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CopilotAlexeyGirinKristinaKasyanovskayasvvaldViktoriaTkacheva
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#5580 - Order of sections for ambiguous bases is wrong - Ambiguous Bases should come first (#8264)
* Initial plan * Fix order of ambiguous bases sections to match requirements Co-authored-by: AlexeyGirin <[email protected]> * fixes * #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label (#8266) * fix: send render-stereo-style per settings; align PNG/SVG with canvas * fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability * Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272) * Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277) * Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280) * Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275) * The function moveOnBond is replaced with getBondLocator.hover() (#8298) The functions declaration of moveOnBond and waitForElementInCanvas are removed * #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252) * First draft * f22 * f3 * f4 * * Initial plan * Disable Symbol and Name fields when Type is not selected Co-authored-by: AlexeyGirin <[email protected]> * Add test to verify Symbol and Name fields are disabled when Type is not selected Co-authored-by: AlexeyGirin <[email protected]> * fixes --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190) * Initial plan * Fix: Update tooltip to show 'minimize window' when expanded Co-authored-by: AlexeyGirin <[email protected]> * fixes * f2 * f3 * f4 * f5 --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * Refactor: #8158 - Replace this union type with a type alias (#8159) * Initial plan * Refactor: Replace union types with type aliases Co-authored-by: AlexeyGirin <[email protected]> * Fix: Remove unused imports after type alias refactoring Co-authored-by: AlexeyGirin <[email protected]> * Fix: Remove unused BackBoneSequenceNode import Co-authored-by: AlexeyGirin <[email protected]> * fixes --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * Refactor: #8168 - Selectors should not be duplicated (#8169) * Initial plan * Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * feat(PO): add ReactionAutoMappingDialog page object (#8244) - Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog. - Introduced `constants.ts` with `AutoMapModeOption` enum. - Removed `applyAutoMapMode` function from `index.ts`. - Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function. - Updated screenshots accordingly. * Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238) * - add test; - add test file; - add screenshots * - add tests; - add screenshots * - add tests; - add test file; - add screenshots * - add tests for API switching from molecules mode to macromolecules; - add screenshots * - delete exeptions * - add test; - add screenshot * #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232) * Initial plan * Add grabbing cursor when dragging monomers from library Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * fixes --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Ivan Maslov <[email protected]> Co-authored-by: Mikhail Zhirnov <[email protected]> * Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279) * #8294 - Do allow to collapse s-groups (superatom type) without name (#8297) * Initial plan * Disable Contract Abbreviation for s-groups without name Co-authored-by: AlexeyGirin <[email protected]> * Use optional chaining to safely check name property Co-authored-by: AlexeyGirin <[email protected]> * Simplify empty name check using optional chaining Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #7936 - Add tooltips to some attachment points in the monomer creation wizard * Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321) * first * 2 * 3 * 10 * 11 * 12 * 13 * 14 * 1111 * Final * f2 * Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320) * - add tests; - add test files; - add screenshots * - add tests; - add test files; - add screenshots * - add tests; - add screenshots * Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324) * #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) * #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module * Update autotests * Update more autotests * Skip failing tests (cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7) * fix --------- Co-authored-by: Nikita Chistousov <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038) * Autotests: 8322 autotests axolabs format support (#8329) * first * Final * Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278) * Backmerge: #8005 – Changing name for attachment points works wrong (#8282) * #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8343) * fix: fix buttons logic * fix: fix primary button logic * #8296 - Make Create Monomer tool disableable (#8346) (#8348) - made create-monomer functionality disableable using buttons config - bumped ketcher to 3.9.0-rc.3 (cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b) * Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148) * Initial plan * Refactor: Replace logical OR (||) with nullish coalescing (??) operator Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218) * Initial plan * Fix Promise rejection to use Error object in FileInputForm Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219) * Initial plan * Fix Promise rejections to use Error objects in remoteStructService Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220) * Initial plan * Refactor: Wrap FileReader error event in Error object for Promise rejection Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349) * fix: menu option mark as connection point disabled * test: fix test * fix: prevent modification list overflow in monomer preview tooltip (#8350) * #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342) * fix: fix Modification drop-down list * fix: fix add-modification-type option * fix: fix error message * fix: add limit on the modififcations fields * #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode * Autotests: 8345 autotests sdf files for librarymonomer information (#8347) * getTopBondByAttributes removal * mapTwoAtoms update * getBottomBondByAttributes removal * fix * Some functions removed * Removing getBottomAtomByAttributes * removing getFirstAtomCoordinatesByAttributes * arrow and plus corrections * removing clickOnPlus * f * f2 * f3 * f4 * Some clean up * fix * а2 * f3 * f4 * some clean up * scu2 * f5 * f6 * f7 * draft * draft2 * Final * fix * f2 * f3 * f4 * f5 * f6 * f7 * f8 * f9 * f10 * f11 * f12 * f13 * f14 * f15 * f16 * f17 * f18 * f19 * f20 * f21 * f22 * f23 * f24 * f25 * f26 * f27 * f28 * Autotests: 8361 autotests some refactoring (#8362) * first * f2 * f3 * f4 * f5 * f6 * f7 * f8 * f9 * f10 * #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360) * - added helm alias field to monomer wizard * - added helm alias field validation * - removed helm alias field from chems * Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372) * - add tests; - add screenshots * - add tests; - add screenshots * - add tests; - add screenshots * - update tests; - add test files; - delete unused 'testData.ts' * Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370) * The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1) * The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2) The function declaration of doubleClickOnBond is removed * #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378) * Initial plan * Add data-topology and data-reacting-center attributes for bonds Co-authored-by: AlexeyGirin <[email protected]> * Improve error handling in getBondFromMoleculeStruct with descriptive comment Co-authored-by: AlexeyGirin <[email protected]> * Improve code quality based on review feedback - simplify null checks and enhance comments Co-authored-by: AlexeyGirin <[email protected]> * fixes * f2 --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375) * Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964) - Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click) - Updated tests: - `atom-properties.spec.ts` - `Template-manipulations.spec.ts` - `right-click.spec.ts` - Replaced direct `getByLabel` usage with `fillLabel` calls: - via new `LabelEditDialog` for long-click cases - via existing `AtomPropertiesDialog` for double-click or context-menu cases * autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests - Implemented longClickOnAtom helper in index.ts - Added setLabel method in LabelEditDialog - Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it - Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review) * Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure * #8200 - Add parameter to Editor to disable saving new monomers to local storage (#8364) * fix: add parameter to Editor to disable saving new monomers to local storage * fix:make monomer library persistence opt‑in via shouldPersist * #7971 - Update the help document (3.9.) (#8384) * Delete documentation/images/FG_chain.gif * Delete documentation/images/Macro-canvas-3.8..png * Delete documentation/images/Library-Tabs-3.8..png * Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png * Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png * Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png * Delete documentation/images/New-Monomer-Micro-3.7..png * Delete documentation/images/New-Monomer-Macro-3.7..png * Delete documentation/images/New-Monomer-Library-3.7..png * Delete documentation/images/Open-Structure-Macro-2-3.0..png * Add files via upload * Update help.md * Update help.md typos * #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892) * #7553 fix fullscreen mode switching dropdown * #7553 fex: implement popup fullscreen mode with proper top-layer targeting * #7553 fix test * fix test * #7553 Remove ref to custom class * #7553 Refactor * #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons (#8365) * fix: add scroll im monomer wizart in popup * fix: fix styles * Autotests: 8376 autotests some refactoring (#8381) * First * f2 * f3 * f4 * f5 * f6 * #8200 - Add parameter to Editor to disable saving new monomers to local storage (#8364) * fix: add parameter to Editor to disable saving new monomers to local storage * fix:make monomer library persistence opt‑in via shouldPersist * #7971 - Update the help document (3.9.) (#8384) * Delete documentation/images/FG_chain.gif * Delete documentation/images/Macro-canvas-3.8..png * Delete documentation/images/Library-Tabs-3.8..png * Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png * Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png * Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png * Delete documentation/images/New-Monomer-Micro-3.7..png * Delete documentation/images/New-Monomer-Macro-3.7..png * Delete documentation/images/New-Monomer-Library-3.7..png * Delete documentation/images/Open-Structure-Macro-2-3.0..png * Add files via upload * Update help.md * Update help.md typos * #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892) * #7553 fix fullscreen mode switching dropdown * #7553 fex: implement popup fullscreen mode with proper top-layer targeting * #7553 fix test * fix test * #7553 Remove ref to custom class * #7553 Refactor * #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons (#8365) * fix: add scroll im monomer wizart in popup * fix: fix styles * f7 --------- Co-authored-by: Kristina <[email protected]> Co-authored-by: Ljubica Milovic <[email protected]> Co-authored-by: KukushkinDmi1riy <[email protected]> * #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388) * #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module * fixes * f2 * f3 --------- Co-authored-by: Alexey Girin <[email protected]> * #8281 - Adjust subscription to library update event of Ketcher API (#8382) * #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225) * Initial plan * Refactor nested ternary in Analyse.jsx into separate method Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224) * Initial plan * Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223) * Initial plan * Refactor: Extract nested ternary operations into independent functions Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222) * Initial plan * Refactor nested ternary operations into if-else statements Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371) * #7905 – Change selection logic * #7905 – Enable Indigo functions * #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point * #7905 – Support undo/redo for reassign attachment point operation * #7905 – Support undo/redo for reassign leaving atom operation * #7905 – Support undo/redo for assign attachment atom operation * #7905 – Fix build failure * #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard * #7905 – Enable layout and clenaup tools, add label to HELM alias input * #7905 – Revert initial notification change * #7905 – Update screenshots * #7905 – Update screenshots * #7905 – Remove outdated test cases * #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288) * Initial plan * Fix sorting of mixed base percentages in tooltip Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336) * #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode * #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure” * #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements * #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met * #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors --------- Co-authored-by: Nikita Chistousov <[email protected]> * #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233) * Initial plan * Fix bond direction change in context menu for stereo bonds Co-authored-by: AlexeyGirin <[email protected]> * Simplify bond type check logic * Fix return statement formatting in useBondTypeChange --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * #8351 Autotests for Ketcher 3.9.0 bugs (#8391) * First draft * Autotests: 8376 autotests some refactoring (#8381) * First * f2 * f3 * f4 * f5 * f6 * #8200 - Add parameter to Editor to disable saving new monomers to local storage (#8364) * fix: add parameter to Editor to disable saving new monomers to local storage * fix:make monomer library persistence opt‑in via shouldPersist * #7971 - Update the help document (3.9.) (#8384) * Delete documentation/images/FG_chain.gif * Delete documentation/images/Macro-canvas-3.8..png * Delete documentation/images/Library-Tabs-3.8..png * Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png * Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png * Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png * Delete documentation/images/New-Monomer-Micro-3.7..png * Delete documentation/images/New-Monomer-Macro-3.7..png * Delete documentation/images/New-Monomer-Library-3.7..png * Delete documentation/images/Open-Structure-Macro-2-3.0..png * Add files via upload * Update help.md * Update help.md typos * #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892) * #7553 fix fullscreen mode switching dropdown * #7553 fex: implement popup fullscreen mode with proper top-layer targeting * #7553 fix test * fix test * #7553 Remove ref to custom class * #7553 Refactor * #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons (#8365) * fix: add scroll im monomer wizart in popup * fix: fix styles * f7 --------- Co-authored-by: Kristina <[email protected]> Co-authored-by: Ljubica Milovic <[email protected]> Co-authored-by: KukushkinDmi1riy <[email protected]> * #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388) * #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module * fixes * f2 * f3 --------- Co-authored-by: Alexey Girin <[email protected]> * draft * 2 * 3 * 4 * 5 * 6 * 7 * #8281 - Adjust subscription to library update event of Ketcher API (#8382) * #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225) * Initial plan * Refactor nested ternary in Analyse.jsx into separate method Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224) * Initial plan * Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223) * Initial plan * Refactor: Extract nested ternary operations into independent functions Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222) * Initial plan * Refactor nested ternary operations into if-else statements Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371) * #7905 – Change selection logic * #7905 – Enable Indigo functions * #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point * #7905 – Support undo/redo for reassign attachment point operation * #7905 – Support undo/redo for reassign leaving atom operation * #7905 – Support undo/redo for assign attachment atom operation * #7905 – Fix build failure * #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard * #7905 – Enable layout and clenaup tools, add label to HELM alias input * #7905 – Revert initial notification change * #7905 – Update screenshots * #7905 – Update screenshots * #7905 – Remove outdated test cases * #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288) * Initial plan * Fix sorting of mixed base percentages in tooltip Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336) * #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode * #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure” * #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements * #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met * #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors --------- Co-authored-by: Nikita Chistousov <[email protected]> * #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233) * Initial plan * Fix bond direction change in context menu for stereo bonds Co-authored-by: AlexeyGirin <[email protected]> * Simplify bond type check logic * Fix return statement formatting in useBondTypeChange --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * fixes * f2 * f3 * f4 --------- Co-authored-by: Kristina <[email protected]> Co-authored-by: Ljubica Milovic <[email protected]> Co-authored-by: KukushkinDmi1riy <[email protected]> Co-authored-by: Nikita Chistousov <[email protected]> Co-authored-by: Copilot <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Roman Rodionov <[email protected]> * Refactor: #8153 - Deprecated APIs should not be used (part 2) (#8154) * Initial plan * Replace deprecated APIs with modern alternatives - Replace all substr() calls with slice() in v3000.js - Replace readAsBinaryString() with readAsArrayBuffer() in fileOpener.js - Replace document.execCommand() and document.queryCommandSupported() with Clipboard API checks in cliparea.jsx Co-authored-by: AlexeyGirin <[email protected]> * f1 --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * Autotests: #7958 - autotests get rid of clickonbond function and replace it with getbondlocatorclick (#8409) * The function clickOnBond is replaced with getBondLocator.click() The function declaration of clickOnBond is removed * The BondType and getBondByIndex are removed from import * #7148 - Number of selected elements in context menu is wrong for sense/antisense chain (#8317) * Initial plan * Fix selection count for sense/antisense chains Co-authored-by: AlexeyGirin <[email protected]> * Fix ESLint error in test Co-authored-by: AlexeyGirin <[email protected]> * Address code review: Use proper type assertion instead of any Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #7735 - System shows inner circles of aromatized benzene rings from collapsed monomers on Molecules canvas (#8197) * Initial plan * Fix aromatic circle rendering for collapsed monomers Added check in ReLoop.show() to skip rendering aromatic circles when all atoms in the loop belong to a contracted MonomerMicromolecule. This prevents internal benzene ring circles from showing when collapsed monomers are displayed in Molecules mode. Co-authored-by: AlexeyGirin <[email protected]> * fixes * f2 * #7500 - Update the monomer preview (#8134) * feat: update the monomer preview * fix: fix code after review * test:update snapshots * test:update snapshots * test:update spanshots * test:update spanshots * test:update spanshots * test: update snapshots * Refactor: #8130 - Fix for many sonar issues (#8131) * Fix accessibility and spacing issues from Sonar reports * fixes * f2 * f3 * f4 * Fix accessibility and spacing issues from Sonar reports * f5 * f6 * f7 * f8 * f9 * f10 * f11 * Refactor: #8093 - Unexpected unknown property "user-focus" (#8094) * Initial plan * Remove invalid CSS property 'user-focus' from RulerArea.module.less Co-authored-by: AlexeyGirin <[email protected]> * Apply prettier formatting to RulerArea.module.less Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * Refactor: #8103 - Use 'String#startsWith' method instead (#8119) * Initial plan * Refactor: #8103 - Use 'String#startsWith' method instead Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * Refactor: Add readonly modifiers to fields only assigned in constructors (part 2) (#8146) * Initial plan * Add readonly modifiers to fields that are only assigned in constructors Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * Refactor: #8151 - Type constituents of unions and intersections should not be redundant (#8152) * Initial plan * Fix redundant types in unions and intersections Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * Refactor: #8160 - Unnecessary constructors should be removed (#8161) * Initial plan * Refactor: Remove unnecessary empty constructors Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * Refactor: #8162 - Make this public static property readonly (#8163) * Initial plan * Add readonly qualifier to public static viewName properties Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * Refactor: #8164 - Duplicated font names should be removed (#8165) * Initial plan * Remove duplicated font names in globals.css Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * Refactor: #8156 - Promises should not be misused (#8170) * Initial plan * Fix promise misuse in fullscreen APIs and async event handler Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * Refactor: #8099 - Remove this redundant type alias and replace its occurrences with "any" (#8171) * Initial plan * Remove redundant type aliases and replace with underlying types Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #4467 - Macro: Ket label should be renamed to Ket Format (#8191) * Initial plan * Rename Ket label to Ket Format in macromolecule editor Co-authored-by: AlexeyGirin <[email protected]> * Fixes * f2 * f3 --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * #7746 - System replace few spaces in monomer name to one space on monomer preview (#8192) * Initial plan * Fix monomer name spacing in preview tooltip by adding white-space: pre-wrap Co-authored-by: AlexeyGirin <[email protected]> * Also fix spacing in AmbiguousMonomerPreview ContentLine Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #7421 - "Ghost image" of CHEM is white (different from "ghost image" of other monomer types) (#8196) * Initial plan * Fix CHEM ghost image color issue Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8067 - Do not save added or updated monomer in local storage (#8135) (#8140) (cherry picked from commit 3474573d9e92d3a64ed305161e126b99f2a0eb76) * #7740 - System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard (#8194) * Initial plan * Disable Symbol and Name fields when Type is not selected Co-authored-by: AlexeyGirin <[email protected]> * Add test to verify Symbol and Name fields are disabled when Type is not selected Co-authored-by: AlexeyGirin <[email protected]> * fixes --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190) * Initial plan * Fix: Update tooltip to show 'minimize window' when expanded Co-authored-by: AlexeyGirin <[email protected]> * fixes * f2 * f3 * f4 * f5 --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * Refactor: #8158 - Replace this union type with a type alias (#8159) * Initial plan * Refactor: Replace union types with type aliases Co-authored-by: AlexeyGirin <[email protected]> * Fix: Remove unused imports after type alias