#9065 System shows natural analog category for phosphates by Copilot · Pull Request #9066 · epam/ketcher

Copilot · 2026-01-31T19:39:36Z

How the feature works? / How did you fix the issue?

Rolled back the RNA builder phosphate grouping change and restored package-lock.json to its pre-change state per feedback, keeping the original natural analogue grouping intact.

Rollback: revert useGroupsData.ts to the pre-change behavior.
Cleanup: remove the added hook test.
Dependencies: restore package-lock.json to its original contents.
UI: Screenshot: https://github.com/user-attachments/assets/52f5a79c-1519-4c15-a5bd-c1574d357486

Check list

unit-tests written
e2e-tests written
documentation updated
PR name follows the pattern #1234 – issue name
branch name doesn't contain '#'
PR is linked with the issue
base branch (master or release/xx) is correct
task status changed to "Code review"
reviewers are notified about the pull request

Original prompt

This section details on the original issue you should resolve

<issue_title>System shows natural analog category for phosphates</issue_title>
<issue_description>Steps to Reproduce

Open Macromolecules mode

Go to Library, RNA tab

Open Phosphate section

Actual behavior
System shows natural analog category for phosphates

Expected behavior
System doesn't show natural analog category for phosphates since it is only aplicable for peptides, bases and nucleotides but not for phosphates

Environment details:

Ketcher Version 3.12.0-rc.2 Build at 2026-01-27; 21:09:05

Indigo Version 1.40.0-rc.1.0-g63d8f2068-wasm32-wasm-clang-19.0.0

Chrome Version 144.0.7559.110 (Official Build) (64-bit)

Win11</issue_description>

Comments on the Issue (you are @copilot in this section)

Fixes System shows natural analog category for phosphates #9065

💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

AlexeyGirin · 2026-02-02T11:59:15Z

@copilot please rollback changes from packages/ketcher-macromolecules/src/components/monomerLibrary/RnaBuilder/RnaElementsView/hooks/useGroupsData.ts file

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

Copilot · 2026-02-02T12:14:41Z

@copilot please rollback changes from packages/ketcher-macromolecules/src/components/monomerLibrary/RnaBuilder/RnaElementsView/hooks/useGroupsData.ts file

Rolled back useGroupsData.ts to its pre-change state and removed the added test; latest screenshot: https://github.com/user-attachments/assets/15c00583-a08e-4091-828a-d521355a4b27. Commit: e3d9797.

AlexeyGirin · 2026-02-02T12:16:04Z

@copilot rollback changes from package-lock.json file

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

Copilot · 2026-02-02T12:30:19Z

@copilot rollback changes from package-lock.json file

Rolled back package-lock.json changes; UI reference screenshot: https://github.com/user-attachments/assets/52f5a79c-1519-4c15-a5bd-c1574d357486. Commit: 68947c7.

…/fix-natural-analog-category-phosphates

* Initial plan * chore: plan phosphate category fix Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * fix: hide phosphate natural analogue groups Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * fixes * f2 * f3 * revert: restore RNA phosphate grouping Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * chore: revert package-lock.json Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * fixes * f2 --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> Co-authored-by: Alexey Girin <alexey_girin@epam.com>

