Releases: epam/ketcher
Ketcher v2.17.0 December 25, 2023
What's Changed
This release includes several bug fixes and new features. Please be aware Ketcher 2.17.0 has been tested with Indigo version 1.17.0 (standalone and remote).
- #3203 - Structure shifting to upper left corner during zoom operations
- #2869 - Preview of monomer structures on canvas
- #3442 - Unused attachment points labels overlaps
- #3554 – Implicit hydrogens for aromatised structures containing Sulphur
- #3544 – option to disable custom query feature
- #3643 - Error appears in DevTool Console after call 'ketcher.setSettings' before templates initialization
- #3636 - Atom display changes to SMARTS notation when any of the Query Properties, such as Aromaticity, Ring membership, Ring size, or Connectivity, is selected.
- #3729 – When merging rings, they are added to canvas at a distorted angle
- Macro: #3443 - Incorrect displaying of monomer attachment point number
- Macro: #2453 -"Clear Canvas" tool
- Macro: #2883 - Modal window to select AP while connecting monomers
- Macro: #3489 - Preview for monomer does not disappear and prevents you from selecting menu in RNA Builder
- Macro: #2369 - "Zoom" tool
- Macro: #2987 - switching between ketcher mode and ketcher macromolecules mode
- Macro: #3498 - When switching from the Macromolecules module to the Molecules module an application crashes
- Macro: #3509 - RNA tab view while opening the RNA tab
- Macro: #3539 – When pull bond away from monomer and press 'Escape', bond remains on canvas
- Macro: #3525 - Wrong usage of AP when establishing a bond between monomers r1 and r2 r2
- Macro: #3475 – Change RNA-preset configuration
- Macro: #3509 - RNA tab view while opening the RNA tab
- Macro: #3542 - after hiding the library panel a residual strip remains concealing content on the canvas
- Macro: #3469 – Snake bonds should be displayed from/to attachment point for R1 and R2
- Macro: #3041 – RNA Builder. Delete presets.
- Macro: #3497 – the "Library" inscription and the "Hide" button are at same height
- Macro: #2925 - Support monomers connection dragging AP
- Macro: #3457 – support import/export mol v3000
- Macro: #3538 - New created preset does not draw on canvas
- Macro: #3537 - default presets do not appear back after cleaning search field
- Autotests: #3474 - Atom settings
- Autotests: #3107 – template manipulations
- Autotests: #3441 - Template Library
- Autotests: #3448 - reagents
- Autotests: #3099 - atom properties
- Autotests: #3523 - Floating windows
- Autotests: #3367 - Create autotests for Load Fragment
- Autotests: #3104 - Create autotests for simple objects
- Autotests: #3103 - Text Tool
Ketcher v2.15.0 November 6, 2023
What's Changed
This release includes several bug fixes and new features. Please be aware Ketcher 2.15.0 has been tested with Indigo version 1.14.0 (standalone and remote).
- #2838 – Bonds between atoms are not centered and not drawn symmetrically
- #2962 – Refactor request: rename attpnt and add type annotation on it
- #3094 – Toolbars are not visible when browser zoomed in
- #3114 – Add support for exporting to InChiKey file format
- #3128 – When dragging and dropping a Functional Group onto the structure, numerous errors appear in the console
- #3119 – The typo in the word "Sciences" and the incorrect spelling of "EPAM" inside the section "About"
- #3075 – replace aromatize and dearomatize icons
- #2623 – Two dividing line between 'Edit...' and 'Single' bond in Bond context menu
- #3070 – Add support for exporting to sdf file format
- #3124 – Remove dividers for items in the same group in bond context menu
- #2389 – Bracket is missing when opening a file RXN v2000/v3000 files with 'S-Group Properties Type = Multiple group'
- #3140 – Add query options to right-click menu
- #3114 – Add support for exporting to inchikey file format
- #3019 – ignorechiralflag setting is not regarded for templates
- #3143 – Modify context menu when right-clicking on an atom and attachment point
- #3224 – Appearing label near the Template after choosing any option in the "Edit" or "Query properties" tab in the context menu disappears when clicking on the canvas
- #3248 – Files with the format InChIKey should be saved with the extension ".inchikey"
- #3208 – Structure disappears after pressing 'Layout' and the app crashes
- #3284 – Application crashes after selecting an attachment point and pressing the right mouse button
- #3024 – Can't copy/paste structure with Repeat count when the number of bonds/atoms is more than 999
- #3462 – Layout should not be called if there are coordinates in extended smiles
Ketcher v2.14.0 (November 2, 2023)
What's Changed
This release includes several bug fixes and new features. Please be aware Ketcher 2.14.0 has been tested with Indigo version 1.14.0 (standalone and remote).
