#3830 – Aromatizing/Dearomatizing changes molecula position (#3837)

* #3830 – Aromatizing/Dearomatizing changes molecula position * #3830 – fixing CI tests
epam · Jan 8, 2024 · 2c9945a · 2c9945a
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diff --git a/...nipula-e6120-lic-structures-with-a-circle-inside-the-cycle-1-chromium-linux.png b/...nipula-e6120-lic-structures-with-a-circle-inside-the-cycle-1-chromium-linux.png
diff --git a/...Aromatic-structures---interchanged-Single-and-Double-bonds-1-chromium-linux.png b/...Aromatic-structures---interchanged-Single-and-Double-bonds-1-chromium-linux.png
diff --git a/...Aromatic-structures---interchanged-Single-and-Double-bonds-2-chromium-linux.png b/...Aromatic-structures---interchanged-Single-and-Double-bonds-2-chromium-linux.png
diff --git a/...Manipu-ff58c-lic-structures-with-a-circle-inside-the-cycle-1-chromium-linux.png b/...Manipu-ff58c-lic-structures-with-a-circle-inside-the-cycle-1-chromium-linux.png
diff --git a/...anipul-880b8-lic-structures-with-a-circle-inside-the-cycle-1-chromium-linux.png b/...anipul-880b8-lic-structures-with-a-circle-inside-the-cycle-1-chromium-linux.png
diff --git a/...hots/Aromatize-Dearomatize-Tool-Cycles-with-Aromatic-Bonds-1-chromium-linux.png b/...hots/Aromatize-Dearomatize-Tool-Cycles-with-Aromatic-Bonds-1-chromium-linux.png
diff --git a/...hots/Aromatize-Dearomatize-Tool-Cycles-with-Aromatic-Bonds-2-chromium-linux.png b/...hots/Aromatize-Dearomatize-Tool-Cycles-with-Aromatic-Bonds-2-chromium-linux.png
diff --git a/...aromatize-Tool-Non-aromatic-structures---Single-bonds-only-1-chromium-linux.png b/...aromatize-Tool-Non-aromatic-structures---Single-bonds-only-1-chromium-linux.png
diff --git a/...aromatize-Tool-Non-aromatic-structures---Single-bonds-only-2-chromium-linux.png b/...aromatize-Tool-Non-aromatic-structures---Single-bonds-only-2-chromium-linux.png
diff --git a/...aromatic-structures---interchanged-Single-and-Double-bonds-1-chromium-linux.png b/...aromatic-structures---interchanged-Single-and-Double-bonds-1-chromium-linux.png
diff --git a/...aromatic-structures---interchanged-Single-and-Double-bonds-2-chromium-linux.png b/...aromatic-structures---interchanged-Single-and-Double-bonds-2-chromium-linux.png
diff --git a/...anipul-0c986-lic-structures-with-a-circle-inside-the-cycle-1-chromium-linux.png b/...anipul-0c986-lic-structures-with-a-circle-inside-the-cycle-1-chromium-linux.png
diff --git a/...anipul-72b71-lic-structures-with-a-circle-inside-the-cycle-2-chromium-linux.png b/...anipul-72b71-lic-structures-with-a-circle-inside-the-cycle-2-chromium-linux.png
diff --git a/...correctly-implicit-Hydrogen-after-aromatize-for-eighth-ket-1-chromium-linux.png b/...correctly-implicit-Hydrogen-after-aromatize-for-eighth-ket-1-chromium-linux.png
diff --git a/...-correctly-implicit-Hydrogen-after-aromatize-for-fifth-ket-1-chromium-linux.png b/...-correctly-implicit-Hydrogen-after-aromatize-for-fifth-ket-1-chromium-linux.png
diff --git a/...-correctly-implicit-Hydrogen-after-aromatize-for-first-ket-1-chromium-linux.png b/...-correctly-implicit-Hydrogen-after-aromatize-for-first-ket-1-chromium-linux.png
diff --git a/...correctly-implicit-Hydrogen-after-aromatize-for-fourth-ket-1-chromium-linux.png b/...correctly-implicit-Hydrogen-after-aromatize-for-fourth-ket-1-chromium-linux.png
diff --git a/...correctly-implicit-Hydrogen-after-aromatize-for-second-ket-1-chromium-linux.png b/...correctly-implicit-Hydrogen-after-aromatize-for-second-ket-1-chromium-linux.png
diff --git a/...orrectly-implicit-Hydrogen-after-aromatize-for-seventh-ket-1-chromium-linux.png b/...orrectly-implicit-Hydrogen-after-aromatize-for-seventh-ket-1-chromium-linux.png
diff --git a/...-correctly-implicit-Hydrogen-after-aromatize-for-sixth-ket-1-chromium-linux.png b/...-correctly-implicit-Hydrogen-after-aromatize-for-sixth-ket-1-chromium-linux.png
diff --git a/...-correctly-implicit-Hydrogen-after-aromatize-for-third-ket-1-chromium-linux.png b/...-correctly-implicit-Hydrogen-after-aromatize-for-third-ket-1-chromium-linux.png
diff --git a/ketcher-autotests/tests/Indigo-Tools/Calculate-CIP-Tool/calculate-cip-tool.spec.ts b/ketcher-autotests/tests/Indigo-Tools/Calculate-CIP-Tool/calculate-cip-tool.spec.ts
@@ -352,8 +352,9 @@ test.describe('Indigo Tools - Calculate CIP Tool', () => {
     Description: New stereobond is added to the Chain structure.
     */
     await openFileAndAddToCanvas('chain-with-stereo-bonds.mol', page);
-    await selectTopPanelButton(TopPanelButton.Calculate, page);
-    await delay(DELAY_IN_SECONDS.TWO);
+    await waitForSpinnerFinishedWork(page, async () => {
+      await selectTopPanelButton(TopPanelButton.Calculate, page);
+    });
     await selectNestedTool(page, BondTool.UP);
     const point = await getBondByIndex(page, { type: BondType.SINGLE }, 5);
     await page.mouse.click(point.x, point.y);