* Fixed flaky tests * fixes * f2 * Update Node.js baseline to 22 (#9026) * Initial plan * update node version references Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * #8999 Refactor: Polynomial regular expression used on uncontrolled data (#9000) * Initial plan * Replace regex trimRight with trimEnd Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * #9003 Refactor: React Router vulnerable to XSS via Open Redirects (#9004) * Initial plan * chore: update react-router to 7.13.0 Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * #9005 Refactor: Next library has a Denial of Service with Server Components - Incomplete Fix Follow-Up (#9006) * Initial plan * chore: upgrade next/react for example-ssr Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * #8987 Labels for monomer natural analog category is missing if filter applied (#8992) * Initial plan * fix: always show monomer group titles in RNA accordion Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * limit natural analog titles to relevant monomer groups Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * fixes --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> Co-authored-by: Alexey Girin <alexey_girin@epam.com> * #9011 Refactor: qs arrayLimit bypass mitigation via parent dependency updates (#9015) * Initial plan * Update qs and body-parser overrides Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Update body-parser via parent dependency Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * #9016 Refactor: update js-yaml dependencies to patched versions without overrides (#9019) * Initial plan * chore: override js-yaml to patched versions Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * chore: bump js-yaml patch versions Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * chore: remove js-yaml overrides and update lock Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Align S-Group subtype combobox width and default option visibility (#8979) * Initial plan * Align S-Group subtype combobox width with other selects Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * fix: show selected empty subtype option Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * fixes * - fixed non specified value * - fixed unit tests * fixes --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> Co-authored-by: Alexey Girin <alexey_girin@epam.com> Co-authored-by: Roman Rodionov <roman_rodionov@epam.com> * Refactor: Potential fix for code scanning alert no. 22: Unvalidated dynamic method call (#9001) * Potential fix for code scanning alert no. 22: Unvalidated dynamic method call Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com> * Fix unvalidated dynamic method call in parseSGroup.js (#9002) * Initial plan * Fix unvalidated dynamic method call in parseSGroup.js Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Optimize security fix by moving constants outside function scope Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> --------- Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com> Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * #9022 Refactor: PostCSS line return parsing error (#9023) * Initial plan * chore: fix package.json trailing comma Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * chore: remove postcss override Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Update CI to Node.js 22.11 (#9037) * #9032 - Flex mode icon is active after ketcher close and open again (#9049) (#9052) * #9032 - Flex mode icon is active after ketcher close and open again - added reset mode button state to default on destroy * - updated ketcher version to 3.12.0-rc.2 (cherry picked from commit d721b77) * #9047 - Leaving group atom position is incorrect for nucleotides created in monomer wizard (#9048) (#9051) - fixed leaving group atom position for nucleotides in monomer creation wizard (cherry picked from commit 34ad31d) * #7153 - Molecule from expanded monomer disappars on switching to Macromolecules mode (#8989) * fix dissapearing molecule from expanded monomer * fixed build * create fragment after removing s group * fixed build * removed redundant * added comment * #8974 autotests for ketcher 3110 bugs (#9031) * add cases * add cases and files * update code and screenshoots * remove step about screenshoot * changes after review * some changes for wariningMessageDialog * add changes * add changes after review * Autotests: 8331 autotests axolabs format support (#8339) * First * second * #9065 System shows natural analog category for phosphates (#9066) * Initial plan * chore: plan phosphate category fix Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * fix: hide phosphate natural analogue groups Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * fixes * f2 * f3 * revert: restore RNA phosphate grouping Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * chore: revert package-lock.json Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * fixes * f2 --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> Co-authored-by: Alexey Girin <alexey_girin@epam.com> * Add fragment selection tool and rename structure selection tooltip (#8973) Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> Co-authored-by: Roman Rodionov <roman_rodionov@epam.com> * Backmerge: #9078 - Update the help document (3.12.) (#9079) * Delete documentation/images/S-Group-Properties-3.6.png * Add files via upload * Update help.md * #9084 - Ketcher saves incorrect attachment points configuration for new nucleotides (#9086) (#9088) (cherry picked from commit 5177c79) * - fixed vulnerability (#9100) * #7915 autotests enable flipping of all expanded monomers in a structure (#9083) * add test cases * add description for tests * #8254 Allow for stereo-bonds (up and down) to be a bond between AA and LGA (#9080) * add test cases * add changes * add svg format for macro * add description for the tests * Update the layout method * # 8383 Introduce library searching using HELM aliases, AxoLabs aliases, and modification types (#9059) * add test cases * update screenshoots * add description for tests * update code and screenshot * #9098 autotests alignment of sense and antisense strings in axolabs format (#9101) * add cases * add screenshots and tests * Changed call for page to the BeforeAll fixture. Stabled some flacky tests (#9107) * add cases (#9112) * #9113 The Copolymer S-Group type should not be displayed unless there are at least two structural repeating units (SRUs) in selection (#9117) * Initial plan * Plan for copolymer s-group availability Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Restrict copolymer s-group option Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Address code review feedback Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Refine copolymer option checks Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Simplify copolymer option logic Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Polish copolymer option filtering Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Tighten copolymer availability check Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Trim sgroup memo dependencies Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Simplify copolymer scheme selection Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Type annotate sgroup test helper Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Memoize schemes and count SRUs Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * #7492 - autotests transform isolated test execution to clear canvas test execution for undo redo actionsspects (#9131) * Isolated test execution has been transformed to clear canvas test execution for undo redo actions. * Screenshots updated * #7493 Transformed isolated test execution to clear canvas test execution for right-click.spec.ts (#9133) * #9119 add expects and change repeating code (#9128) * add expects and change repeating code * add changes for failed test * #9108 Incorrect valence for nitrogen (#9124) * Initial plan * Allow nitrogen valence 5 Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * fixes --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> Co-authored-by: Alexey Girin <alexey_girin@epam.com> * #9126 Some keyboard shortcuts don't work on Macromolecules canvas (#9127) * Initial plan * Fix macromolecules hotkeys Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Adjust macromolecule hotkey tests Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Clarify sequence-mode hotkey comment Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Document bond hotkey options Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Refactor bond hotkey helper Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Tidy hotkey comments Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Revert macromolecule hotkey tests Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Fixes --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> Co-authored-by: Alexey Girin <alexey_girin@epam.com> * refactor: reEmage and resimpleObject toggle points logic (#9222) * 9151:constructor should have readonly (#9241) * refactor:use nullish coeliscine (#9242) * Fix attachment point sorting comparator (#9281) * Fix reduce call in DistanceSnapView with initial value (#9268) * test: document intentional noop helper (#9264) * fix(core): avoid unused ClearTool instantiation in test (#9206) * Fix dialog keyboard handler accessibility issue (#9200) * fix(core): make EmptySnakeLayoutNode non-empty (#9265) * #9227 - The return value of "useState" should be destructured and named symmetrically (#9228) * Initial plan * Fix useState asymmetric naming: rename isStuctureChecking to isStructureChecking Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * #9223- Redundant casts and non-null assertions should be avoided (#9224) * Initial plan * Remove redundant TypeScript casts and non-null assertions Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * Fix type errors: properly handle false values and keep necessary cast Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * #9223- remove redundant type assertion for actionmenu --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * #9217 - React props should be read-only (#9219) * Initial plan * Make React props read-only in 5 components Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * Remove package-lock.json from commit * Remove package-lock.json from commit Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * Restore