refactoring Co-authored-by: AlexeyGirin <[email protected]> * Fix: Remove unused BackBoneSequenceNode import Co-authored-by: AlexeyGirin <[email protected]> * fixes --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * Refactor: #8168 - Selectors should not be duplicated (#8169) * Initial plan * Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * feat(PO): add ReactionAutoMappingDialog page object (#8244) - Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog. - Introduced `constants.ts` with `AutoMapModeOption` enum. - Removed `applyAutoMapMode` function from `index.ts`. - Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function. - Updated screenshots accordingly. * Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238) * - add test; - add test file; - add screenshots * - add tests; - add screenshots * - add tests; - add test file; - add screenshots * - add tests for API switching from molecules mode to macromolecules; - add screenshots * - delete exeptions * - add test; - add screenshot * #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232) * Initial plan * Add grabbing cursor when dragging monomers from library Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #5570 - PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label (#8266) * fix: send render-stereo-style per settings; align PNG/SVG with canvas * fix: replace nested ternary with if/else in getSerilizedServerOptions (renderStereoStyle) for readability * Backmerge: #8040 – R2 attachment point is missing for vinU monomer (#8272) * Backmerge: #7978 – Create monomer process changes atom of not related part of the molecule (#8277) * Backmerge: #8002 – No validation message shown for minimal monomer structure in Monomer Wizard (#8280) * Backmerge: #8070 – Existing Presets in the library disappear after adding new preset via API (#8275) * The function moveOnBond is replaced with getBondLocator.hover() (#8298) The functions declaration of moveOnBond and waitForElementInCanvas are removed * #7984 autotests allow for modification of the attachment points in the monomer creation wizard part 2 (#8252) * First draft * f22 * f3 * f4 * * Initial plan * Disable Symbol and Name fields when Type is not selected Co-authored-by: AlexeyGirin <[email protected]> * Add test to verify Symbol and Name fields are disabled when Type is not selected Co-authored-by: AlexeyGirin <[email protected]> * fixes --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * #3742 - Macro: Wrong tooltip for "minimize window" button (shows "expand window") (#8190) * Initial plan * Fix: Update tooltip to show 'minimize window' when expanded Co-authored-by: AlexeyGirin <[email protected]> * fixes * f2 * f3 * f4 * f5 --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * Refactor: #8158 - Replace this union type with a type alias (#8159) * Initial plan * Refactor: Replace union types with type aliases Co-authored-by: AlexeyGirin <[email protected]> * Fix: Remove unused imports after type alias refactoring Co-authored-by: AlexeyGirin <[email protected]> * Fix: Remove unused BackBoneSequenceNode import Co-authored-by: AlexeyGirin <[email protected]> * fixes --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * Refactor: #8168 - Selectors should not be duplicated (#8169) * Initial plan * Fix duplicate CSS/LESS selectors in globals.css and Accordion.module.less Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * feat(PO): add ReactionAutoMappingDialog page object (#8244) - Added `ReactionAutoMappingDialog.ts` PO for reaction auto-mapping dialog. - Introduced `constants.ts` with `AutoMapModeOption` enum. - Removed `applyAutoMapMode` function from `index.ts`. - Updated tests (`image-files.spec.ts`, `reaction-am-tool-veryfing-button.spec.ts`) to use PO instead of old function. - Updated screenshots accordingly. * Autotests: #7996 - autotests tests for expanding the snap functionality to monomer groups inside of a structure (#8238) * - add test; - add test file; - add screenshots * - add tests; - add screenshots * - add tests; - add test file; - add screenshots * - add tests for API switching from molecules mode to macromolecules; - add screenshots * - delete exeptions * - add test; - add screenshot * #7373 - "Grabbing hand" mouse cursor is absent on grabbing monomers from the library (#8232) * Initial plan * Add grabbing cursor when dragging monomers from library Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * fixes --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Ivan Maslov <[email protected]> Co-authored-by: Mikhail Zhirnov <[email protected]> * Backmerge: #8000 – Monomer Wizard allows creation of monomer with Functional Group (#8279) * #8294 - Do allow to collapse s-groups (superatom type) without name (#8297) * Initial plan * Disable Contract Abbreviation for s-groups without name Co-authored-by: AlexeyGirin <[email protected]> * Use optional chaining to safely check name property Co-authored-by: AlexeyGirin <[email protected]> * Simplify empty name check using optional chaining Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #7936 - Add tooltips to some attachment points in the monomer creation wizard * Autotests: #8268 autotests continuation of attachment points editing in the monomer creation wizard (#8321) * first * 2 * 3 * 10 * 11 * 12 * 13 * 14 * 1111 * Final * f2 * Autotests: #8239 - autotests tests for improving snake layout logic to include small molecules (#8320) * - add tests; - add test files; - add screenshots * - add tests; - add test files; - add screenshots * - add tests; - add screenshots * Backmerge: #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) (#8324) * #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module (#8271) * #8270 – Migrate to Indigo v1.37.0-rc.2 in-browser module * Update autotests * Update more autotests * Skip failing tests (cherry picked from commit b060f735c154dbb2b8c292f78c8409e6199000a7) * fix --------- Co-authored-by: Nikita Chistousov <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8038) * Autotests: 