of Flex modes and switch through modes
• #​4744 – When changing zoom level in macro mode, there is no percentage indication
• #​4739 – Pasting IDT structures via clipboard does not work
• #​4740 – Delete of cycled sequence from the canvas causes delete of another cycled sequence bond that makes it non-cycled
• #​4764 – IDT label is not shown or shown but layout is broken after load sequence from ket
• #​4726 – Delete of nucleoside symbol turns another nucleoside to nucleotide
• #​4777 – Incorrect valence for carbon atom in ring with attachment point after saving and reopening file
• #​4801 – Cut operation for attachment points makes canvas inaccessible/in-operational and delete entire molecule
• #​4708 – Forbid merging cyclic sequences on delete in Sequence mode
• #​4823 – In sequence mode, each press adds two characters and when deleted, also removes two
• #​4824 – Cycled chain breaks sequence canvas and entire app
• #​4839 – System loses connections to molecule R2 if there is no R1 attachment point
• #​4836 – Molecule changes position after saving and opening from file
• #​4840 – Paste from clipboard does not work for molecules in macro mode
• #​4879 – Save to mol for micro and macro structures connected through attachment points works wrong
• #​4973 – Connection between molecule and monomer lost after opening and saving to ket

v2.21.0: Ketcher v2.21.0 June 28, 2024

Compare Source

What's Changed

New features

• #​3734 - Displaying modified nucleotide chains in sequence representation
• #​3824 - Modify nucleotides from sequence in RNA builder
• #​4374 - RNA builder should be highlighted in Edit mode. Canvas should be disabled
• #​3894 - Paste from clipboard in sequence mode

Bugfixes and improvements

• #​4238 - getKet function return ket file without selection flags
• #​4174 - Buttons in paste from clipboard window change their position when zoomed more than 175 percent
• #​4172 - 'leavingGroup' section does not contain information about number of atoms
• #​4144 - Connection of bond to atom inside s-group supergroup cause it connected incorrectly in terms of layout
• #​3986 - Selected RNA preset not discards when mouse moved
• #​3957 - Atom Query feature export System lost MOST Substitution count values export to Molfile
• #​4356 - Clear canvas button doesn't work in Sequence mode
• #​4454 - 'Update sequence' modal window: don't close RNA-builder after pressing 'Cancel' in modal window.
• #​4455 - 'Update sequence' modal window: display the number of nucleotides to be changed
• #​3919 - After pressing Snake mode, attachment points stick out in different directions and not attached to the bonds
• #​3899 - Attachment points do not disappear when hover is removed from some monomers.
• #​4487 - RNA builder: Cancel button doesn't work
• #​4507 - When expanding structures, added to the canvas via Clipboard, an error appears in the Console
• #​3843 - System doesn't filter out and do execute html tags and javascript in custom query feature text
• #​3816 - RNA Builder allows creating an invalid preset with disconnected sugar
• #​4399 - Different chains shown by the same sequence in sequence mode (system ignores sugar presence)
• #​4405 - Switching to Sequence mode causes page freeze
• #​4568 - Pasted sequences are not visible in the Snake mode
• #​4548 - Cyclic chains disappear from canvas when try to Edit in the sequence mode
• #​4508 - In the Text-editing mode, when selecting nucleotides linked through phosphates R2-R2, an error appears in the Console
• #​4871 - Migrate to Indigo v1.20.0 in-browser module

v2.20.0: Ketcher v2.20.0 April 30, 2024

Compare Source

What's Changed

This release includes several bug fixes and new features. Please be aware Ketcher 2.20.0 has been tested with Indigo version 1.19.0 (standalone and remote).

