6383 dna antisense chains (#6571)

* 6368 Introduce the creation of DNA antisense chains * 6368 Introduce the creation of DNA antisense chains * 6368 Introduce the creation of DNA antisense chains * 6368 Introduce the creation of DNA antisense chains * 6368 Introduce the creation of DNA antisense chains * 6368 Introduce the creation of DNA antisense chains * - updated screenshots * updated screenshots * updated screenshots --------- Co-authored-by: Aleksandr Afanasev <[email protected]> Co-authored-by: Roman Rodionov <[email protected]>
epam · Feb 28, 2025 · 36d3df1 · 36d3df1
1 parent 5b3ca32
commit 36d3df1
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Showing 16 changed files with 86 additions and 38 deletions.
diff --git a/ketcher-autotests/tests/Macromolecule-editor/Antisense-Chains/antisense-chain-layout.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Antisense-Chains/antisense-chain-layout.spec.ts
@@ -663,7 +663,7 @@ test(`5. Check that backbones should be placed parallel to each other`, async ()
   await selectAllStructuresOnCanvas(page);
   await callContextMenuForMonomer(page, 0);
   const createAntisenseStrandOption = page
-    .getByTestId('create_antisense_chain')
+    .getByTestId('create_antisense_rna_chain')
     .first();
   await createAntisenseStrandOption.click();
 

diff --git a/ketcher-autotests/tests/Macromolecule-editor/Antisense-Chains/antisense-chains.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Antisense-Chains/antisense-chains.spec.ts
@@ -922,7 +922,7 @@ for (const monomer of monomers.filter((m) => m.eligibleForAntisense)) {
     await callContextMenuForMonomer(page, monomer.monomerLocatorIndex);
 
     const createAntisenseStrandOption = page
-      .getByTestId('create_antisense_chain')
+      .getByTestId('create_antisense_rna_chain')
       .first();
 
     // Checking presence of Create Antisense Strand option on the context menu and enabled
@@ -963,7 +963,7 @@ for (const monomer of monomers.filter(
     await callContextMenuForMonomer(page, monomer.monomerLocatorIndex);
 
     const createAntisenseStrandOption = page
-      .getByTestId('create_antisense_chain')
+      .getByTestId('create_antisense_rna_chain')
       .first();
     const createAntisenseStrandOptionPresent =
       (await createAntisenseStrandOption.count()) > 0;
@@ -2184,7 +2184,7 @@ for (const chain of chainWithExtraBondToBase) {
     await callContextMenuForMonomer(page, chain.monomerLocatorIndex);
 
     const createAntisenseStrandOption = page
-      .getByTestId('create_antisense_chain')
+      .getByTestId('create_antisense_rna_chain')
       .first();
     const createAntisenseStrandOptionPresent =
       (await createAntisenseStrandOption.count()) > 0;
@@ -2372,7 +2372,7 @@ for (const monomer1 of shortMonomerList) {
       await callContextMenuForMonomer(page, monomer1.monomerLocatorIndex);
 
       const createAntisenseStrandOption = page
-        .getByTestId('create_antisense_chain')
+        .getByTestId('create_antisense_rna_chain')
         .first();
 
       if (
@@ -2449,7 +2449,7 @@ test(`5. Check that all non R1-R2 connections of backbone monomers (except R3-R1
   await callContextMenuForMonomer(page, chain.monomerLocatorIndex);
 
   const createAntisenseStrandOption = page
-    .getByTestId('create_antisense_chain')
+    .getByTestId('create_antisense_rna_chain')
     .first();
 
   // Checking presence of Create Antisense Strand option on the context menu and enabled
@@ -2500,7 +2500,7 @@ test(`6. Check that every nucleotide (sugar and phosphate are part of the backbo
   await callContextMenuForMonomer(page, chain.monomerLocatorIndex);
 
   const createAntisenseStrandOption = page
-    .getByTestId('create_antisense_chain')
+    .getByTestId('create_antisense_rna_chain')
     .first();
 