- #2958 – Atom label disappears after updating R-Group attachment point to none
- #2742 – Attachment point selection edition and deletion
- #2833 – Lookup Abbreviations window disappears when user change browser tab
- #2595 – draw selection outline correctly for hovered structures
- #1859 – Save structure window: formats in drop-down list is not ordered
- #2679 – Highlight colors for Simple Objects do not match the new design
- #2982 – ignore abbreviation lookup for repetitive keystrokes
- #2911 – Add all-scroll for selected structure
- #3022 – Some structures from Template library have incorrect chiral flag
- #3000 – remove unused code in the ketcher-core
- #2679 – Highlight colors for Simple Objects do not match the new design
- #2957 – Incorrect order of Hydrogen symbol in abbreviation of the atoms when adding them to the structure
- #2332 – Add peptide monomers to canvas (by click)
- #2963 – Copy/Cut/Paste + Undo/Redo makes objects appear randomly on the canvas, their initial amount increases
- #2642 – Refactoring request: remove duplicate shared utils functions
- #2912 – fix memory leak for ketcher when it is opened inside modal
- #2793 – Selection tool: Incorrect selection view
- #2948 – Bond thickness is not changed via Ketcher API
- #3091 – Cannot open CDX files on Mac
- #2541 – missing tool word for arrow filled triangle
- #2939 – Merge preview of abbreviated structures
- #3133 – Merge preview stops appearing after hovering over a terminal atoms
- #3209 – expand the number of ignored keys for abbreviations lookup
- #3238 – Enhanced stereochemistry is disabled via right-click for stereocenters after pasting structure through API in Ket format
Ketcher v2.13.0 (September 28, 2023)
What's Changed
This release includes several bug fixes and new features. Please be aware Ketcher 2.13.0 has been tested with Indigo version 1.13.0 (standalone and remote).
- #2765 – Introduce to .ket file specification attachment point information for super atoms
- #2600 – Preview peptide monomers in Library
- #2854 – Multiple repeating S-groups: limit on maximum count
- #2128 – Automatically adjust zoom when opening a structure
- #2751 – RNA builder. Collapsing panel with RNA components
- #2779 – Add automated tests
- #2902 – Fix test failures in 'localhost' environments due to design changes
- #2009 – Incorrect positioning of data s-group labels
- #2467 – update documentation about the RGroup attachment points
- #2760 – Snap partially selected structure to an attachment bond when rotated
- #2111 – Position newly added bond so that mouse cursor is over its atom
- #2774 – Structure with r group isnt opened
- #2817 – Rotation tool: cancel rotation by pressing 'right click' button
- #2790 – Missing warning message when pasting copied structure via the "Paste" button
- #2854 – Multiple repeating S-groups: limit on maximum count
- #2128 – Automatically adjust zoom when opening a structure
- #2765 – Introduce to .ket file specification attachment point information for super atoms
- #197 – Attachment points should be within R-Group brackets
- #2916 – Allow zoom change via ctrl+scroll
- #2078 – Center molecules after layout
- #2933 – Migrate to Indigo v1.13.0-rc.1 in-browser module
- #2940 – No modal windows are opened during R-Group adding
- #2966 – Error message after opening saved png file
- #2949 – Attachment points should be within S-Group brackets
- #2985 – Ctrl+Scroll for zooming is not working
- #2989 – Error message appears when copypaste structure with s group properties functional groups and salts and solvents
- #3006 – The canvas view moves in the direction of the cursor
- #3025 – Stereo flag is separated from the structure and each time you click on 'Layout' button zoom decreases
- #3097 – Apply auto zoom and centering for api
- #2849 – When zoom out or zoom in, atoms and templates are located not under the mouse cursor
- #3176 – Drawing gets broken after dragging a Functional Group onto an atom
Ketcher 2.12.0 (August 11, 2023)
What's Changed
This release includes several bug fixes and new features. Please be aware Ketcher 2.12.0 has been tested with Indigo version 1.12.0 (standalone and remote).