8322 autotests axolabs format support (#8329) * first * Final * Backmerge: #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine) (#8278) * Backmerge: #8005 – Changing name for attachment points works wrong (#8282) * #7932 - Add warning messages to the monomer creation wizard in case of unusual leaving group atoms (#8343) * fix: fix buttons logic * fix: fix primary button logic * #8296 - Make Create Monomer tool disableable (#8346) (#8348) - made create-monomer functionality disableable using buttons config - bumped ketcher to 3.9.0-rc.3 (cherry picked from commit aff299e32b9aee2dd502ca82ad4ab70e607aac9b) * Refactor: Replace logical OR (||) with nullish coalescing (??) operator for safer default values (#8148) * Initial plan * Refactor: Replace logical OR (||) with nullish coalescing (??) operator Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8214 - Refactor: Expected the Promise rejection reason to be an Error (part 1) (#8218) * Initial plan * Fix Promise rejection to use Error object in FileInputForm Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8215 - Refactor: Expected the Promise rejection reason to be an Error (part 2) (#8219) * Initial plan * Fix Promise rejections to use Error objects in remoteStructService Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8216 - Refactor: Expected the Promise rejection reason to be an Error (part 3) (#8220) * Initial plan * Refactor: Wrap FileReader error event in Error object for Promise rejection Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #7997 - For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled (#8349) * fix: menu option mark as connection point disabled * test: fix test * fix: prevent modification list overflow in monomer preview tooltip (#8350) * #8328 - Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically) (#8342) * fix: fix Modification drop-down list * fix: fix add-modification-type option * fix: fix error message * fix: add limit on the modififcations fields * #8334 -Preview: Ketcher crashes completely when switching from Wizard mode to Macro mode * Autotests: 8345 autotests sdf files for librarymonomer information (#8347) * getTopBondByAttributes removal * mapTwoAtoms update * getBottomBondByAttributes removal * fix * Some functions removed * Removing getBottomAtomByAttributes * removing getFirstAtomCoordinatesByAttributes * arrow and plus corrections * removing clickOnPlus * f * f2 * f3 * f4 * Some clean up * fix * а2 * f3 * f4 * some clean up * scu2 * f5 * f6 * f7 * draft * draft2 * Final * fix * f2 * f3 * f4 * f5 * f6 * f7 * f8 * f9 * f10 * f11 * f12 * f13 * f14 * f15 * f16 * f17 * f18 * f19 * f20 * f21 * f22 * f23 * f24 * f25 * f26 * f27 * f28 * Autotests: 8361 autotests some refactoring (#8362) * first * f2 * f3 * f4 * f5 * f6 * f7 * f8 * f9 * f10 * #7928 - Allow for setting of HELM alias in the monomer creation wizard (#8360) * - added helm alias field to monomer wizard * - added helm alias field validation * - removed helm alias field from chems * Autotests: #8341 - autotests tests for add ability to update monomers library api in sdf format (#8372) * - add tests; - add screenshots * - add tests; - add screenshots * - add tests; - add screenshots * - update tests; - add test files; - delete unused 'testData.ts' * Autotests: #7960 - autotests get rid of doubleclickonbond function and replace it with getbondlocatordblclick (#8370) * The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 1) * The function doubleClickOnBond is replaced with getBondLocator.dblclick(part 2) The function declaration of doubleClickOnBond is removed * #8377 - Add data-topology and data-reacting-center attributes for bonds (#8378) * Initial plan * Add data-topology and data-reacting-center attributes for bonds Co-authored-by: AlexeyGirin <[email protected]> * Improve error handling in getBondFromMoleculeStruct with descriptive comment Co-authored-by: AlexeyGirin <[email protected]> * Improve code quality based on review feedback - simplify null checks and enhance comments Co-authored-by: AlexeyGirin <[email protected]> * fixes * f2 --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#8375) * Autotests: #7964 - add LabelEditDialog page object and update atom editing tests (#7964) - Added new PO `LabelEditDialog.ts` for label editing modal (opened via long left click) - Updated tests: - `atom-properties.spec.ts` - `Template-manipulations.spec.ts` - `right-click.spec.ts` - Replaced direct `getByLabel` usage with `fillLabel` calls: - via new `LabelEditDialog` for long-click cases - via existing `AtomPropertiesDialog` for double-click or context-menu cases * autotests(#7964): add longClickOnAtom and setLabel, refactor label editing tests - Implemented longClickOnAtom helper in index.ts - Added setLabel method in LabelEditDialog - Updated atom-properties.spec.ts and view-only-mode.spec.ts to reuse it - Used setOptions instead of fillLabel+apply in template-manipulations.spec.ts (per review) * Removed no used import pressButton from is-query-structure-selected.spec.ts, because of git push failure * #8200 - Add parameter to Editor to disable saving new monomers to local storage (#8364) * fix: add parameter to Editor to disable saving new monomers to local storage * fix:make monomer library persistence opt‑in via shouldPersist * #7971 - Update the help document (3.9.) (#8384) * Delete documentation/images/FG_chain.gif * Delete documentation/images/Macro-canvas-3.8..png * Delete documentation/images/Library-Tabs-3.8..png * Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png * Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png * Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png * Delete documentation/images/New-Monomer-Micro-3.7..png * Delete documentation/images/New-Monomer-Macro-3.7..png * Delete documentation/images/New-Monomer-Library-3.7..png * Delete documentation/images/Open-Structure-Macro-2-3.0..png * Add files via upload * Update help.md * Update help.md typos * #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892) * #7553 