diff --git a/...tructure-7ded6-tereo-labels-various-structure-combinations-1-chromium-linux.png b/...tructure-7ded6-tereo-labels-various-structure-combinations-1-chromium-linux.png
diff --git a/...tructure-88a7a-tereo-labels-various-structure-combinations-1-chromium-linux.png b/...tructure-88a7a-tereo-labels-various-structure-combinations-1-chromium-linux.png
diff --git a/...tructure-68afd-tereo-labels-various-structure-combinations-1-chromium-linux.png b/...tructure-68afd-tereo-labels-various-structure-combinations-1-chromium-linux.png
diff --git a/...tructure-f49d8-tereo-labels-various-structure-combinations-1-chromium-linux.png b/...tructure-f49d8-tereo-labels-various-structure-combinations-1-chromium-linux.png
diff --git a/...tructure-219bb-tereo-labels-various-structure-combinations-1-chromium-linux.png b/...tructure-219bb-tereo-labels-various-structure-combinations-1-chromium-linux.png
diff --git a/...tructure-45bb8-tereo-labels-various-structure-combinations-1-chromium-linux.png b/...tructure-45bb8-tereo-labels-various-structure-combinations-1-chromium-linux.png
diff --git a/...tructure-a7ec2-tereo-labels-various-structure-combinations-1-chromium-linux.png b/...tructure-a7ec2-tereo-labels-various-structure-combinations-1-chromium-linux.png
diff --git a/...-new-s-d6c2b-nipulations-with-structure-with-stereo-labels-1-chromium-linux.png b/...-new-s-d6c2b-nipulations-with-structure-with-stereo-labels-1-chromium-linux.png
diff --git a/...l-Aromatize-Undo-with-structure-that-contain-stereo-labels-1-chromium-linux.png b/...l-Aromatize-Undo-with-structure-that-contain-stereo-labels-1-chromium-linux.png
diff --git a/...l-Aromatize-Undo-with-structure-that-contain-stereo-labels-2-chromium-linux.png b/...l-Aromatize-Undo-with-structure-that-contain-stereo-labels-2-chromium-linux.png
diff --git a/...l-Aromatize-Undo-with-structure-that-contain-stereo-labels-3-chromium-linux.png b/...l-Aromatize-Undo-with-structure-that-contain-stereo-labels-3-chromium-linux.png
diff --git a/...Indigo-Tools---Calculate-CIP-Tool-Check-tooltip-and-labels-1-chromium-linux.png b/...Indigo-Tools---Calculate-CIP-Tool-Check-tooltip-and-labels-1-chromium-linux.png
diff --git a/...IP-Tool-Copy-Paste-of-structure-that-contain-stereo-labels-1-chromium-linux.png b/...IP-Tool-Copy-Paste-of-structure-that-contain-stereo-labels-1-chromium-linux.png
diff --git a/...-atom--0d78c-nipulations-with-structure-with-stereo-labels-1-chromium-linux.png b/...-atom--0d78c-nipulations-with-structure-with-stereo-labels-1-chromium-linux.png
diff --git a/...-atom--36b50-nipulations-with-structure-with-stereo-labels-2-chromium-linux.png b/...-atom--36b50-nipulations-with-structure-with-stereo-labels-2-chromium-linux.png
diff --git a/...-bond--b8f39-nipulations-with-structure-with-stereo-labels-2-chromium-linux.png b/...-bond--b8f39-nipulations-with-structure-with-stereo-labels-2-chromium-linux.png
diff --git a/...-bond--bc4cb-nipulations-with-structure-with-stereo-labels-1-chromium-linux.png b/...-bond--bc4cb-nipulations-with-structure-with-stereo-labels-1-chromium-linux.png
diff --git a/...Tool-Layout-Undo-with-structure-that-contain-stereo-labels-2-chromium-linux.png b/...Tool-Layout-Undo-with-structure-that-contain-stereo-labels-2-chromium-linux.png