- #2471 – When you try to add a structure to a canvas with an expanded functional group, an EDIT ABBREVIATION window appears
- #2650 – Move renderStruct function from ketcher-react to ketcher-core
- #2625 – Rotation tool: cancel rotation by pressing "Escape" key
- #2632 – Refactoring request: improve Editor tools in 'ketcher-react'
- #1905 – Refactor Render class: convert raphaelRender.js to TypeScript and add necessary types
- #2423 – Hotkeys for atoms don't work on Functional Groups and Salts abbreviations
- #2689 – Make cyclopentadiene ring systems fusion without valence errors
- #2584 #2750 – Selection tool: add flip and delete buttons & Rotation Tool: non-selected end of the selected bond should be the rotation center
- #2599 – Rotation tool: label rotation
- #2447 – peptide monomer library
- #2165 – Change attachment point visualization to IUPAC style
- #2745 – move selected structures using arrow keys
- #2626 – Move Icon and IconButton components to ketcher-react and re-use the same icons
- #2766 – Can not open .rxn files with S-Group properties
- #2773 – refactoring request remove warnings from build logs for linters
- #2780 – Add ability to run a project under windows os without using unix subsystems
- #2753 – Snap arrows to horizontal and vertical orientation
- #2781 – Refactoring request: restrict usage of "any" type and not-null-assertion for new code
- #2731 – Lookup abbreviations using the keyboard
- #2738 – Migrate to Indigo v1.12.0 in-browser module
- #2707 – Update ketcher toolbar UI styles
- #2753 – Snap arrows to horizontal and vertical orientation
- #2467 – Ketcher needs to correctly parse and represent attachment point information for super atoms for mol v2000 format
- #2804 – Selected Atom appears in the left upper corner of canvas
- #2803 – When user moves mouse, there is a constant update in the '3D Viewer' window
- #2812 – Tooltip for Data S-Group does not appear
- #2810 – Part of the structure disappears when opening a contracted Superatom with multiple connection points
- #2824 – tooltip for sl button is showing custom template instead structure library backmerge
- #2805 – horizontal and vertical flips are working incorrectly (affect position) with some atoms, texts and functional groups
- #2825 – The structure when moving with arrows on the keyboard disappears beyond the edges of canvas
- #2806 – All inner space of selected Functional Group is highlighted if structure selected via CTRL+A
- #2839 – Buttons have changed their position on the toolbars and margin and padding of toolbars are increased
- #2837 – Programmatically scroll buttons do not appear
- #2865 – Incorrect display of carbon in attachment points for functional groups
- #2864 – Incorrect display angle of attachment points for functional groups
- #2867 – Incorrect display of the 'tBu' functional group
- #2879 – Incorrect display of attachment points for some Functional Groups
Ketcher 2.11.0 (July 10, 2023)
This release includes several bug fixes, performance improvements and new features. Please be aware Ketcher 2.11.0 has been tested with Indigo version 1.12.0 (standalone and remote).