fix fullscreen mode switching dropdown * #7553 fex: implement popup fullscreen mode with proper top-layer targeting * #7553 fix test * fix test * #7553 Remove ref to custom class * #7553 Refactor * #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons (#8365) * fix: add scroll im monomer wizart in popup * fix: fix styles * Autotests: 8376 autotests some refactoring (#8381) * First * f2 * f3 * f4 * f5 * f6 * #8200 - Add parameter to Editor to disable saving new monomers to local storage (#8364) * fix: add parameter to Editor to disable saving new monomers to local storage * fix:make monomer library persistence opt‑in via shouldPersist * #7971 - Update the help document (3.9.) (#8384) * Delete documentation/images/FG_chain.gif * Delete documentation/images/Macro-canvas-3.8..png * Delete documentation/images/Library-Tabs-3.8..png * Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png * Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png * Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png * Delete documentation/images/New-Monomer-Micro-3.7..png * Delete documentation/images/New-Monomer-Macro-3.7..png * Delete documentation/images/New-Monomer-Library-3.7..png * Delete documentation/images/Open-Structure-Macro-2-3.0..png * Add files via upload * Update help.md * Update help.md typos * #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892) * #7553 fix fullscreen mode switching dropdown * #7553 fex: implement popup fullscreen mode with proper top-layer targeting * #7553 fix test * fix test * #7553 Remove ref to custom class * #7553 Refactor * #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons (#8365) * fix: add scroll im monomer wizart in popup * fix: fix styles * f7 --------- Co-authored-by: Kristina <[email protected]> Co-authored-by: Ljubica Milovic <[email protected]> Co-authored-by: KukushkinDmi1riy <[email protected]> * #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388) * #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module * fixes * f2 * f3 --------- Co-authored-by: Alexey Girin <[email protected]> * #8281 - Adjust subscription to library update event of Ketcher API (#8382) * #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225) * Initial plan * Refactor nested ternary in Analyse.jsx into separate method Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224) * Initial plan * Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223) * Initial plan * Refactor: Extract nested ternary operations into independent functions Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222) * Initial plan * Refactor nested ternary operations into if-else statements Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371) * #7905 – Change selection logic * #7905 – Enable Indigo functions * #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point * #7905 – Support undo/redo for reassign attachment point operation * #7905 – Support undo/redo for reassign leaving atom operation * #7905 – Support undo/redo for assign attachment atom operation * #7905 – Fix build failure * #7905 – Do not apply toggle explicit hydrogens for leaving group atoms in monomer creation wizard * #7905 – Enable layout and clenaup tools, add label to HELM alias input * #7905 – Revert initial notification change * #7905 – Update screenshots * #7905 – Update screenshots * #7905 – Remove outdated test cases * #5520 - Percentages for mixed bases ain't sorted from biggest to smallest in tooltip (#8288) * Initial plan * Fix sorting of mixed base percentages in tooltip Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode (#8336) * #7970 - Include 'Create cyclic structure' option in the context menu for Flex mode * #8366 – Preview: Wrong name in context menu - “Circular layout” should be “Create cyclic structure” * #8369 – Preview: Circular layout option is active even when structure does not meet minimal closure requirements * #8368 - Preview: Context menu incorrectly allows “Circular layout” even when selection criteria are not met * #8367 - Preview: Undo does not revert Circular layout - structure disappears, ghost bonds remain and cause console errors --------- Co-authored-by: Nikita Chistousov <[email protected]> * #4188 - Choosing wedged/hashed bond direction doesn't work from right-clicking context menu (#8233) * Initial plan * Fix bond direction change in context menu for stereo bonds Co-authored-by: AlexeyGirin <[email protected]> * Simplify bond type check logic * Fix return statement formatting in useBondTypeChange --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> Co-authored-by: Alexey Girin <[email protected]> * #8351 Autotests for Ketcher 3.9.0 bugs (#8391) * First draft * Autotests: 8376 autotests some refactoring (#8381) * First * f2 * f3 * f4 * f5 * f6 * #8200 - Add parameter to Editor to disable saving new monomers to local storage (#8364) * fix: add parameter to Editor to disable saving new monomers to local storage * fix:make monomer library persistence opt‑in via shouldPersist * #7971 - Update the help document (3.9.) (#8384) * Delete documentation/images/FG_chain.gif * Delete documentation/images/Macro-canvas-3.8..png * Delete documentation/images/Library-Tabs-3.8..png * Delete documentation/images/Selection-for-Creating-a-Monomer-3.7..png * Delete documentation/images/Entering-the-Monomer-Creation-Wizard-3.7..png * Delete documentation/images/Exiting-the-Monomer-Creation-Wizard-3.7..png * Delete documentation/images/New-Monomer-Micro-3.7..png * Delete documentation/images/New-Monomer-Macro-3.7..png * Delete documentation/images/New-Monomer-Library-3.7..png * Delete documentation/images/Open-Structure-Macro-2-3.0..png * Add files via upload * Update help.md * Update help.md typos * #7553 - Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode (#7892) * #7553 fix fullscreen mode switching dropdown * #7553 fex: implement popup fullscreen mode with proper top-layer targeting * #7553 fix test * fix test * #7553 Remove ref to custom class * #7553 Refactor * #8337 - Preview: No limit on the number of added modification fields; new fields extend beyond the visible wizard area and shift action buttons (#8365) * fix: add scroll im monomer wizart in popup * fix: fix styles * f7 --------- Co-authored-by: Kristina <[email protected]> Co-authored-by: Ljubica Milovic <[email protected]> Co-authored-by: KukushkinDmi1riy <[email protected]> * #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module (#8388) * #8385 – Migrate to Indigo v1.38.0-rc.1 in-browser module * fixes * f2 * f3 --------- Co-authored-by: Alexey Girin <[email protected]> * draft * 2 * 3 * 4 * 5 * 6 * 7 * #8281 - Adjust subscription to library update event of Ketcher API (#8382) * #8212 - Refactor: Extract this nested ternary operation into an independent statement (part 4) (#8225) * Initial plan * Refactor nested ternary in Analyse.jsx into separate method Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8211 - Refactor: Extract this nested ternary operation into an independent statement (part 3) (#8224) * Initial plan * Refactor: Extract nested ternary operation in MainRow.jsx into renderCell function Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8210 - Refactor: Extract this nested ternary operation into an independent statement (part 2) (#8223) * Initial plan * Refactor: Extract nested ternary operations into independent functions Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #8209 - Refactor: Extract this nested ternary operation into an independent statement (part 1) (#8222) * Initial plan * Refactor nested ternary operations into if-else statements Co-authored-by: AlexeyGirin <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: AlexeyGirin <[email protected]> * #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard (#8371) * #7905 – Change selection logic * #7905 – Enable Indigo functions * #7905 – Support undo/redo for assigning attachment point via leaving atom and removing as assigned attachment point * #7905 – Support undo/redo for reassign attachment point operation * #7905 – Support undo/redo for reassign leaving atom operation * #7905 – Support undo/…
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‎ketcher-autotests/tests/specs/Chromium-popup/Bugs/ketcher-3.3.0-bugs.spec.ts-snapshots/Ketcher-bugs-in-3-3-0-Case-11-RNA-Builder-sec-10040-rresponding-monomer-in-library-on-first-click-3-chromium-popup-linux.png‎

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‎ketcher-autotests/tests/specs/Chromium-popup/Bugs/ketcher-3.3.0-bugs.spec.ts-snapshots/Ketcher-bugs-in-3-3-0-Case-11-RNA-Builder-sec-7921c-rresponding-monomer-in-library-on-first-click-1-chromium-popup-linux.png‎

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‎ketcher-autotests/tests/specs/Chromium-popup/Library/arrow-button-on-library-cards.spec.ts-snapshots/Arrow-button-on-Library-cards-Case-2-Verify-t-7d66c--Phosphates-Nucleotides-and-CHEMs-in-Library-4-chromium-popup-linux.png‎

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‎ketcher-autotests/tests/specs/Chromium-popup/Library/color-of-nucleobases.spec.ts‎

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@@ -11,6 +11,7 @@ import { Library } from '@tests/pages/macromolecules/Library';
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import { MacromoleculesTopToolbar } from '@tests/pages/macromolecules/MacromoleculesTopToolbar';
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import {
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clickOnCanvas,
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moveMouseAway,
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openFileAndAddToCanvasAsNewProject,
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takeEditorScreenshot,
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takeElementScreenshot,
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*/
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await Library(page).openRNASection(RNASection.Bases);
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await Library(page).selectMonomer(base);
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await moveMouseAway(page);
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await takeMonomerLibraryScreenshot(page, {
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hideMonomerPreview: true,
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hideMacromoleculeEditorScrollBars: true,

‎ketcher-autotests/tests/specs/Chromium-popup/Library/color-of-nucleobases.spec.ts-snapshots/Color-of-Nucleobases-Case-1-Check-that-cl6pur-f626b-their-colour-changed-to-CAD3DD-see-mockups-1-chromium-popup-linux.png‎

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‎ketcher-autotests/tests/specs/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts-snapshots/Macro-Micro-Switcher-Check-that-Pressing-Clean-Up-button-not-erase-all-macromolecules-from-canvas-1-chromium-linux.png‎

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‎ketcher-autotests/tests/specs/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts-snapshots/Macro-Micro-Switcher-Check-that-Pressing-Layout-button-not-erase-all-macromolecules-from-canvas-1-chromium-linux.png‎

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‎ketcher-autotests/tests/specs/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts-snapshots/Macro-Micro-Switcher-Check-that-for-CHEMs-mono-c2074--to-micro-mode-restricted-remove-abbreviation-1-chromium-linux.png‎

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‎ketcher-autotests/tests/specs/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts-snapshots/Macro-Micro-Switcher-Check-that-the-Ket-struct-7b663-oard-in-Macro-mode-is-visible-in-Micro-mode-1-chromium-linux.png‎

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‎ketcher-autotests/tests/specs/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts-snapshots/Macro-Micro-Switcher-Check-that-the-Mol-struct-36f81-board-in-Macro-mode-is-visible-in-Micro-mode-1-chromium-linux.png‎

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