#4726 - Delete of nucleoside symbol turns another nucleoside to nucle…

…otide (#4789)

- skip phosphate add/delete logic for middle/beginning of chain
- restricted entering symbols before phosphate
- updated screenshot

ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-edit.spec.ts

@@ -3,7 +3,6 @@ import {
   moveMouseAway,
   openFileAndAddToCanvasMacro,
   selectSequenceLayoutModeTool,
-  selectSingleBondTool,
   selectSnakeLayoutModeTool,
   SequenceType,
   startNewSequence,
@@ -187,37 +186,36 @@ test.describe('Sequence edit mode', () => {
     await takeEditorScreenshot(page);
   });
 
-  test('Bonds between existing and new nucleotides adhere to RNA monomer connection rules', async ({
+  test('Check that when adding new nucleotides to beginning of a row, order of chains not changes in Sequence mode', async ({
     page,
   }) => {
     /*
-    Test case: #3650
-    Description: Phosphate R2 of first nucleotide should be connected with the sugar R1 of next nucleotide.
+    Test case: #4340
+    Description: After adding new nucleotides to beginning of a row, order of chains not changes in Sequence mode.
     */
-    await openFileAndAddToCanvasMacro('KET/rna-g.ket', page);
-    await page.getByText('G').locator('..').first().click({ button: 'right' });
+    await openFileAndAddToCanvasMacro('KET/atuc.ket', page);
+    await takeEditorScreenshot(page);
+    await clickOnSequenceSymbol(page, 'T', { button: 'right' });
     await page.getByTestId('edit_sequence').click();
+    await page.keyboard.press('ArrowLeft');
     await enterSequence(page, 'u');
-    await page.keyboard.press('Escape');
-    await selectSnakeLayoutModeTool(page);
-    await selectSingleBondTool(page);
-    await page.getByText('P').locator('..').nth(1).hover();
     await takeEditorScreenshot(page);
   });
 
-  test('Check that when adding new nucleotides to beginning of a row, order of chains not changes in Sequence mode', async ({
+  test('Adding symbols before separate phosphate should be restricted', async ({
     page,
   }) => {
     /*
-    Test case: #4340
-    Description: After adding new nucleotides to beginning of a row, order of chains not changes in Sequence mode.
+    Github ticket: https://github.com/epam/ketcher/issues/4726
+    Description: It was decided to restrict adding symbols before separate phosphate to prevent adding of nucleosides
+    by entering symbols before the phosphate.
     */
-    await openFileAndAddToCanvasMacro('KET/atuc.ket', page);
-    await takeEditorScreenshot(page);
-    await clickOnSequenceSymbol(page, 'T', { button: 'right' });
+    await openFileAndAddToCanvasMacro('KET/rna-g.ket', page);
+    await page.getByText('G').locator('..').first().click({ button: 'right' });
     await page.getByTestId('edit_sequence').click();
-    await page.keyboard.press('ArrowLeft');
     await enterSequence(page, 'u');
+    await page.keyboard.press('Escape');
+    await selectSnakeLayoutModeTool(page);
     await takeEditorScreenshot(page);
   });
 });

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

@@ -430,24 +430,26 @@ export class SequenceMode extends BaseMode {
   }
 
   private connectNodes(
-    node: SubChainNode | undefined,
-    nextNode: SubChainNode | undefined,
+    firstNodeToConnect: SubChainNode | undefined,
+    secondNodeToConnect: SubChainNode | undefined,
     modelChanges: Command,
     newNodePosition: Vec2,
+    nextNodeInSameChain?: SubChainNode,
   ) {
     if (
-      !node ||
-      node instanceof EmptySequenceNode ||
-      !nextNode ||
-      nextNode instanceof EmptySequenceNode
+      !firstNodeToConnect ||
+      firstNodeToConnect instanceof EmptySequenceNode ||
+      !secondNodeToConnect ||
+      secondNodeToConnect instanceof EmptySequenceNode
     ) {
       return;
     }
 
     const editor = CoreEditor.provideEditorInstance();
-    const nodeR2Bond = node.lastMonomerInNode.attachmentPointsToBonds?.R2;
+    const nodeR2Bond =
+      firstNodeToConnect.lastMonomerInNode.attachmentPointsToBonds?.R2;
     const nextNodeR1Bond =
-      nextNode?.firstMonomerInNode?.attachmentPointsToBonds.R1;
+      secondNodeToConnect?.firstMonomerInNode?.attachmentPointsToBonds.R1;
 
     if (nodeR2Bond || nextNodeR1Bond) {
       editor.events.error.dispatch(
@@ -458,21 +460,23 @@ export class SequenceMode extends BaseMode {
     }
 
     if (
-      node instanceof Nucleoside &&
-      (nextNode instanceof Nucleotide || nextNode instanceof Nucleoside)
+      nextNodeInSameChain instanceof EmptySequenceNode &&
+      firstNodeToConnect instanceof Nucleoside &&
+      (secondNodeToConnect instanceof Nucleotide ||
+        secondNodeToConnect instanceof Nucleoside)
     ) {
       modelChanges.merge(
         this.bondNodesThroughNewPhosphate(
           newNodePosition,
-          node.lastMonomerInNode,
-          nextNode.firstMonomerInNode,
+          firstNodeToConnect.lastMonomerInNode,
+          secondNodeToConnect.firstMonomerInNode,
         ),
       );
     } else {
       modelChanges.merge(
         editor.drawingEntitiesManager.createPolymerBond(
-          node.lastMonomerInNode,
-          nextNode.firstMonomerInNode,
+          firstNodeToConnect.lastMonomerInNode,
+          secondNodeToConnect.firstMonomerInNode,
           AttachmentPointName.R2,
           AttachmentPointName.R1,
         ),
@@ -582,8 +586,7 @@ export class SequenceMode extends BaseMode {
 
       if (
         nodeBeforeSelection instanceof Nucleoside &&
-        (nodeAfterSelection instanceof Nucleotide ||
-          nodeAfterSelection instanceof Nucleoside)
+        nodeAfterSelection instanceof Nucleotide
       ) {
         modelChanges.merge(
           this.bondNodesThroughNewPhosphate(
@@ -916,6 +919,14 @@ export class SequenceMode extends BaseMode {
     const newNodePosition = this.getNewNodePosition();
     let modelChanges;
     const previousNodeInSameChain = SequenceRenderer.previousNodeInSameChain;
+
+    if (
+      currentNode instanceof MonomerSequenceNode &&
+      currentNode.monomer instanceof Phosphate
+    ) {
+      return;
+    }
+
     if (currentNode instanceof EmptySequenceNode && previousNodeInSameChain) {
       if (!this.isR2Free(previousNodeInSameChain)) {
         this.showMergeWarningModal(editor);
@@ -978,6 +989,7 @@ export class SequenceMode extends BaseMode {
       firstNodeOfNewFragment,
       modelChanges,
       newNodePosition,
+      currentNode,
     );
 
     this.connectNodes(