What's changed
- #2653 Migrate to Indigo v1.12.0-rc.1 in-browser module
- #2088 Selection Tool: use rounded rectangles for selection of bonds and atom labels
- #2213 Data S-Group: 'Field value' text when placed on a structure becomes hard to access
- #2566 Improve page loading performance
- #2576 Right click menu shown for highlighted Functional Group instead of clicked
- #2619 Add ketcher api method getCDXml() for retrieving molecule in CDXml format
- #2127 Change esc behaviour logic for selection tool
- #2597 Rotation tool: fix selection box for expanded s-groups
- #2596 Rotation tool: Use steps for increasing/decreasing the size of the rotation wheel
- #2340 Sliders changed to checkboxes in 'Settings'
- #2463 Rotation Tool: display predefined rotation angles and current angle
- #2517 Incorrect rendering of superatom with multiple connection points
- #2512 Toolbar arrow is active after the Ketcher with iFrame is loaded and disappears when you click on it
- #2492 Add a function to detect when opened file is loaded
- #2288 Tooltip appears after dragging abbreviation and stay on canvas until release click
- #2276 Click & drag an 'Atom' on FG, Salts and Solvents, FG connected with Atom forms many atoms
- #1835 Extra textarea is shown, when Ketcher is not full-screen
- #2460 Structure on canvas becomes 'undefined' when atom is hovered and Functional Group selected using hotkey
- #1994 Salts and Solvents: Edit notification appears instead of replacing new Salt or Solvent
- #2267 Using Template Tool, Salts and Solvents should replace Atoms, Functional Groups, and Salts and Solvents
- #2428 Atom letter is drawn at the cursor after user selects structure/part of structure on the canvas and then click atom on the toolbar
- #2490 When atoms are selected, pressing atoms hotkey opens a modal window instead of an instant replacement
- #2196 The Save button is active for empty canvas
- #2483 Pressing Clear Canvas with Reaction Arrow under mouse cursor causes errors in DevTool console
- #2090 Selection Tool: support rotation using in-place handle
- #2411 Move to vite from react-app-rewired for example project development build
- #2379 Can't open v3000 mol file with assigned Alias
- #1997 RXN 2000 and 3000 import: When importing, the structure becomes unreadable
- #2383 When hovering over a data s-group label - hover rectangle should appear around it and tooltip should be shown
- #1930 Reagents: When opening Daylight SMILES and Extended SMILES files with reagent the original structure is distorted bug externalIssue depends on external services such as Indigo service
- #2376 Edit abbreviation window doesn't appear when user trying to add structure to a functional group or salt, allowing user to modify it
- #2449 Structure with R-Group isn't opened correctly from v3000 mol file
- #2335 Structure with R-Group Fragment Tool pasted into square brackets of the copied structure
- #2655 Add dynamic load for Miew
- #2624 Rotation tool: incorrect selection box for s-groups
- #2669 Atom placed with atom tool have incorrect hover border
- #2634 S-Group Polymer label has character limit
- #2694 Improve performance of Templates Modal
- #2681 Calculate CIP: stereolabels appears under structure
- #2679 Highlight colors for Simple Objects do not match the new design
- #2683 Missing circles to expand reaction arrows by
- #2680 Reaction arrow and text don't rotate with rotated objects
- #2717 Tooltip for S-Group appears in upper left area of canvas
- #2719 Preview images for Functional Groups and Salts and Solvents are less readable
- #2734 Tooltip for Multiple group and SRU Polymer appears in upper left area of canvas
Ketcher 2.10.0 (June 6, 2023)
This release includes several bug fixes, improvements, and new features. Please be aware Ketcher 2.10.0 has been tested with Indigo version 1.11.0 (standalone and remote).