   // Checking presence of Create Antisense Strand option on the context menu and enabled
@@ -2589,7 +2589,7 @@ test(`7. Check that every nucleoside (not a nucleotide, sugar is connected throu
   await callContextMenuForMonomer(page, chain.monomerLocatorIndex);
 
   const createAntisenseStrandOption = page
-    .getByTestId('create_antisense_chain')
+    .getByTestId('create_antisense_rna_chain')
     .first();
 
   // Checking presence of Create Antisense Strand option on the context menu and enabled
@@ -2637,7 +2637,7 @@ test(`8. Check that all other monomers in the backbone that are not a part of th
   await callContextMenuForMonomer(page, chain.monomerLocatorIndex);
 
   const createAntisenseStrandOption = page
-    .getByTestId('create_antisense_chain')
+    .getByTestId('create_antisense_rna_chain')
     .first();
 
   // Checking presence of Create Antisense Strand option on the context menu and enabled
@@ -2688,7 +2688,7 @@ test(`9. Check that the antisense chain should be "flipped" in relation to the s
   await callContextMenuForMonomer(page, chain.monomerLocatorIndex);
 
   const createAntisenseStrandOption = page
-    .getByTestId('create_antisense_chain')
+    .getByTestId('create_antisense_rna_chain')
     .first();
 
   // Checking presence of Create Antisense Strand option on the context menu and enabled
@@ -2824,7 +2824,7 @@ test(`13. Validate that creating, deleting, and modifying the antisense chain su
   await callContextMenuForMonomer(page, chain.monomerLocatorIndex);
 
   const createAntisenseStrandOption = page
-    .getByTestId('create_antisense_chain')
+    .getByTestId('create_antisense_rna_chain')
     .first();
 
   // Checking presence of Create Antisense Strand option on the context menu and enabled
@@ -2889,7 +2889,7 @@ test(`14. Validate that both sense and antisense strands can be exported correct
   await callContextMenuForMonomer(page, chain.monomerLocatorIndex);
 
   const createAntisenseStrandOption = page
-    .getByTestId('create_antisense_chain')
+    .getByTestId('create_antisense_rna_chain')
     .first();
 
   // Checking presence of Create Antisense Strand option on the context menu and enabled
@@ -2944,7 +2944,7 @@ test(`15. Ensure that switching between (Flex, Snake, Sequence) modes does not b
   await callContextMenuForMonomer(page, chain.monomerLocatorIndex);
 
   const createAntisenseStrandOption = page
-    .getByTestId('create_antisense_chain')
+    .getByTestId('create_antisense_rna_chain')
     .first();
 
   // Checking presence of Create Antisense Strand option on the context menu and enabled
@@ -2988,7 +2988,7 @@ test(`16. Ensure that switching between macro and micro modes does not break the
   await callContextMenuForMonomer(page, chain.monomerLocatorIndex);
 
   const createAntisenseStrandOption = page
-    .getByTestId('create_antisense_chain')
+    .getByTestId('create_antisense_rna_chain')
     .first();
 
   // Checking presence of Create Antisense Strand option on the context menu and enabled
@@ -3031,7 +3031,7 @@ test(`17. Verify that copying the sense and antisense strand and pasting it with
   await callContextMenuForMonomer(page, chain.monomerLocatorIndex);
 
   const createAntisenseStrandOption = page
-    .getByTestId('create_antisense_chain')
+    .getByTestId('create_antisense_rna_chain')
     .first();
 
   // Checking presence of Create Antisense Strand option on the context menu and enabled

diff --git a/...backbo-68bef-oside-directly-copied-to-the-antisense-strand-1-chromium-linux.png b/...backbo-68bef-oside-directly-copied-to-the-antisense-strand-1-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
@@ -43,18 +43,25 @@ test.describe('Sequence mode edit in RNA Builder', () => {
     await waitForMonomerPreview(page);
 
