#5678 - Introduce creating antisense chains

packages/ketcher-core/__tests__/application/editor/tools/SelectRectangleTool.test.ts

@@ -147,9 +147,6 @@ describe('Select Rectangle Tool', () => {
     jest
       .spyOn(BaseMonomerRenderer.prototype, 'redrawEnumeration')
       .mockImplementation(() => {});
-    jest
-      .spyOn(BaseMonomerRenderer.prototype, 'reDrawChainBeginning')
-      .mockImplementation(() => {});
     const fn = jest
       .spyOn(window, 'requestAnimationFrame')
       .mockImplementation((func) => {

packages/ketcher-core/src/application/editor/Editor.ts

@@ -55,6 +55,7 @@ import { ViewModel } from 'application/render/view-model/ViewModel';
 import { HandTool } from 'application/editor/tools/Hand';
 import { HydrogenBond } from 'domain/entities/HydrogenBond';
 import { ToolName } from 'application/editor/tools/types';
+import { BaseMonomerRenderer } from 'application/render';
 
 interface ICoreEditorConstructorParams {
   theme;
@@ -230,6 +231,16 @@ export class CoreEditor {
           !(eventData.polymerBond instanceof HydrogenBond))
       ) {
         this.events.rightClickPolymerBond.dispatch(event, eventData);
+      } else if (
+        eventData instanceof BaseMonomerRenderer &&
+        eventData.monomer.selected
+      ) {
+        this.events.rightClickSelectedMonomers.dispatch(
+          event,
+          this.drawingEntitiesManager.selectedEntities
+            .filter(([, drawingEntity]) => drawingEntity instanceof BaseMonomer)
+            .map(([, drawingEntity]) => drawingEntity as BaseMonomer),
+        );
       } else if (isClickOnCanvas) {
         this.events.rightClickCanvas.dispatch(event);
       }
@@ -271,6 +282,20 @@ export class CoreEditor {
     this.events.changeSequenceTypeEnterMode.add((mode: SequenceType) =>
       this.onChangeSequenceTypeEnterMode(mode),
     );
+    this.events.createAntisenseChain.add(() => {
+      this.onCreateAntisenseChain();
+    });
+    this.events.copySelectedStructure.add(() => {
+      this.mode.onCopy();
+    });
+    this.events.deleteSelectedStructure.add(() => {
+      const command = new Command();
+      const history = new EditorHistory(this);
+
+      command.merge(this.drawingEntitiesManager.deleteSelectedEntities());
+      history.update(command);
+      this.renderersContainer.update(command);
+    });
   }
 
   private onEditSequence(sequenceItemRenderer: BaseSequenceItemRenderer) {
@@ -301,6 +326,14 @@ export class CoreEditor {
     this.sequenceTypeEnterMode = mode;
   }
 
+  private onCreateAntisenseChain() {
+    const modelChanges = this.drawingEntitiesManager.createAntisenseChain();
+    const history = new EditorHistory(this);
+
+    this.renderersContainer.update(modelChanges);
+    history.update(modelChanges);
+  }
+
   private onSelectMonomer(monomer: MonomerItemType) {
     if (this.mode instanceof SequenceMode) {
       this.mode.insertMonomerFromLibrary(monomer);
@@ -626,6 +659,18 @@ export class CoreEditor {
         struct,
         this.drawingEntitiesManager,
       );
+
+    if (this.mode instanceof SnakeMode) {
+      modelChanges.merge(
+        this.drawingEntitiesManager.applySnakeLayout(
+          this.canvas.width.baseVal.value,
+          true,
+          true,
+          false,
+        ),
+      );
+    }
+
     this.renderersContainer.update(modelChanges);
     ketcher?.editor.clear();
     this._type = EditorType.Macromolecules;