What's Changed
- #2273 When user selects and moves atom on Functional Group or Salt it doesn't replaces atom in the structure
- #2113 Hovered structure gets into the saved molecule
- #2062 RXN v2000: Detection molecule above/below arrow as reagent doesn't work
- #2362 Remove appearance of a tooltip under mouse cursor for Functional Groups/Salts and Solvents abbreviations
- #2403 Wrong tooltip and label in 'Extended Table'
- #2421 Add locators and/or functions for tools sub-menus
- #2029 Completely replace yarn with npm commands throughout the project
- #2355 Add DisableQueryElements parameter to disable query elements from extended table
- #2246 Multiple bond editing changes bond types to all selected bonds
- #2425 The cancel button does not reverse adding template to expanded and contracted functional group main
- #2446 Structures are drawn outside the viewbox, when changing rendering options
- #2427 When moving a structure outside of the canvas, structure does not move smoothly
- #2353 CTRL+SHIFT+0 hotkey not working for 'Zoom 100%'
- #2402 Atom under mouse cursor on click and drag freezes on canvas if you move cursor away from dragged atom
- #1855 Make benzene rings fused rings connection without valence errors
- #2456 Update KET json schema to support explicit implicit hydrogens
- #2441 Add a warning message about localStorage to templates window
- #2052 Expand collapse unknown super atom
- #2482 Ketcher with iFrame loads with scrollbars activated
- #2442 When mouse hovering on atom or bond hotkey CTRL+Z (Undo) is not working
- #2420 Hotkey (Del) can't delete Functional Groups and Salts abbreviation
- #2454 After clicking undo button edit abbreviation popup do not appear
- #2245 Settings:
Terminal and Heterois not selected as default andonoption is not working - #225 Add support for stereo cip values in ket format
- #2458 Migrate to Indigo v1.11.0-rc.1 in-browser module
- #2257 Unable to add a bond to a functional group by bond tool
- #1865 Extended SMILES saved from Ketcher might be invalid for RDKit
- #2516 When create Superatom part of the structure disappears
- #2528 Erase tool does not completely remove the Functional Groups if it selecting via the hot key CTRL + A
- #2530 Tooltip for created Data S-Group not appears after hover on it
- #2113 Hovered structure gets into the saved molecule
- #2420 Hotkey (Del) can't delete Functional Groups and Salts abbreviation
- #2548 If name of Superatom matches abbreviation in Custom Templates, then tooltip is shown on hover
- #2517 File with Superatom opens without part of structure
- #2273 When user selects and moves atom on Functional Group or Salt it doesn't replaces atom in the structure
- #2585 Change behaviour of "Show hydrogen labels" setting so the "on" value works the same way as "terminal and hetero"
- #2614 Contracted unknown superatom is parsed as expanded, and brackets with name are lost
- #2636 Unable to contract or expand Unknown Superatoms that are parsed via API in MolV3000, KET, CDX, CDXML, CML, Base64CDX formats
- #2656 After opening or pasting an unknown superatom onto canvas, it becomes non-interactive
Ketcher 2.9.0 (May 8, 2023)
This release includes several bug fixes, improvements, and new features. Please be aware Ketcher 2.9.0 has been tested with Indigo version 1.10.0 (standalone and remote).
Notably, the following changes have been made:
Features
#1996 – The bond context menu now has the ability to attach or edit s groups. Additionally, when a Data S-Group or S-Group is selected, right-clicking on an atom or bond will open the S-Group Properties window.
#2192 – The canvas will now automatically expand when moving the structure off the page.
#2329 – Unknown super-atoms can now be expanded and collapsed.
#2005 – CDX export has been added to the output formats list.
#2161 – The ignore-chiral-flag parameter has been added to ketcher settings.
Bug Fixes
#2135 – Functional groups can now be merged into nearby structures.
#2169 – A warning in the console that occurred when the About icon was clicked has been fixed.
#2033 – Atoms now properly protrude beyond the expanded view in Abbreviations.
#2026 – The erase tool's hotkey (Del) can now delete arrows and plus signs.
#1456 – The selected file format in the Save Structure window now matches the mockup.
#2110 – The incorrect merging of functional groups has been fixed.
#2257 – It is now possible to add a bond to a Function Group.
#2247 – Clicking outside of a context menu doesn't apply the currently selected tool.
#2216 – The S-Group pop-up tool tip is no longer positioned so that it overlaps the structure.
#2123 – The hover effect now appears after clicking on bonds or atoms.
#1954 – The selected structure now draws at the mouse cursor after closing the Templates window.
#2330 – Atom editing via the right-click menu is now applied.
#2316 – When hovering over the label R/S, the Indigo system information is not visible.
Improvements
#2093 – The s group menus have been combined, and the generic s group has been removed.