     // should see correct context menu title and available 'modify_in_rna_builder' button
-    await takeEditorScreenshot(page);
+    await takeEditorScreenshot(page, {
+      hideMonomerPreview: true,
+    });
     await page.getByTestId('modify_in_rna_builder').click();
     // should see uploaded nucleotide data to RNA Builder and disabled "Update" button
     // should see disabled top bar's selectors
     // should see disabled top undo/redo/open buttons
+    await moveMouseAway(page);
     await takePageScreenshot(page);
     await page.getByTestId(SUGAR).click();
     // should see disabled and nondisabled sugars
-    await takeMonomerLibraryScreenshot(page);
+    await takeMonomerLibraryScreenshot(page, {
+      hideMonomerPreview: true,
+    });
     await selectMonomer(page, Sugars._25R);
     // should see updated sugar, updated title of preset and nondisabled "Update" button
-    await takeRNABuilderScreenshot(page);
+    await takeRNABuilderScreenshot(page, {
+      hideMonomerPreview: true,
+    });
     await pressSaveButton(page);
     // should see updated nucleotide in chain
     // should see nondisabled top bar's selectors

diff --git a/...-builde-568bf-ected-without-an-adjacent-nucleoside-to-left-1-chromium-linux.png b/...-builde-568bf-ected-without-an-adjacent-nucleoside-to-left-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-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/...edit-in-RNA-Builder-Select-one-nucleotide-and-modify-sugar-1-chromium-linux.png b/...edit-in-RNA-Builder-Select-one-nucleotide-and-modify-sugar-1-chromium-linux.png
diff --git a/...edit-in-RNA-Builder-Select-one-nucleotide-and-modify-sugar-4-chromium-linux.png b/...edit-in-RNA-Builder-Select-one-nucleotide-and-modify-sugar-4-chromium-linux.png
diff --git a/...lder-Select-two-nucleotides-and-modify-sugar-and-phosphate-2-chromium-linux.png b/...lder-Select-two-nucleotides-and-modify-sugar-and-phosphate-2-chromium-linux.png
diff --git a/packages/ketcher-core/src/application/editor/Editor.ts b/packages/ketcher-core/src/application/editor/Editor.ts
@@ -384,8 +384,8 @@ export class CoreEditor {
     this.events.changeSequenceTypeEnterMode.add((mode: SequenceType) =>
       this.onChangeSequenceTypeEnterMode(mode),
     );
-    this.events.createAntisenseChain.add(() => {
-      this.onCreateAntisenseChain();
+    this.events.createAntisenseChain.add((isDnaAntisense: boolean) => {
+      this.onCreateAntisenseChain(isDnaAntisense);
     });
     this.events.copySelectedStructure.add(() => {
       this.mode.onCopy();
@@ -428,8 +428,9 @@ export class CoreEditor {
     this.sequenceTypeEnterMode = mode;
   }
 
-  private onCreateAntisenseChain() {
-    const modelChanges = this.drawingEntitiesManager.createAntisenseChain();
+  private onCreateAntisenseChain(isDnaAntisense: boolean) {
+    const modelChanges =
+      this.drawingEntitiesManager.createAntisenseChain(isDnaAntisense);
     const history = new EditorHistory(this);
 
     this.renderersContainer.update(modelChanges);

diff --git a/packages/ketcher-core/src/application/editor/modes/SequenceMode.ts b/packages/ketcher-core/src/application/editor/modes/SequenceMode.ts
@@ -1202,6 +1202,7 @@ export class SequenceMode extends BaseMode {
                       previousTwoStrandedNode?.antisenseNode instanceof
                       EmptySequenceNode
                     )),
+                false,
               );
 
             if (antisenseNodeCreationResult && currentTwoStrandedNode) {

diff --git a/packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts b/packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts
@@ -2526,8 +2526,8 @@ export class DrawingEntitiesManager {
     };
   }
 
