#4388 - Macro: Allow Nucleoside of sequence edit in RNA builder

epam · Apr 24, 2024 · a71acc2 · a71acc2
1 parent ca3b83f
commit a71acc2
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Showing 58 changed files with 710 additions and 211 deletions.
diff --git a/...elect--fad51-owLeft-then-paste-ket-from-clipboard-and-undo-2-chromium-linux.png b/...elect--fad51-owLeft-then-paste-ket-from-clipboard-and-undo-2-chromium-linux.png
diff --git a/...e-for-view-mode-Copy-paste-selection-with-rectangular-tool-1-chromium-linux.png b/...e-for-view-mode-Copy-paste-selection-with-rectangular-tool-1-chromium-linux.png
diff --git a/...e-for-view-mode-Copy-paste-selection-with-rectangular-tool-2-chromium-linux.png b/...e-for-view-mode-Copy-paste-selection-with-rectangular-tool-2-chromium-linux.png
diff --git a/...elect--0f3ce-with-Ctrl-Lclick-then-copy-and-paste-and-undo-3-chromium-linux.png b/...elect--0f3ce-with-Ctrl-Lclick-then-copy-and-paste-and-undo-3-chromium-linux.png
diff --git a/...elect--87e1a-with-Ctrl-Lclick-then-copy-and-paste-and-undo-1-chromium-linux.png b/...elect--87e1a-with-Ctrl-Lclick-then-copy-and-paste-and-undo-1-chromium-linux.png
diff --git a/...elect--e2c16-with-Ctrl-Lclick-then-copy-and-paste-and-undo-2-chromium-linux.png b/...elect--e2c16-with-Ctrl-Lclick-then-copy-and-paste-and-undo-2-chromium-linux.png
diff --git a/...otests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-edit-in-rna-builder.spec.ts b/...otests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-edit-in-rna-builder.spec.ts
@@ -47,6 +47,66 @@ test.describe('Sequence mode edit in RNA Builder', () => {
     await takePageScreenshot(page);
   });
 
+  test('Select nucleoside and phosphate and modify sugar and phosphate as it one nucleotide', async ({
+    page,
+  }) => {
+    // Coordinates for rectangle selection
+    const startX = 300;
+    const startY = 100;
+    const endX = 400;
+    const endY = 200;
+    await selectRectangleArea(page, startX, startY, endX, endY);
+    await clickOnSequenceSymbol(page, 'T', { button: 'right', nthNumber: 2 });
+    // should see correct context menu title and available 'modify_in_rna_builder' button
+    await takeEditorScreenshot(page);
+    await page.getByTestId('modify_in_rna_builder').click();
+    // should see uploaded nucleotide (nucleoside + phosphate) data to RNA Builder and disabled "Update" button
+    await takeRNABuilderScreenshot(page);
+    // Update Sugar
+    await page.getByTestId(SUGAR).click();
+    await page.getByTestId('25R___2,5-Ribose').click();
+    await moveMouseAway(page);
+    // Update Phosphate
+    await page.getByTestId(PHOSPHATE).click();
+    await page.getByTestId('bP___Boranophosphate').click();
+    await moveMouseAway(page);
+    // should see updated sugar and phosphate, updated title of preset and nondisabled "Update" button
+    await takeRNABuilderScreenshot(page);
+    await page.getByTestId('save-btn').click();
+    await takePageScreenshot(page);
+  });
+
+  test('Select nucleotide, nucleoside and modify sugar and phosphate. nucleoside should become nucleotide', async ({
+    page,
+  }) => {
+    // Coordinates for rectangle selection
+    const startX = 280;
+    const startY = 100;
+    const endX = 320;
+    const endY = 200;
+    await selectRectangleArea(page, startX, startY, endX, endY);
+    await clickOnSequenceSymbol(page, 'T', { button: 'right', nthNumber: 2 });
+    // should see correct context menu title and available 'modify_in_rna_builder' button
+    await takeEditorScreenshot(page);
+    await page.getByTestId('modify_in_rna_builder').click();
+    // should see uploaded data to RNA Builder and disabled "Update" button
+    await takeRNABuilderScreenshot(page);
+    // Update Sugar
+    await page.getByTestId(SUGAR).click();
+    await page.getByTestId('25R___2,5-Ribose').click();
+    await moveMouseAway(page);
+    // Update Phosphate
+    await page.getByTestId(PHOSPHATE).click();
+    await page.getByTestId('bP___Boranophosphate').click();
+    await moveMouseAway(page);
+    // should see updated sugar and phosphate of preset and nondisabled "Update" button
+    await takeRNABuilderScreenshot(page);
+    await page.getByTestId('save-btn').click();
+    // Click 'Yes' in modal
+    await page.getByText('Yes').click();
+    await takePageScreenshot(page);
+  });
+
   test('Select one nucleotide and cancel modification', async ({ page }) => {
     await clickOnSequenceSymbol(page, 'T');
     await clickOnSequenceSymbol(page, 'T', { button: 'right' });
@@ -93,7 +153,7 @@ test.describe('Sequence mode edit in RNA Builder', () => {
     await takeEditorScreenshot(page);
   });
 