#1681 – React has been upgraded to version 18, and react-contextmenu has been replaced with react-contexify.
#1456 – The design of the Save Structure Select has been fixed.
#2241 – The Template window will now open with the previously opened tab.
#1990 – Functional groups now connect with another functional group on click-and-drag.
#2173 – The font size drop-down now collapses.
#2255 – The in-browser module has been migrated to Indigo v1.10.0-rc.4.
#1886 – The keyboard shortcuts for atoms, bonds, zoom, and functions have been changed.
Other Changes
Update bug_report.md - add test case field
#2319 – A previous change that caused an inability to add a bond to a Function Group has been reverted.
#2321 – Indigo v1.10.0-rc.4 has been migrated to the in-browser module.
#2341 – The help.md page has been updated to reflect keyboard shortcut changes.
New Contributors
Full Changelog: v2.8.0...v2.9.0
Contributors
Assets 4
Ketcher 2.8.0 (March 23, 2023)
#2132 Migrate to Indigo v1.10.0-rc.1 in-browser module
#2130 Custom Templates: When drag an abbreviation preview is not hide
#2129 Adding custom s-groups to bonds incorrectly selects atoms instead of the bond by default
#2086 Dragging a selected s-group sometimes duplicates it
#1818 Persist user settings
#2091 Using paste tool (or new template tool) - clearing the canvas causes console errors
#2112 The hand tool is still following the cursor when moving outside the canvas
#1889 Add ability to flip a part of structure
#2108 Input fields in some modals lose focus when typing
#2109 Console error when adding sGroups to canvas
#2104 JS error is thrown, when clicking on a canvas after right click on a bond with "Data S-Group" tool selected
#2043 Thumbnail images are not readable in Template Dialog
#2084 When we double click on the selected atom we get error in console
#2105 Unable to select data s-group type
#1988 Abbreviations: User can make changes to the abbreviations of Functional Groups and Salts and Solvents
#2045 Functional Groups: The functional group is not added to one of the H3C
#2083 Error when deleting stereo bond via context-menu
#1995 Bond context menu: move non-query bonds to 1st level, add dots to Edit item
#2085 Selection is reset when using context menu
#1887 Add s-group data for atom or bond without selection
#2060 Don't break the selection if the user's cursor goes beyond the canvas
#1902 Save hotkey CTRL+S: An atom or structure copied to the clipboard is saved with coordinates
#2051 S-groups are not interactive when cursor is outside of the hover area
#2038 Charge Tool Hot key: Pressing the hot button (5) on an atom applies the opposite charge
#2057 Move enhanced stereochemistry icon to left toolbar
#2065 Remove "Chiral" label from text of absolute flag
#2072 Remove hardcoded ENABLE_POLYMER_EDITOR flag from build scripts
#1951 Selection rectangle is displayed incorrectly for functional groups with longer names
#1987 Ketcher should not display explicit valence for functional groups
#2003 MDL Molfile v2000: Incorrect padding for M ALS
#2035 Changing the logic of interaction with the 'Selection tool' hotkey
#1931 Reagents: An error message appears when opening the file RXN v3000 with reagent
#2040 Template Library: When you select edit any template, the edit window does not appear
#1899 Add right-click menu for atoms
#2049 App crashes, when clicking on "Save" button
#2046 Remove excessive warnings in template dialog
#2011 Reaction Mapping Tool: Manual mapping of atoms does not work
#1872 Add right-click menu for bonds
#1999 S-Group: Hover over the S-Group displays always acetaldehyde
#1836 SMILES format: Structure is missing and a new structure is formed when "Paste from clipboard" or "Open from file" if reaction consists of two or more reaction arrows and structures. #
#1837 RXN files: structure is missing when "Paste from clipboard" or "Open from file" if reaction consists of two or more reaction arrows and structures.
Ketcher 2.7.2 (February 8, 2023)
What's Changed
- #2125: Functional groups get merged into nearby structures by @KonstantinEpam23 in #2188
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Full Changelog: v2.7.1...v2.7.2