packages/ketcher-core/src/application/editor/editorEvents.ts

@@ -36,6 +36,7 @@ export function resetEditorEvents() {
     rightClickSequence: new Subscription(),
     rightClickCanvas: new Subscription(),
     rightClickPolymerBond: new Subscription(),
+    rightClickSelectedMonomers: new Subscription(),
     editSequence: new Subscription(),
     startNewSequence: new Subscription(),
     turnOnSequenceEditInRNABuilderMode: new Subscription(),
@@ -53,6 +54,9 @@ export function resetEditorEvents() {
     doubleClickOnSequenceItem: new Subscription(),
     openConfirmationDialog: new Subscription(),
     mouseUpAtom: new Subscription(),
+    createAntisenseChain: new Subscription(),
+    copySelectedStructure: new Subscription(),
+    deleteSelectedStructure: new Subscription(),
   };
 }
 resetEditorEvents();
@@ -73,6 +77,7 @@ export const renderersEvents: ToolEventHandlerName[] = [
   'rightClickSequence',
   'rightClickCanvas',
   'rightClickPolymerBond',
+  'rightClickSelectedMonomers',
   'editSequence',
   'startNewSequence',
   'turnOnSequenceEditInRNABuilderMode',

packages/ketcher-core/src/application/editor/modes/BaseMode.ts

@@ -105,8 +105,8 @@ export abstract class BaseMode {
 
   abstract scrollForView(): void;
 
-  onCopy(event: ClipboardEvent) {
-    if (this.checkIfTargetIsInput(event)) {
+  onCopy(event?: ClipboardEvent) {
+    if (event && this.checkIfTargetIsInput(event)) {
       return;
     }
     const editor = CoreEditor.provideEditorInstance();
@@ -162,7 +162,7 @@ export abstract class BaseMode {
     );
     if (isClipboardAPIAvailable()) {
       navigator.clipboard.writeText(serializedKet);
-    } else {
+    } else if (event) {
       legacyCopy(event.clipboardData, {
         'text/plain': serializedKet,
       });

packages/ketcher-core/src/application/editor/modes/SequenceMode.ts

@@ -32,11 +32,13 @@ import assert from 'assert';
 import {
   getPeptideLibraryItem,
   getRnaPartLibraryItem,
+  getSugarBySequenceType,
 } from 'domain/helpers/rna';
 import {
   peptideNaturalAnalogues,
   RNA_DNA_NON_MODIFIED_PART,
   rnaDnaNaturalAnalogues,
+  RnaDnaNaturalAnaloguesEnum,
 } from 'domain/constants/monomers';
 import { SubChainNode } from 'domain/entities/monomer-chains/types';
 import { isNumber, uniq } from 'lodash';
@@ -106,7 +108,7 @@ export class SequenceMode extends BaseMode {
     // Prevent rearranging chains (and recalculating the layout) when switching to sequence mode,
     // only recalculate after changes in the sequence
     const modelChanges = needReArrangeChains
-      ? editor.drawingEntitiesManager.reArrangeChains(
+      ? editor.drawingEntitiesManager.applySnakeLayout(
           editor.canvas.width.baseVal.value,
           true,
           false,
@@ -494,19 +496,28 @@ export class SequenceMode extends BaseMode {
   }
 
   private handleRnaDnaNodeAddition(
-    enteredSymbol: string,
+    enteredSymbol: RnaDnaNaturalAnaloguesEnum | string,
     currentNode: SubChainNode,
     newNodePosition: Vec2,
   ) {
     if (!rnaDnaNaturalAnalogues.includes(enteredSymbol)) {
       return undefined;
     }
 
+    const editor = CoreEditor.provideEditorInstance();
     const modelChanges = new Command();
     const { modelChanges: addedNodeModelChanges, node: nodeToAdd } =
       currentNode instanceof Nucleotide || currentNode instanceof Nucleoside
-        ? Nucleotide.createOnCanvas(enteredSymbol, newNodePosition)
-        : Nucleoside.createOnCanvas(enteredSymbol, newNodePosition);
+        ? Nucleotide.createOnCanvas(
+            enteredSymbol,
+            newNodePosition,
+            getSugarBySequenceType(editor.sequenceTypeEnterMode),
+          )
+        : Nucleoside.createOnCanvas(
+            enteredSymbol,
+            newNodePosition,
+            getSugarBySequenceType(editor.sequenceTypeEnterMode),
+          );
 
