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@renovate renovate bot commented Apr 29, 2024

This PR contains the following updates:

Package Change Age Adoption Passing Confidence
ketcher-core (source) 2.18.0 -> 2.25.0 age adoption passing confidence

Release Notes

epam/ketcher (ketcher-core)

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

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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

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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

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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

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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

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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

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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

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