diff --git a/...ation-wi-ce307-ture-including-stereo-properties-R-S-labels-1-chromium-linux.png b/...ation-wi-ce307-ture-including-stereo-properties-R-S-labels-1-chromium-linux.png
diff --git a/...ation-wi-eeefa-ture-including-stereo-properties-E-Z-labels-1-chromium-linux.png b/...ation-wi-eeefa-ture-including-stereo-properties-E-Z-labels-1-chromium-linux.png
diff --git a/...-Tool-Operation-with-a-structure-without-stereo-properties-1-chromium-linux.png b/...-Tool-Operation-with-a-structure-without-stereo-properties-1-chromium-linux.png
diff --git a/...e-stru-c535a-nipulations-with-structure-with-stereo-labels-1-chromium-linux.png b/...e-stru-c535a-nipulations-with-structure-with-stereo-labels-1-chromium-linux.png
diff --git a/...opdown-6dfaf-After-the-manual-mapping-with-incorrect-pairs-2-chromium-linux.png b/...opdown-6dfaf-After-the-manual-mapping-with-incorrect-pairs-2-chromium-linux.png
diff --git a/...opdown-77a0a-After-the-manual-mapping-with-incorrect-pairs-4-chromium-linux.png b/...opdown-77a0a-After-the-manual-mapping-with-incorrect-pairs-4-chromium-linux.png
diff --git a/...opdown-90f04-After-the-manual-mapping-with-incorrect-pairs-3-chromium-linux.png b/...opdown-90f04-After-the-manual-mapping-with-incorrect-pairs-3-chromium-linux.png
diff --git a/...opdown-996d6-er-the-manual-mapping-with-incorrect-ordering-3-chromium-linux.png b/...opdown-996d6-er-the-manual-mapping-with-incorrect-ordering-3-chromium-linux.png
diff --git a/.../Verifying-buttons-on-reaction-am-tool-dropdown-Clear-mode-1-chromium-linux.png b/.../Verifying-buttons-on-reaction-am-tool-dropdown-Clear-mode-1-chromium-linux.png
diff --git a/.../Verifying-buttons-on-reaction-am-tool-dropdown-Clear-mode-2-chromium-linux.png b/.../Verifying-buttons-on-reaction-am-tool-dropdown-Clear-mode-2-chromium-linux.png
diff --git a/.../Verifying-buttons-on-reaction-am-tool-dropdown-Clear-mode-3-chromium-linux.png b/.../Verifying-buttons-on-reaction-am-tool-dropdown-Clear-mode-3-chromium-linux.png
diff --git a/.../Verifying-buttons-on-reaction-am-tool-dropdown-Clear-mode-4-chromium-linux.png b/.../Verifying-buttons-on-reaction-am-tool-dropdown-Clear-mode-4-chromium-linux.png
diff --git a/.../Verifying-buttons-on-reaction-am-tool-dropdown-Clear-mode-5-chromium-linux.png b/.../Verifying-buttons-on-reaction-am-tool-dropdown-Clear-mode-5-chromium-linux.png
diff --git a/...ttons-on-reaction-am-tool-dropdown-Half-reaction-on-canvas-1-chromium-linux.png b/...ttons-on-reaction-am-tool-dropdown-Half-reaction-on-canvas-1-chromium-linux.png
diff --git a/...tion-am-tool-dropdown-Verifying-of-the-correct-automapping-1-chromium-linux.png b/...tion-am-tool-dropdown-Verifying-of-the-correct-automapping-1-chromium-linux.png
diff --git a/...tion-am-tool-dropdown-Verifying-of-the-correct-automapping-2-chromium-linux.png b/...tion-am-tool-dropdown-Verifying-of-the-correct-automapping-2-chromium-linux.png
diff --git a/...tion-am-tool-dropdown-Verifying-of-the-correct-automapping-3-chromium-linux.png b/...tion-am-tool-dropdown-Verifying-of-the-correct-automapping-3-chromium-linux.png
diff --git a/...ion-am-tool-dropdown-With-autoMapping-Compare-the-behavior-2-chromium-linux.png b/...ion-am-tool-dropdown-With-autoMapping-Compare-the-behavior-2-chromium-linux.png