     modelChanges.merge(addedNodeModelChanges);
 

packages/ketcher-core/src/application/editor/modes/SnakeMode.ts

@@ -27,7 +27,7 @@ export class SnakeMode extends BaseMode {
     // we need just redraw canvas to apply new bond view style (straight instead of curved)
     const modelChanges = _isUndo
       ? new Command()
-      : editor.drawingEntitiesManager.reArrangeChains(
+      : editor.drawingEntitiesManager.applySnakeLayout(
           editor.canvas.width.baseVal.value,
           true,
         );

packages/ketcher-core/src/application/editor/operations/modes/snake.ts

@@ -2,6 +2,7 @@ import { Operation } from 'domain/entities/Operation';
 import { RenderersManager } from 'application/render/renderers/RenderersManager';
 
 export class RecalculateCanvasMatrixOperation implements Operation {
+  public priority = 1;
   constructor(
     private recalculateCanvasMatrixModelChange: () => void,
     private invertRecalculateCanvasMatrixModelChange: () => void,

packages/ketcher-core/src/application/editor/operations/monomer/index.ts

@@ -128,6 +128,7 @@ export class MonomerItemModifyOperation implements Operation {
     public revertMonomerItem: () => BaseMonomer,
   ) {
     this.monomer = monomer;
+    this.execute();
   }
 
   public execute() {

packages/ketcher-core/src/application/editor/operations/polymerBond/index.ts

@@ -18,14 +18,15 @@ import { PolymerBond } from 'domain/entities/PolymerBond';
 import { RenderersManager } from 'application/render/renderers/RenderersManager';
 import { Operation } from 'domain/entities/Operation';
 import { BaseMonomer } from 'domain/entities/BaseMonomer';
+import { HydrogenBond } from 'domain/entities';
 
 export class PolymerBondAddOperation implements Operation {
   public polymerBond;
   public priority = 1;
   constructor(
     private addPolymerBondChangeModel: (
-      polymerBond?: PolymerBond,
-    ) => PolymerBond,
+      polymerBond?: PolymerBond | HydrogenBond,
+    ) => PolymerBond | HydrogenBond,
     private deletePolymerBondChangeModel: (polymerBond) => void,
   ) {
     this.polymerBond = this.addPolymerBondChangeModel();
@@ -45,11 +46,11 @@ export class PolymerBondAddOperation implements Operation {
 export class PolymerBondDeleteOperation implements Operation {
   public priority = -1;
   constructor(
-    public polymerBond: PolymerBond,
+    public polymerBond: PolymerBond | HydrogenBond,
     private deletePolymerBondChangeModel: () => void,
     private finishPolymerBondCreationModelChange: (
-      polymerBond?: PolymerBond,
-    ) => PolymerBond,
+      polymerBond?: PolymerBond | HydrogenBond,
+    ) => PolymerBond | HydrogenBond,
   ) {
     this.deletePolymerBondChangeModel();
   }

packages/ketcher-core/src/application/editor/tools/Bond.ts

@@ -143,7 +143,6 @@ class PolymerBond implements BaseTool {
       this.editor.drawingEntitiesManager.hidePolymerBondInformation(
         renderer.polymerBond,
       );
-    this.editor.renderersContainer.markForRecalculateBegin();
     this.editor.renderersContainer.update(modelChanges);
   }
 
@@ -157,7 +156,6 @@ class PolymerBond implements BaseTool {
       this.editor.drawingEntitiesManager.showPolymerBondInformation(
         renderer.polymerBond,
       );
-    this.editor.renderersContainer.markForRecalculateBegin();
     this.editor.renderersContainer.update(modelChanges);
   }
 
@@ -188,7 +186,6 @@ class PolymerBond implements BaseTool {
         );
     }
 
-    this.editor.renderersContainer.markForRecalculateBegin();
     this.editor.renderersContainer.update(modelChanges);
   }
 