-  private static get antisenseChainBasesMap() {
-    return {
+  private static antisenseChainBasesMap(isDnaAntisense: boolean) {
+    const antisenseMap = {
       [RnaDnaNaturalAnaloguesEnum.ADENINE]: RnaDnaNaturalAnaloguesEnum.URACIL,
       [RnaDnaNaturalAnaloguesEnum.CYTOSINE]: RnaDnaNaturalAnaloguesEnum.GUANINE,
       [RnaDnaNaturalAnaloguesEnum.GUANINE]: RnaDnaNaturalAnaloguesEnum.CYTOSINE,
@@ -2545,6 +2545,12 @@ export class DrawingEntitiesManager {
       [StandardAmbiguousRnaBase.S]: StandardAmbiguousRnaBase.S,
       [StandardAmbiguousRnaBase.V]: StandardAmbiguousRnaBase.B,
     };
+    if (isDnaAntisense) {
+      antisenseMap[RnaDnaNaturalAnaloguesEnum.ADENINE] =
+        RnaDnaNaturalAnaloguesEnum.THYMINE;
+    }
+
+    return antisenseMap;
   }
 
   public markMonomerAsAntisense(monomer: BaseMonomer) {
@@ -2700,8 +2706,11 @@ export class DrawingEntitiesManager {
     );
   }
 
-  private static getAntisenseBaseLabel(rnaBase: RNABase | AmbiguousMonomer) {
-    return DrawingEntitiesManager.antisenseChainBasesMap[
+  private static getAntisenseBaseLabel(
+    rnaBase: RNABase | AmbiguousMonomer,
+    isDnaAntisense: boolean,
+  ) {
+    return DrawingEntitiesManager.antisenseChainBasesMap(isDnaAntisense)[
       rnaBase instanceof AmbiguousMonomer
         ? rnaBase.monomerItem.label
         : rnaBase.monomerItem.props.MonomerNaturalAnalogCode
@@ -2711,23 +2720,27 @@ export class DrawingEntitiesManager {
   public static createAntisenseNode(
     node: Nucleoside | Nucleotide,
     needAddPhosphate = false,
+    isDnaAntisense: boolean,
   ) {
     const antisenseBaseLabel = DrawingEntitiesManager.getAntisenseBaseLabel(
       node.rnaBase,
+      isDnaAntisense,
     );
 
     if (!antisenseBaseLabel) {
       return;
     }
-
+    const sugarName = isDnaAntisense
+      ? RNA_DNA_NON_MODIFIED_PART.SUGAR_DNA
+      : RNA_DNA_NON_MODIFIED_PART.SUGAR_RNA;
     return (needAddPhosphate ? Nucleotide : Nucleoside).createOnCanvas(
       antisenseBaseLabel,
       node.monomer.position.add(new Vec2(0, 3)),
-      RNA_DNA_NON_MODIFIED_PART.SUGAR_RNA,
+      sugarName,
     );
   }
 
-  public createAntisenseChain() {
+  public createAntisenseChain(isDnaAntisense: boolean) {
     const editor = CoreEditor.provideEditorInstance();
     const command = new Command();
     const selectedMonomers = this.selectedEntities
@@ -2741,7 +2754,10 @@ export class DrawingEntitiesManager {
             (node) =>
               (node instanceof Nucleotide || node instanceof Nucleoside) &&
               Boolean(
-                DrawingEntitiesManager.getAntisenseBaseLabel(node.rnaBase),
+                DrawingEntitiesManager.getAntisenseBaseLabel(
+                  node.rnaBase,
+                  isDnaAntisense,
+                ),
               ) &&
               node.monomer.selected,
           ),
@@ -2796,7 +2812,11 @@ export class DrawingEntitiesManager {
 