-  test('Select entire chain and see disabled modify_in_rna_builder button', async ({
+  test('Select entire chain and see enabled modify_in_rna_builder button', async ({
     page,
   }) => {
     await page.keyboard.down('Control');
@@ -102,7 +162,7 @@ test.describe('Sequence mode edit in RNA Builder', () => {
     // should see the whole chain selected
     await takeEditorScreenshot(page);
     await clickOnSequenceSymbol(page, 'T', { button: 'right' });
-    // should see correct context menu title and disabled 'modify_in_rna_builder' button
+    // should see correct context menu title and enabled 'modify_in_rna_builder' button
     await takeEditorScreenshot(page);
   });
 });
diff --git a/...-entir-0092b-and-see-disabled-modify-in-rna-builder-button-1-chromium-linux.png b/...-entir-0092b-and-see-disabled-modify-in-rna-builder-button-1-chromium-linux.png
diff --git a/...-entir-f3387-and-see-disabled-modify-in-rna-builder-button-2-chromium-linux.png b/...-entir-f3387-and-see-disabled-modify-in-rna-builder-button-2-chromium-linux.png
diff --git a/...-entire-chain-and-see-enabled-modify-in-rna-builder-button-1-chromium-linux.png b/...-entire-chain-and-see-enabled-modify-in-rna-builder-button-1-chromium-linux.png
diff --git a/...-entire-chain-and-see-enabled-modify-in-rna-builder-button-2-chromium-linux.png b/...-entire-chain-and-see-enabled-modify-in-rna-builder-button-2-chromium-linux.png
diff --git a/...-nucle-2386e-dify-sugar-and-phosphate-as-it-one-nucleotide-2-chromium-linux.png b/...-nucle-2386e-dify-sugar-and-phosphate-as-it-one-nucleotide-2-chromium-linux.png
diff --git a/...t-nucle-29a1e-hosphate-nucleoside-should-become-nucleotide-3-chromium-linux.png b/...t-nucle-29a1e-hosphate-nucleoside-should-become-nucleotide-3-chromium-linux.png
diff --git a/...-nucle-3234e-dify-sugar-and-phosphate-as-it-one-nucleotide-4-chromium-linux.png b/...-nucle-3234e-dify-sugar-and-phosphate-as-it-one-nucleotide-4-chromium-linux.png
diff --git a/...-nucle-323a0-dify-sugar-and-phosphate-as-it-one-nucleotide-3-chromium-linux.png b/...-nucle-323a0-dify-sugar-and-phosphate-as-it-one-nucleotide-3-chromium-linux.png
diff --git a/...t-nucle-403dc-hosphate-nucleoside-should-become-nucleotide-4-chromium-linux.png b/...t-nucle-403dc-hosphate-nucleoside-should-become-nucleotide-4-chromium-linux.png
diff --git a/...t-nucle-5df02-hosphate-nucleoside-should-become-nucleotide-2-chromium-linux.png b/...t-nucle-5df02-hosphate-nucleoside-should-become-nucleotide-2-chromium-linux.png
diff --git a/...-nucle-fafd5-dify-sugar-and-phosphate-as-it-one-nucleotide-1-chromium-linux.png b/...-nucle-fafd5-dify-sugar-and-phosphate-as-it-one-nucleotide-1-chromium-linux.png
diff --git a/...t-nucle-fc129-hosphate-nucleoside-should-become-nucleotide-1-chromium-linux.png b/...t-nucle-fc129-hosphate-nucleoside-should-become-nucleotide-1-chromium-linux.png
diff --git a/...de-selection-for-edit-mode-Select-letters-with-LClick-drag-1-chromium-linux.png b/...de-selection-for-edit-mode-Select-letters-with-LClick-drag-1-chromium-linux.png