@@ -229,7 +226,6 @@ class PolymerBond implements BaseTool {
         );
     }
 
-    this.editor.renderersContainer.markForRecalculateBegin();
     this.editor.renderersContainer.update(modelChanges);
   }
 
@@ -257,7 +253,6 @@ class PolymerBond implements BaseTool {
           this.bondRenderer?.polymerBond,
         );
 
-      this.editor.renderersContainer.markForRecalculateBegin();
       this.editor.renderersContainer.update(modelChanges);
     }
   }
@@ -276,7 +271,6 @@ class PolymerBond implements BaseTool {
           attachmentPointRenderer.monomer,
           this.bondRenderer?.polymerBond,
         );
-      this.editor.renderersContainer.markForRecalculateBegin();
       this.editor.renderersContainer.update(modelChanges);
     }
   }
@@ -329,8 +323,6 @@ class PolymerBond implements BaseTool {
       this.editor.renderersContainer.update(modelChanges);
       this.editor.renderersContainer.deletePolymerBond(
         this.bondRenderer.polymerBond,
-        false,
-        false,
       );
       this.bondRenderer = undefined;
       event.stopPropagation();
@@ -448,8 +440,6 @@ class PolymerBond implements BaseTool {
       this.editor.renderersContainer.update(modelChanges);
       this.editor.renderersContainer.deletePolymerBond(
         this.bondRenderer.polymerBond,
-        false,
-        false,
       );
       this.bondRenderer = undefined;
       this.history.update(modelChanges);
@@ -520,8 +510,6 @@ class PolymerBond implements BaseTool {
     this.isBondConnectionModalOpen = false;
     this.editor.renderersContainer.deletePolymerBond(
       this.bondRenderer.polymerBond,
-      false,
-      false,
     );
     this.bondRenderer = undefined;
   };

packages/ketcher-core/src/application/editor/tools/SelectRectangle.ts

@@ -278,7 +278,6 @@ class SelectRectangle implements BaseTool {
       this.editor.drawingEntitiesManager.showPolymerBondInformation(
         renderer.polymerBond,
       );
-    this.editor.renderersContainer.markForRecalculateBegin();
     this.editor.renderersContainer.update(modelChanges);
   }
 
@@ -293,7 +292,6 @@ class SelectRectangle implements BaseTool {
       this.editor.drawingEntitiesManager.hidePolymerBondInformation(
         renderer.polymerBond,
       );
-    this.editor.renderersContainer.markForRecalculateBegin();
     this.editor.renderersContainer.update(modelChanges);
   }
 

packages/ketcher-core/src/application/editor/tools/Tool.ts

@@ -50,6 +50,8 @@ interface ToolEventHandler {
 
   rightClickPolymerBond?(event: Event): void;
 
+  rightClickSelectedMonomers?(event: Event): void;
+
   editSequence?(): void;
 
   startNewSequence?(): void;

packages/ketcher-core/src/application/render/renderers/AmbiguousMonomerRenderer.ts

@@ -44,7 +44,8 @@ export class AmbiguousMonomerRenderer extends BaseMonomerRenderer {
 
     this.monomerRenderer = new MonomerRenderer(new EmptyMonomer());
     this.monomerSymbolElementsIds = monomerSymbolElementsIds;
-    this.CHAIN_BEGINNING = this.monomerRenderer.CHAIN_BEGINNING;
+    this.CHAIN_START_TERMINAL_INDICATOR_TEXT =
+      this.monomerRenderer.CHAIN_START_TERMINAL_INDICATOR_TEXT;
   }
 
   protected appendBody(
@@ -122,9 +123,6 @@ export class AmbiguousMonomerRenderer extends BaseMonomerRenderer {
     if (this.enumerationElementPosition) {
       this.appendEnumeration();
     }
-    if (this.CHAIN_BEGINNING) {
-      this.appendChainBeginning();
-    }
   }
 
   private appendPreviewAttachmentPoint(