package-lock.json to original state --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * #9211 - Switch cases should end with an unconditional "break" statement (#9212) * Initial plan * Initial analysis - identify switch case fall-through issues Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * Fix switch case fall-through in action/index.js and state/index.js Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * Refactor to reduce code duplication in switch cases Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * Add JSDoc and improve variable naming Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * Revert "Initial analysis - identify switch case fall-through issues" This reverts commit 2286028. --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * #9259 - If statements should not be the only statement in else blocks (#9261) * Initial plan * Refactor: Replace nested if in else block with else if in CoreAtom.ts Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * #9293 Autotests: Cyclic imports in autotests (#9294) * Initial plan * fix(autotests): remove circular imports in tests utilities and monomer dialog Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * refactor(autotests): eliminate remaining cyclic imports in tests Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * refactor(autotests): rollback requested files and replace delay helper calls Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * fixes * f2 --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> Co-authored-by: Alexey Girin <alexey_girin@epam.com> * #9251 - Redundant React fragments should be removed (#9252) * Initial plan * Remove redundant React fragment in ErrorsCheck component Co-authored-by: oguzhanduran <86467364+oguzhanduran@users.noreply.github.com> * Remove package-lock.json changes from PR Co-authored-by: oguzhanduran <86467364+oguzhanduran@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: oguzhanduran <86467364+oguzhanduran@users.noreply.github.com> * #9236 - Ternary operators should not be nested (#9247) * Initial plan * Refactor nested ternary operators in 4 files Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * 9236 - undo changes for package-lock * 9236 - refactor nested arrays for period table * 9236 - extract modification type attribute logic to reusable utility --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * 9167:fixed all branches in a conditional structure should not have exactly same implementation issue (#9230) * #9193:Refactor:(TypeScript) Objects and classes converted or coerced t… (#9196) * 9183:Refactor:(TypeScript) Objects and classes converted or coerced to strings should define * 9183/fix:delete unnecessary file * 9183/refactor:fix according to copilot review comment * fix:remove unused function * 9279: create cross-platform script for app build and run (#9280) * #9298: (TypeScript) Two branches in a conditional structure should not have exactly the same implementation (#9300) * refactor:implement duplicate branch cleanup in 2 reported lications * Revert "refactor:implement duplicate branch cleanup in 2 reported lications" This reverts commit 95dabd1. * refactor two branches same implementations * #9207- Unused React typed props should be removed (#9214) * 9207/fix:remove unused props * fix:refactor accroding comments * fix:rename current to diaog element * #9195 - Refactor: Use optional chaining instead of manual null checks (#9201) * Initial plan * Refactor: Use optional chaining instead of manual null checks Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * Fix prettier formatting issues Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * Fix code review issues: correct atom lookup and improve if statement logic Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * #9195 fix test issues * #9195 fix undo changes for package-lock * 9195 - replace undefineds with null * #9195 - replace null with undefined * #9195 - replace some undefineds with null --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * #9238 - Refactor: (TypeScript) Non-interactive DOM elements should not have interactive ARIA roles (#9262) * Enhance accessibility by adding ARIA roles and attributes to various components * Refactor ARIA roles to improve accessibility and semantic structure in ColorPicker, Form components, and SpecialSymbolsButton * Refactor ColorPicker to streamline ID generation for palette * fix snapshots * 9174: fix selector duplicated issue (#9302) * #9255 - Spacing between inline elements should be explicit (#9256) * Initial plan * Fix ambiguous JSX whitespace in RnaPresetTabs.tsx Co-authored-by: oguzhanduran <86467364+oguzhanduran@users.noreply.github.com> * Use explicit JSX space expression {' '} as per lint rule Co-authored-by: oguzhanduran <86467364+oguzhanduran@users.noreply.github.com> * Format JSX space expression on single line as per image Co-authored-by: oguzhanduran <86467364+oguzhanduran@users.noreply.github.com> * Use regular space instead of {' '} JSX expression Co-authored-by: oguzhanduran <86467364+oguzhanduran@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: oguzhanduran <86467364+oguzhanduran@users.noreply.github.com> * 9162 used collection