diff --git a/...de-selection-for-edit-mode-Select-letters-with-LClick-drag-2-chromium-linux.png b/...de-selection-for-edit-mode-Select-letters-with-LClick-drag-2-chromium-linux.png
diff --git a/...e-Select-letters-with-Shift-ArrowLeft-then-delete-and-undo-1-chromium-linux.png b/...e-Select-letters-with-Shift-ArrowLeft-then-delete-and-undo-1-chromium-linux.png
diff --git a/...e-Select-letters-with-Shift-ArrowLeft-then-delete-and-undo-2-chromium-linux.png b/...e-Select-letters-with-Shift-ArrowLeft-then-delete-and-undo-2-chromium-linux.png
diff --git a/...e-Select-letters-with-Shift-ArrowLeft-then-delete-and-undo-3-chromium-linux.png b/...e-Select-letters-with-Shift-ArrowLeft-then-delete-and-undo-3-chromium-linux.png
diff --git a/...e-Select-letters-with-Shift-ArrowLeft-then-delete-and-undo-4-chromium-linux.png b/...e-Select-letters-with-Shift-ArrowLeft-then-delete-and-undo-4-chromium-linux.png
diff --git a/...-for-edit-mode-Select-letters-with-Shift-ArrowRight-button-1-chromium-linux.png b/...-for-edit-mode-Select-letters-with-Shift-ArrowRight-button-1-chromium-linux.png
diff --git a/...-for-edit-mode-Select-letters-with-Shift-ArrowRight-button-2-chromium-linux.png b/...-for-edit-mode-Select-letters-with-Shift-ArrowRight-button-2-chromium-linux.png
diff --git a/...lection-for-view-mode-Select-entire-chain-with-Ctrl-Lclick-1-chromium-linux.png b/...lection-for-view-mode-Select-entire-chain-with-Ctrl-Lclick-1-chromium-linux.png
diff --git a/...e-selection-for-view-mode-Select-letters-with-Shift-Lclick-1-chromium-linux.png b/...e-selection-for-view-mode-Select-letters-with-Shift-Lclick-1-chromium-linux.png
diff --git a/...r-view-mode-Select-letters-with-rectangular-selection-tool-1-chromium-linux.png b/...r-view-mode-Select-letters-with-rectangular-selection-tool-1-chromium-linux.png
diff --git a/...ence-Mode-Open-monomers-chains-and-switch-to-sequence-mode-2-chromium-linux.png b/...ence-Mode-Open-monomers-chains-and-switch-to-sequence-mode-2-chromium-linux.png
diff --git a/...-flex-view-to-sequence-view-to-snake-view-and-back-to-flex-1-chromium-linux.png b/...-flex-view-to-sequence-view-to-snake-view-and-back-to-flex-1-chromium-linux.png
diff --git a/...-flex-view-to-sequence-view-to-snake-view-and-back-to-flex-2-chromium-linux.png b/...-flex-view-to-sequence-view-to-snake-view-and-back-to-flex-2-chromium-linux.png
diff --git a/...-flex-view-to-sequence-view-to-snake-view-and-back-to-flex-3-chromium-linux.png b/...-flex-view-to-sequence-view-to-snake-view-and-back-to-flex-3-chromium-linux.png
diff --git a/ketcher-autotests/tests/utils/macromolecules/sequence.ts b/ketcher-autotests/tests/utils/macromolecules/sequence.ts
@@ -3,9 +3,13 @@ import { Page } from '@playwright/test';
 export async function clickOnSequenceSymbol(
   page: Page,
   symbolText: string,
-  clickOptions?: { button: 'right' | 'left' },
+  clickOptions?: { button?: 'right' | 'left'; nthNumber?: number },
 ) {
-  const symbolLocator = await getSequenceSymbolLocator(page, symbolText);
+  const symbolLocator = getSequenceSymbolLocator(
+    page,
+    symbolText,
+    clickOptions?.nthNumber,
+  );
   await symbolLocator.click(clickOptions);
 }
 