diff --git a/...ion-am-tool-dropdown-With-autoMapping-Compare-the-behavior-3-chromium-linux.png b/...ion-am-tool-dropdown-With-autoMapping-Compare-the-behavior-3-chromium-linux.png
diff --git a/...ion-am-tool-dropdown-With-autoMapping-Compare-the-behavior-4-chromium-linux.png b/...ion-am-tool-dropdown-With-autoMapping-Compare-the-behavior-4-chromium-linux.png
diff --git a/...opdown-a4c7c-er-the-manual-mapping-with-incorrect-ordering-2-chromium-linux.png b/...opdown-a4c7c-er-the-manual-mapping-with-incorrect-ordering-2-chromium-linux.png
diff --git a/...opdown-d3b56-er-the-manual-mapping-with-incorrect-ordering-4-chromium-linux.png b/...opdown-d3b56-er-the-manual-mapping-with-incorrect-ordering-4-chromium-linux.png
diff --git a/...action-am-tool-dropdown-full-reaction-on-canvas-Alter-mode-1-chromium-linux.png b/...action-am-tool-dropdown-full-reaction-on-canvas-Alter-mode-1-chromium-linux.png
diff --git a/...action-am-tool-dropdown-full-reaction-on-canvas-Alter-mode-4-chromium-linux.png b/...action-am-tool-dropdown-full-reaction-on-canvas-Alter-mode-4-chromium-linux.png
diff --git a/...tion-am-tool-dropdown-full-reaction-on-canvas-Discard-mode-1-chromium-linux.png b/...tion-am-tool-dropdown-full-reaction-on-canvas-Discard-mode-1-chromium-linux.png
diff --git a/...tion-am-tool-dropdown-full-reaction-on-canvas-Discard-mode-4-chromium-linux.png b/...tion-am-tool-dropdown-full-reaction-on-canvas-Discard-mode-4-chromium-linux.png
diff --git a/...eaction-am-tool-dropdown-full-reaction-on-canvas-Keep-mode-1-chromium-linux.png b/...eaction-am-tool-dropdown-full-reaction-on-canvas-Keep-mode-1-chromium-linux.png
diff --git a/...eaction-am-tool-dropdown-full-reaction-on-canvas-Keep-mode-4-chromium-linux.png b/...eaction-am-tool-dropdown-full-reaction-on-canvas-Keep-mode-4-chromium-linux.png
diff --git a/...s-Actions-on-the-reaction-with-non-default-reaction-arrows-3-chromium-linux.png b/...s-Actions-on-the-reaction-with-non-default-reaction-arrows-3-chromium-linux.png
diff --git a/...shots/Bond-Tool-Aromatic---Ring-inside-the-cycle-structure-2-chromium-linux.png b/...shots/Bond-Tool-Aromatic---Ring-inside-the-cycle-structure-2-chromium-linux.png
diff --git a/...shots/Bond-Tool-Aromatic---Ring-inside-the-cycle-structure-3-chromium-linux.png b/...shots/Bond-Tool-Aromatic---Ring-inside-the-cycle-structure-3-chromium-linux.png
diff --git a/...tional-Group-Tools3-Check-aromatize-dearomatize-tool-on-FG-1-chromium-linux.png b/...tional-Group-Tools3-Check-aromatize-dearomatize-tool-on-FG-1-chromium-linux.png
diff --git a/...tional-Group-Tools3-Check-aromatize-dearomatize-tool-on-FG-2-chromium-linux.png b/...tional-Group-Tools3-Check-aromatize-dearomatize-tool-on-FG-2-chromium-linux.png
diff --git a/...apshots/Create-and-Save-Templates-Create-Template---saving-1-chromium-linux.png b/...apshots/Create-and-Save-Templates-Create-Template---saving-1-chromium-linux.png
diff --git a/...s/Undo-Redo-Actions-Undo-Redo-Mapping-tool-template-action-2-chromium-linux.png b/...s/Undo-Redo-Actions-Undo-Redo-Mapping-tool-template-action-2-chromium-linux.png