New features

• #​3650 - Remove and insert nucleotides in sequences (sequence representation)
• #​3861 - Insertion mode for nucleotide entry (switch RNA/DNA/Peptide)
• #​4146 - UI for Open/Save As FASTA
• #​4109 - UI for Save As Sequence
• #​3819 - Selection in sequence representation for view mode
• #​3819 - Selection in sequence representation edit mode
• #​3876 - Nucleotide preview in sequence representation

Bugfixes and improvements

• #​3005 - Unable to 'undo' the paste action, if there is no reset to Select tool
• #​3902 - If open a macro file and put in center of canvas in micro mode then switch to macro, structure is not in center of canvas*
• #​3750 - Add search menu clear button
• #​4173 - the pop-up window does not appear in fullscreen mode after clicking the “Open” button and the “Save as” button
• #​4231 - Maximum call stack size exceeded error appears during snake layout for large chains
• #​3663 - After clicking the 'Duplicate and Edit' button and subsequently clicking 'Cancel,' the preset remains saved.
• #​4241 - Pasting large cyclodextrins structure cause Ketcher to freeze
• #​4271 - The Uncaught TypeError appears in the DevTool Console, when scrolling until it stops, using the Shift+Left arrow, in the Text-editing mode
• #​4295 - Cannot save FASTA using the Remote mode
• #​4286 - Editing grid disappears but editing mode is on
• #​4297 - When removing nucleotides from the canvas, the preview of the nucleotide does not disappear, if you leave the cursor over it
• #​4192 - Export to SVG/PNG ignores "Show hydrogen labels" option
• #​3775 - Phenylalanine mustard is displayed incorrectly in the Structure library
• #​4296 - When pressing the Enter or the Spacebar, the “Edit mode” drop-down opens and closes randomly in the Text-editing mode
• #​4028 - When monomers are selected Del and Backspace hotkey delete selected monomers and switches to Erase tool
• #​4356 - Clear canvas button doesn't work in Sequence mode
• #​4369 - Del button works as Backspace button that is wrong
• #​4329 - Cyclic chains disappear from canvas when switching to sequence mode
• #​4252 - Migrate to Indigo v1.19.0 in-browser module

v2.19.0: Ketcher v2.19.0 April 23, 2024

Compare Source

What's Changed

This release includes several bug fixes and new features. Please be aware Ketcher 2.19.0 has been tested with Indigo version 1.18.0 (standalone and remote).

New features

• #​3648 - Displaying unmodified nucleotide chains in sequence representation
• #​3869 - Left-to-right ("Snake-like") layout for RNA
• #​3870 - RNA layout change while switching from sequence to flex and snake modes
• #​3728 - Add group selection for macromolecules
• #​4519 - Macro: Add Pyrro and AspOH peptides to monomer library

Bugfixes and improvements

• #​3827 - Add fixes in group selection for macromolecules
• #​3736 - System marks availiable connection point as unavaliable in Select Connection Point dialog
• #​2177 - library.svg file for templates does not seem to be used
• #​3862 - UI modal window to open and save sequence format
• #​4047 - System doesn't save selection state for atom wrapped into R-Group
• #​3017 - Using setMolecule with molfile does not rescale bond lengths
• #​3891 - Aromatize/Dearomatize of having abbreviation (Salts and Solvents) on the canvas causes spontaneous random de-abbreviation
• #​3893 - Remove explicit hydrogens feature changes layout of simple molecules
• #​3918 - When deleting part of a structure using a hotkey Del, and preview of structure is under mouse cursor, an error occurs.
• #​4088 - System print out subscripted text imperfectly
• #​4154 - Cannot select bonds when we add molecule with addFragment, setMolecule or Paste from clipboard
• #​4255 - Hand tool coordinates on canvas calculated are not correct
• #​4167 - Migrate to Indigo v1.18.0 in-browser module

---

Configuration

📅 Schedule: Branch creation - At any time (no schedule defined), Automerge - At any time (no schedule defined).

🚦 Automerge: Disabled by config. Please merge this manually once you are satisfied.

♻ Rebasing: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox.

🔕 Ignore: Close this PR and you won't be reminded about this update again.

---

• If you want to rebase/retry this PR, check this box

---

This PR was generated by Mend Renovate. View the repository job log.