diff --git a/packages/ketcher-core/src/application/editor/Editor.ts b/packages/ketcher-core/src/application/editor/Editor.ts
@@ -3,7 +3,7 @@ import { SequenceType, Struct, Vec2 } from 'domain/entities';
 import {
   BaseTool,
   IRnaPreset,
-  LabeledNucleotideWithPositionInSequence,
+  LabeledNodesWithPositionInSequence,
   isBaseTool,
   Tool,
   ToolConstructorInterface,
@@ -197,7 +197,7 @@ export class CoreEditor {
       this.onTurnOffSequenceEditInRNABuilderMode(),
     );
     this.events.modifySequenceInRnaBuilder.add(
-      (updatedSelection: LabeledNucleotideWithPositionInSequence[]) =>
+      (updatedSelection: LabeledNodesWithPositionInSequence[]) =>
         this.onModifySequenceInRnaBuilder(updatedSelection),
     );
     this.events.changeSequenceTypeEnterMode.add((mode: SequenceType) =>
@@ -238,7 +238,7 @@ export class CoreEditor {
   }
 
   private onModifySequenceInRnaBuilder(
-    updatedSelection: LabeledNucleotideWithPositionInSequence[],
+    updatedSelection: LabeledNodesWithPositionInSequence[],
   ) {
     if (!(this.mode instanceof SequenceMode)) {
       return;

diff --git a/packages/ketcher-core/src/application/editor/modes/SequenceMode.ts b/packages/ketcher-core/src/application/editor/modes/SequenceMode.ts
@@ -7,9 +7,9 @@ import {
   NodesSelection,
   SequenceRenderer,
 } from 'application/render/renderers/sequence/SequenceRenderer';
-import { AttachmentPointName, MonomerItemType } from 'domain/types';
+import { AttachmentPointName } from 'domain/types';
 import { Command } from 'domain/entities/Command';
-import { BaseMonomer, SequenceType, Vec2 } from 'domain/entities';
+import { BaseMonomer, Phosphate, SequenceType, Vec2 } from 'domain/entities';
 import { BaseRenderer } from 'application/render/renderers/internal';
 import { EmptySequenceNode } from 'domain/entities/EmptySequenceNode';
 import { Nucleoside } from 'domain/entities/Nucleoside';
@@ -34,7 +34,7 @@ import { ChainsCollection } from 'domain/entities/monomer-chains/ChainsCollectio
 import { DrawingEntitiesManager } from 'domain/entities/DrawingEntitiesManager';
 import { Chain } from 'domain/entities/monomer-chains/Chain';
 import { MonomerSequenceNode } from 'domain/entities/MonomerSequenceNode';
-import { LabeledNucleotideWithPositionInSequence } from 'application/editor/tools/Tool';
+import { LabeledNodesWithPositionInSequence } from 'application/editor/tools/Tool';
 
 const naturalAnalogues = uniq([
   ...rnaDnaNaturalAnalogues,
@@ -154,53 +154,102 @@ export class SequenceMode extends BaseMode {
   }
 
   public modifySequenceInRnaBuilder(
-    updatedSelection: LabeledNucleotideWithPositionInSequence[],
+    updatedSelection: LabeledNodesWithPositionInSequence[],
   ) {
     const editor = CoreEditor.provideEditorInstance();
     const history = new EditorHistory(editor);
     const modelChanges = new Command();
 
     // Update Nucleotides one by one
-    for (const labeledNucleotide of updatedSelection) {
-      const nodeIndexOverall = labeledNucleotide.nodeIndexOverall;
+    for (const labeledNucleoelement of updatedSelection) {
+      const nodeIndexOverall = labeledNucleoelement.nodeIndexOverall;
 
       if (nodeIndexOverall === undefined) return;
 
       // Create monomerItem(s) based on label
-      const sugarMonomerItem = getRnaPartLibraryItem(
-        editor,
-        labeledNucleotide.sugarLabel,
-      );
-      const baseMonomerItem = getRnaPartLibraryItem(
-        editor,
-        labeledNucleotide.baseLabel,
-      );
-      const phosphateMonomerItem = getRnaPartLibraryItem(
-        editor,
-        labeledNucleotide.phosphateLabel,
-      );
+      let sugarMonomerItem;
+      let baseMonomerItem;
+      let phosphateMonomerItem;
+      if (labeledNucleoelement.sugarLabel) {
+        sugarMonomerItem = getRnaPartLibraryItem(
+          editor,
+          labeledNucleoelement.sugarLabel,
+        );
+      }
+      if (labeledNucleoelement.baseLabel) {
+        baseMonomerItem = getRnaPartLibraryItem(
+          editor,
+          labeledNucleoelement.baseLabel,
+        );
+      }
+      if (labeledNucleoelement.phosphateLabel) {
+        phosphateMonomerItem = getRnaPartLibraryItem(
+          editor,
+          labeledNucleoelement.phosphateLabel,
+        );
+      }
 
       const currentNode = SequenceRenderer.getNodeByPointer(nodeIndexOverall);
 