contents (#9208) * #9209 - Refactor: (JavaScript) Loop counters should not be assigned within the loop body (#9237) * Refactor loop structures to use while instead of for for improved readability in utils.js and v3000.js * Refactor spacebarsplit function for improved readability and maintainability * refactor: update according to Sonar errors (#9272) * #9160-(TypeScript) Unused assignments should be removed (#9226) * 9160/refactor:remove unused assignments * 9160/refactor:remove unused assignments * 9160/refactor:try to pass test in github * remove ubused assignments * fix:remove unnnessacary changes from structeditor * fix:revert * remove unused assigments * refactor:use lodash for form and structeditor * #8187 It is possible to create preset with empty name (#9075) * Initial plan * fix: reject empty monomer group template names Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * fix: keep preset template updates while validating names Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * test: cover whitespace-only preset names Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * fix: clarify empty preset name error text Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * #9276- Literals should not be used for promise rejection #9276iterals should not be used for promise rejection (#9277) * 9276: fix promise rejection for literal usage * normalizeError utility added * added normalizeError utility into all necessary files * #9269: add anput references to labels for iframe in examples (#9275) * refactor: simplify async handling in cut and keydown event methods (#9305) * Support for enhanced stereochemistry markings in macromolecules mode (#9095) * Initial plan * Add stereoLabel support to CoreAtom and AtomRenderer for macromolecules mode Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Fix magic number in positionStereoLabel method Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * fixed size of stereolabel * fixed displaying abs stereoflags * fixed moving stereolabel after moving second bonds atom --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> Co-authored-by: Aleksei Proskurnov <proskurn@gmail.com> * #9282 - Empty collections should not be accessed or iterated (#9284) * Fix empty collection access in sequence tests and sgroup action * Fix: Always initialize `attachmentPoints` as an empty array, disregarding `attrs.attachmentPoints`. * #9218 - Unused methods of React components should be removed (#9221) * refactor analyse dialog to remove unused class methods * refactor: move analyseItems constant outside of Analyse component to prevent re-declaration * #9202 - Make EditorHistory constructor private and add getInstance accessor (#9213) * Fix EditorHistory constructor return by using static accessor * fix: Disable `no-use-before-define` ESLint rule for the `_instance` property. * style: format EditorHistory.update arguments for improved readability. * refactor: improve type safety of EditorHistory singleton by adding an instance type guard. * Update auto_assign.yml to simplify assignee groups (#9270) Removed developers and QA groups from auto assign configuration. * #8896- fix assertion error when adding ket file to canvas (#9315) * #9260 - Refactor: Constructors should not contain asynchronous operations (#9296) * Initial plan * refactor: move async monomers library init out of CoreEditor constructor Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * #9260 - undo the changes on package-lock --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> * Introducing rotation of monomers in Macromolecules mode (#9094) * Initial plan * Add rotation and flip functionality for monomers in Macromolecules mode Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Add interactive rotation handle functionality with 15° snapping Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> * Address code review feedback: extract constants, improve comments Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> Co-authored-by: Roman Rodionov <roman_rodionov@epam.com> * fixes * f2 * f3 * f5 * f6 --------- Co-authored-by: Ieva Bendikiene <bendikiene16@gmail.com> Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com> Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com> Co-authored-by: Roman Rodionov <roman_rodionov@epam.com> Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com> Co-authored-by: aproskurnov <proskurn@gmail.com> Co-authored-by: AnnaKosol <annakosolapova24@gmail.com> Co-authored-by: Ljubica Milovic <ljubica_milovic@epam.com> Co-authored-by: Pavel Lukin <124054458+zefiris87@users.noreply.github.com> Co-authored-by: Yaroslav Kovalsky <71060724+YatsekTest@users.noreply.github.com> Co-authored-by: SergeiBakirov <sergei_bakirov@epam.com> Co-authored-by: Yurii Danylenko <Givchik228@gmail.com> Co-authored-by: Gulia <83670176+guliaisaeva@users.noreply.github.com> Co-authored-by: azamatalt <108387789+azamatalt@users.noreply.github.com> Co-authored-by: beyzaevcen <95762073+beyzaevcen@users.noreply.github.com> Co-authored-by: oguzhanduran <86467364+oguzhanduran@users.noreply.github.com> Co-authored-by: Yurii Danylenko <yurii_danylenko@epam.com> Co-authored-by: umutzd-alt <umutozdemir997@outlook.com>