diff --git a/...pshots/Open-Ketcher-Verify-Aromatize-and-Dearomatize-icons-2-chromium-linux.png b/...pshots/Open-Ketcher-Verify-Aromatize-and-Dearomatize-icons-2-chromium-linux.png
diff --git a/...pshots/Open-Ketcher-Verify-Aromatize-and-Dearomatize-icons-3-chromium-linux.png b/...pshots/Open-Ketcher-Verify-Aromatize-and-Dearomatize-icons-3-chromium-linux.png
diff --git a/ketcher-autotests/tests/test-data/KET/structure-with-stereo-bonds-expected.ket b/ketcher-autotests/tests/test-data/KET/structure-with-stereo-bonds-expected.ket
@@ -14,24 +14,24 @@
             {
                 "label": "C",
                 "location": [
-                    11.775473354321095,
-                    -8.187600977368211,
+                    12.101912830334278,
+                    -7.750100691265916,
                     0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    12.641368581131388,
-                    -8.68759904432894,
+                    12.967808057144572,
+                    -8.250098758226644,
                     0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    13.507464079537838,
-                    -8.187600977368211,
+                    13.833903555551021,
+                    -7.750100691265916,
                     0
                 ],
                 "cip": "R",
@@ -40,8 +40,8 @@
             {
                 "label": "C",
                 "location": [
-                    14.373459442146208,
-                    -8.68759904432894,
+                    14.699898918159391,
+                    -8.250098758226644,
                     0
                 ],
                 "cip": "S",
@@ -50,40 +50,40 @@
             {
                 "label": "C",
                 "location": [
-                    15.23945480475458,
-                    -8.187600977368211,
+                    15.565894280767763,
+                    -7.750100691265916,
                     0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    16.105551256835295,
-                    -8.68759904432894,
+                    16.43199073284848,
+                    -8.250098758226644,
                     0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    16.97164580156748,
-                    -8.187600977368211,
+                    17.29808527758066,
+                    -7.750100691265916,
                     0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    13.507464079537838,
-                    -7.187506614997213,
+                    13.833903555551021,
+                    -6.750006328894918,
                     0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    14.373459442146208,
-                    -9.687493135103784,
+                    14.699898918159391,
+                    -9.249992849001488,
                     0
                 ]
             }
@@ -147,11 +147,6 @@
                 ],
                 "stereo": 6
             }
-        ],
-        "stereoFlagPosition": {
-            "x": 16.97164580156748,
-            "y": 6.187506614997213,
-            "z": 0
-        }
+        ]
     }
 }
diff --git a/ketcher-autotests/tests/test-data/structure-with-stereo-bonds-expectedV2000.mol b/ketcher-autotests/tests/test-data/structure-with-stereo-bonds-expectedV2000.mol
@@ -1,5 +1,5 @@
 