         if (node instanceof Nucleotide || node instanceof Nucleoside) {
           const antisenseNodeCreationResult =
-            DrawingEntitiesManager.createAntisenseNode(node, false);
+            DrawingEntitiesManager.createAntisenseNode(
+              node,
+              false,
+              isDnaAntisense,
+            );
 
           if (!antisenseNodeCreationResult) {
             return;

diff --git a/...es/src/components/contextMenu/SelectedMonomersContextMenu/SelectedMonomersContextMenu.tsx b/...es/src/components/contextMenu/SelectedMonomersContextMenu/SelectedMonomersContextMenu.tsx
@@ -29,8 +29,24 @@ export const SelectedMonomersContextMenu = ({
       title: 'Copy',
     },
     {
-      name: 'create_antisense_chain',
-      title: 'Create Antisense Strand',
+      name: 'create_antisense_rna_chain',
+      title: 'Create Antisense RNA Strand',
+      separator: false,
+      disabled: isAntisenseCreationDisabled(selectedMonomers),
+      hidden: ({ props }: { props?: { selectedMonomers?: BaseMonomer[] } }) => {
+        return !props?.selectedMonomers?.some((selectedMonomer) => {
+          return (
+            (selectedMonomer instanceof RNABase &&
+              getSugarFromRnaBase(selectedMonomer)) ||
+            (selectedMonomer instanceof Sugar &&
+              getRnaBaseFromSugar(selectedMonomer))
+          );
+        });
+      },
+    },
+    {
+      name: 'create_antisense_dna_chain',
+      title: 'Create Antisense DNA Strand',
       separator: true,
       disabled: isAntisenseCreationDisabled(selectedMonomers),
       hidden: ({ props }: { props?: { selectedMonomers?: BaseMonomer[] } }) => {
@@ -55,8 +71,11 @@ export const SelectedMonomersContextMenu = ({
       case 'copy':
         editor.events.copySelectedStructure.dispatch();
         break;
-      case 'create_antisense_chain':
-        editor.events.createAntisenseChain.dispatch();
+      case 'create_antisense_rna_chain':
+        editor.events.createAntisenseChain.dispatch(false);
+        break;
+      case 'create_antisense_dna_chain':
+        editor.events.createAntisenseChain.dispatch(true);
         break;
       case 'delete':
         editor.events.deleteSelectedStructure.dispatch();

diff --git a/...omolecules/src/components/contextMenu/SequenceItemContextMenu/SequenceItemContextMenu.tsx b/...omolecules/src/components/contextMenu/SequenceItemContextMenu/SequenceItemContextMenu.tsx
@@ -116,7 +116,7 @@ export const SequenceItemContextMenu = ({
     {
       name: SequenceItemContextMenuNames.createDnaAntisenseStrand,
       title: 'Create DNA antisense strand',
-      disabled: true,
+      disabled: isAntisenseCreationDisabled(extractedBaseMonomers),
       hidden: isAntisenseOptionHidden,
     },
     {
@@ -184,10 +184,10 @@ export const SequenceItemContextMenu = ({
         editor.events.editSequence.dispatch(props.sequenceItemRenderer);
         break;
       case SequenceItemContextMenuNames.createRnaAntisenseStrand:
-        editor.events.createAntisenseChain.dispatch();
+        editor.events.createAntisenseChain.dispatch(false);
         break;
       case SequenceItemContextMenuNames.createDnaAntisenseStrand:
-        // TODO: implement createDnaAntisenseStrand
+        editor.events.createAntisenseChain.dispatch(true);
         break;
       default:
         break;
-Original file line number
+Diff line change
@@ Expand Up / @@ -1202,6 +1202,7 @@ export class SequenceMode extends BaseMode { @@
                           previousTwoStrandedNode?.antisenseNode instanceof
                           EmptySequenceNode
                         )),
+                    false,
                   );
                 if (antisenseNodeCreationResult && currentTwoStrandedNode) {
@@ Expand Down @@