Initial plan

218d385

Copilot AI assigned Copilot and AlexeyGirin Jan 31, 2026

Copilot started work on behalf of AlexeyGirin January 31, 2026 19:39

View session

Copilot AI and others added 2 commits January 31, 2026 19:43

chore: plan phosphate category fix

ec66c05

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

fix: hide phosphate natural analogue groups

bbb32a9

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

Copilot AI changed the title ~~[WIP] Fix natural analog category display for phosphates~~ Hide natural analogue grouping for RNA phosphates Jan 31, 2026

Copilot AI requested a review from AlexeyGirin January 31, 2026 20:36

Copilot finished work on behalf of AlexeyGirin January 31, 2026 20:36

fixes

0afd424

AlexeyGirin marked this pull request as ready for review January 31, 2026 20:54

auto-assign Bot requested review from NataliaLoginova, Zhirnoff and svvald January 31, 2026 20:54

AlexeyGirin added Fixed by ChatGPT5 Ready for approve labels Jan 31, 2026

AlexeyGirin added 2 commits February 1, 2026 16:08

f2

c142c4c

f3

d2e6d69

AlexeyGirin changed the title ~~Hide natural analogue grouping for RNA phosphates~~ #9065 System shows natural analog category for phosphates Feb 1, 2026

Copilot started work on behalf of AlexeyGirin February 2, 2026 11:59

View session

revert: restore RNA phosphate grouping

e3d9797

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

Copilot AI changed the title ~~#9065 System shows natural analog category for phosphates~~ Rollback RNA phosphate grouping change Feb 2, 2026

Copilot finished work on behalf of AlexeyGirin February 2, 2026 12:15

Copilot started work on behalf of AlexeyGirin February 2, 2026 12:16

View session

chore: revert package-lock.json

68947c7

Co-authored-by: AlexeyGirin <26869421+AlexeyGirin@users.noreply.github.com>

Copilot AI changed the title ~~Rollback RNA phosphate grouping change~~ Rollback RNA phosphate grouping change and package-lock updates Feb 2, 2026

Copilot finished work on behalf of AlexeyGirin February 2, 2026 12:30

AlexeyGirin added 2 commits February 2, 2026 16:18

Merge branch 'master' of https://github.com/epam/ketcher into copilot…

e6f9085

…/fix-natural-analog-category-phosphates

fixes

277d4ca

AlexeyGirin changed the title ~~Rollback RNA phosphate grouping change and package-lock updates~~ #9065 System shows natural analog category for phosphates Feb 2, 2026

f2

8c79377

AlexeyGirin requested review from rrodionov91 and removed request for AlexeyGirin, NataliaLoginova and Zhirnoff February 2, 2026 15:48

rrodionov91 approved these changes Feb 2, 2026

View reviewed changes

rrodionov91 merged commit 4d92f18 into master Feb 2, 2026
15 checks passed

rrodionov91 deleted the copilot/fix-natural-analog-category-phosphates branch February 2, 2026 16:27

Navigation Menu

Repository navigation

#9065 System shows natural analog category for phosphates - #9066

#9065 System shows natural analog category for phosphates#9066
rrodionov91 merged 11 commits into
masterfrom
copilot/fix-natural-analog-category-phosphates

Copilot AI commented Jan 31, 2026 •

edited

Loading

Uh oh!

AlexeyGirin commented Feb 2, 2026

Uh oh!

Copilot AI commented Feb 2, 2026

Uh oh!

AlexeyGirin commented Feb 2, 2026

Uh oh!

Copilot AI commented Feb 2, 2026

Uh oh!

Uh oh!

Reviewers

Uh oh!

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

Conversation

Copilot AI commented Jan 31, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

How the feature works? / How did you fix the issue?

Check list

Comments on the Issue (you are @copilot in this section)

Uh oh!

AlexeyGirin commented Feb 2, 2026

Uh oh!

Copilot AI commented Feb 2, 2026

Uh oh!

AlexeyGirin commented Feb 2, 2026

Uh oh!

Copilot AI commented Feb 2, 2026

Uh oh!

Uh oh!

Reviewers

Uh oh!

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

Copilot AI commented Jan 31, 2026 •

edited

Loading