-  Ketcher 10152310222D 1   1.00000     0.00000     0
+  Ketcher  1 52414 52D 1   1.00000     0.00000     0
 
   9  8  0  0  0  0  0  0  0  0999 V2000
    12.1019   -7.7501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

diff --git a/ketcher-autotests/tests/test-data/structure-with-stereo-bonds-expectedV3000.mol b/ketcher-autotests/tests/test-data/structure-with-stereo-bonds-expectedV3000.mol
@@ -1,5 +1,5 @@
 
-  -INDIGO-10152310232D
+  -INDIGO-01052414052D
 
   0  0  0  0  0  0  0  0  0  0  0 V3000
 M  V30 BEGIN CTAB

diff --git a/packages/ketcher-core/src/application/editor/editor.types.ts b/packages/ketcher-core/src/application/editor/editor.types.ts
@@ -32,7 +32,7 @@ export type FloatingToolsParams = {
 export interface Editor {
   isDitrty: () => boolean;
   setOrigin: () => void;
-  struct: (struct?: Struct) => Struct;
+  struct: (struct?: Struct, needToCenterStruct?: boolean) => Struct;
   structToAddFragment: (struct: Struct) => Struct;
   subscribe: (eventName: string, handler: (data?: any) => any) => any;
   unsubscribe: (eventName: string, subscriber: any) => void;

diff --git a/packages/ketcher-react/src/script/editor/Editor.ts b/packages/ketcher-react/src/script/editor/Editor.ts
@@ -267,22 +267,27 @@ class Editor implements KetcherEditor {
     this.struct(undefined);
   }
 
-  renderAndRecoordinateStruct(struct: Struct) {
+  renderAndRecoordinateStruct(struct: Struct, needToCenterStruct = true) {
     const action = fromNewCanvas(this.render.ctab, struct);
     this.update(action);
-    this.centerStruct();
+    if (needToCenterStruct) {
+      this.centerStruct();
+    }
     return this.render.ctab.molecule;
   }
 
-  struct(value?: Struct): Struct {
+  struct(value?: Struct, needToCenterStruct = true): Struct {
     if (arguments.length === 0) {
       return this.render.ctab.molecule;
     }
 
     this.selection(null);
     const struct = value || new Struct();
 
-    const molecule = this.renderAndRecoordinateStruct(struct);
+    const molecule = this.renderAndRecoordinateStruct(
+      struct,
+      needToCenterStruct,
+    );
 
     this.hoverIcon.create();
     return molecule;

diff --git a/packages/ketcher-react/src/script/ui/state/server/index.js b/packages/ketcher-react/src/script/ui/state/server/index.js
@@ -152,6 +152,7 @@ export function serverTransform(method, data, struct) {
           load(loadedStruct, {
             rescale: method === 'layout',
             reactionRelayout: method === 'clean',
+            method,
           }),
         );
       })

diff --git a/packages/ketcher-react/src/script/ui/state/shared.ts b/packages/ketcher-react/src/script/ui/state/shared.ts
@@ -102,7 +102,7 @@ export function load(struct: Struct, options?) {
     const server = state.server;
     const errorHandler = editor.errorHandler;
     options = options || {};
-    let { isPaste, ...otherOptions } = options;
+    let { isPaste, method, ...otherOptions } = options;
     otherOptions = {
       ...otherOptions,
       'dearomatize-on-load': editor.options()['dearomatize-on-load'],
@@ -170,11 +170,13 @@ export function load(struct: Struct, options?) {
           dispatch(onAction({ tool: 'paste', opts: parsedStruct }));
         }
       } else {
-        editor.struct(parsedStruct);
+        editor.struct(parsedStruct, method === 'layout');
       }
 
       editor.zoomAccordingContent(parsedStruct);
-      if (!isPaste) {
+
+      const isIndigoFunctionCalled = !!method;
+      if (!isPaste && !isIndigoFunctionCalled) {
         editor.centerStruct();
       }