-      // Update monomerItem objects
-      modelChanges.merge(
-        editor.drawingEntitiesManager.modifyMonomerItem(
-          currentNode.sugar,
-          sugarMonomerItem as MonomerItemType,
-        ),
-      );
-      modelChanges.merge(
-        editor.drawingEntitiesManager.modifyMonomerItem(
-          currentNode.rnaBase,
-          baseMonomerItem as MonomerItemType,
-        ),
-      );
-      modelChanges.merge(
-        editor.drawingEntitiesManager.modifyMonomerItem(
-          currentNode.phosphate,
-          phosphateMonomerItem as MonomerItemType,
-        ),
-      );
+      // Update Sugar monomerItem object
+      if (currentNode.sugar && sugarMonomerItem) {
+        modelChanges.merge(
+          editor.drawingEntitiesManager.modifyMonomerItem(
+            currentNode.sugar,
+            sugarMonomerItem,
+          ),
+        );
+      }
+      // Update Base monomerItem object
+      if (currentNode.rnaBase && baseMonomerItem) {
+        modelChanges.merge(
+          editor.drawingEntitiesManager.modifyMonomerItem(
+            currentNode.rnaBase,
+            baseMonomerItem,
+          ),
+        );
+      }
+
+      // Update monomerItem object or add Phosphate
+      if (phosphateMonomerItem) {
+        // Update Phosphate monomerItem object for Nucleotide
+        if (currentNode instanceof Nucleotide) {
+          modelChanges.merge(
+            editor.drawingEntitiesManager.modifyMonomerItem(
+              currentNode.phosphate,
+              phosphateMonomerItem,
+            ),
+          );
+          // Add Phosphate to Nucleoside
+        } else if (currentNode instanceof Nucleoside) {
+          const sugarR2 = currentNode.sugar.attachmentPointsToBonds.R2;
+          const nextMonomerInSameChain = sugarR2?.secondMonomer;
+
+          // Remove existing bond connection between Nucleoside Sugar and next node in case of any
+          if (sugarR2) {
+            modelChanges.merge(
+              editor.drawingEntitiesManager.deletePolymerBond(sugarR2),
+            );
+          }
+
+          modelChanges.merge(
+            this.bondNodesThroughNewPhosphate(
+              new Vec2(0, 0),
+              currentNode.sugar,
+              nextMonomerInSameChain,
+              labeledNucleoelement.phosphateLabel,
+            ),
+          );
+          // Update Phosphate monomerItem object
+        } else if (currentNode.monomer instanceof Phosphate) {
+          modelChanges.merge(
+            editor.drawingEntitiesManager.modifyMonomerItem(
+              currentNode.monomer,
+              phosphateMonomerItem,
+            ),
+          );
+        }
+      }
     }
 
     // Refresh UI
@@ -282,12 +331,13 @@ export class SequenceMode extends BaseMode {
   private bondNodesThroughNewPhosphate(
     position: Vec2,
     previousMonomer: BaseMonomer,
-    nextMonomer: BaseMonomer,
+    nextMonomer?: BaseMonomer,
+    phosphate?: string,
   ) {
     const editor = CoreEditor.provideEditorInstance();
     const phosphateLibraryItem = getRnaPartLibraryItem(
       editor,
-      RNA_DNA_NON_MODIFIED_PART.PHOSPHATE,
+      phosphate || RNA_DNA_NON_MODIFIED_PART.PHOSPHATE,
     );
 
     assert(phosphateLibraryItem);
@@ -309,14 +359,16 @@ export class SequenceMode extends BaseMode {
       ),
     );
 
-    modelChanges.merge(
-      editor.drawingEntitiesManager.createPolymerBond(
-        additionalPhosphate,
-        nextMonomer,
-        AttachmentPointName.R2,
-        AttachmentPointName.R1,
-      ),
-    );
+    if (nextMonomer) {
+      modelChanges.merge(
+        editor.drawingEntitiesManager.createPolymerBond(
+          additionalPhosphate,
+          nextMonomer,
+          AttachmentPointName.R2,
+          AttachmentPointName.R1,
+        ),
+      );
+    }
 
     return modelChanges;
   }

diff --git a/packages/ketcher-core/src/application/editor/tools/Tool.ts b/packages/ketcher-core/src/application/editor/tools/Tool.ts
@@ -1,4 +1,4 @@
-import { MonomerItemType } from 'domain/types';
+import { MonomerItemType, Entities } from 'domain/types';
 
 interface ToolEventHandler {
   click?(event: Event): void;
@@ -76,11 +76,14 @@ export interface IRnaPreset {
   presetInList?: IRnaPreset;
 }
 
-export type LabeledNucleotideWithPositionInSequence = {
-  baseLabel: string;
-  sugarLabel: string;
-  phosphateLabel: string;
+export type LabeledNodesWithPositionInSequence = {
+  type: Entities;
   nodeIndexOverall: number;
+  baseLabel?: string;
+  sugarLabel?: string;
+  phosphateLabel?: string;
+  isNucleosideConnectedAndSelectedWithPhosphate?: boolean;
+  hasR1Connection?: boolean;
 };
 
 export interface Tool extends ToolEventHandler {