#6252 - allow creation of antisense chains in sequence mode (#6516)

* feat: Add antisense logic in menu dropdown

* feat: Reuse antisense logic in menu dropdown from other view

* feat: Update rerender for sequence mode

* feat: Update Playwright tests

* feat: Update Playwright test

* - updated screenshots

---------

Co-authored-by: Roman Rodionov <[email protected]>

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

@@ -266,6 +266,7 @@ test.describe('Sequence mode selection for view mode', () => {
     await takeEditorScreenshot(page);
     await page.getByText('G').first().click({ button: 'right' });
     await page.getByTestId('edit_sequence').click();
+    await moveMouseAway(page);
     await takeEditorScreenshot(page);
   });
 });

packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts

@@ -96,6 +96,7 @@ import {
   StandardAmbiguousRnaBase,
 } from 'domain/constants/monomers';
 import { Chain } from 'domain/entities/monomer-chains/Chain';
+import { ReinitializeModeOperation } from 'application/editor/operations/modes';
 import {
   SnakeLayoutModel,
   SnakeLayoutNode,
@@ -2897,6 +2898,10 @@ export class DrawingEntitiesManager {
       this.applySnakeLayout(editor.canvas.width.baseVal.value, true, true),
     );
 
+    if (editor.mode instanceof SequenceMode) {
+      command.addOperation(new ReinitializeModeOperation());
+    }
+
     command.setUndoOperationsByPriority();
 
     return command;

packages/ketcher-macromolecules/src/components/contextMenu/SelectedMonomersContextMenu/SelectedMonomersContextMenu.tsx

@@ -5,113 +5,23 @@ import { KETCHER_MACROMOLECULES_ROOT_NODE_SELECTOR } from 'ketcher-react';
 import { useAppSelector } from 'hooks';
 import { selectEditor } from 'state/common';
 import {
-  AmbiguousMonomer,
   BaseMonomer,
   getRnaBaseFromSugar,
   getSugarFromRnaBase,
-  isRnaBaseOrAmbiguousRnaBase,
-  KetAmbiguousMonomerTemplateSubType,
   RNABase,
   Sugar,
 } from 'ketcher-core';
 import { ContextMenu } from 'components/contextMenu/ContextMenu';
+import { isAntisenseCreationDisabled } from './helpers';
 
 type SelectedMonomersContextMenuType = {
   selectedMonomers: BaseMonomer[];
 };
 
-const getMonomersCode = (monomers: BaseMonomer[]) => {
-  return monomers
-    .map((monomer) => monomer.monomerItem.props.MonomerNaturalAnalogCode)
-    .sort()
-    .join('');
-};
-const isSenseBase = (monomer: BaseMonomer | AmbiguousMonomer) => {
-  const { monomerItem } = monomer;
-  const isNaturalAnalogue =
-    monomerItem.props.MonomerNaturalAnalogCode === 'A' ||
-    monomerItem.props.MonomerNaturalAnalogCode === 'C' ||
-    monomerItem.props.MonomerNaturalAnalogCode === 'G' ||
-    monomerItem.props.MonomerNaturalAnalogCode === 'T' ||
-    monomerItem.props.MonomerNaturalAnalogCode === 'U';
-  if (isNaturalAnalogue) {
-    return true;
-  }
-  if (!monomer.monomerItem.isAmbiguous) {
-    return false;
-  }
-
-  if (
-    (monomer as AmbiguousMonomer).subtype ===
-    KetAmbiguousMonomerTemplateSubType.MIXTURE
-  ) {
-    return false;
-  }
-
-  const N1 = 'ACGT';
-  const N2 = 'ACGU';
-  const B1 = 'CGT';
-  const B2 = 'CGU';
-  const D1 = 'AGT';
-  const D2 = 'AGU';
-  const H1 = 'ACT';
-  const H2 = 'ACU';
-  const K1 = 'GT';
-  const K2 = 'GU';
-  const W1 = 'AT';
-  const W2 = 'AU';
-  const Y1 = 'CT';
-  const Y2 = 'CU';
-  const M = 'AC';
-  const R = 'AG';
-  const S = 'CG';
-  const V = 'ACG';
-  const ambigues = [
-    N1,
-    N2,
-    B1,
-    B2,
-    D1,
-    D2,
-    H1,
-    H2,
-    K1,
-    K2,
-    W1,
-    W2,
-    Y1,
-    Y2,
-    M,
-    R,
-    S,
-    V,
-  ];
-  const code = getMonomersCode((monomer as AmbiguousMonomer).monomers);
-  return ambigues.some((v) => v === code);
-};
-
 export const SelectedMonomersContextMenu = ({
   selectedMonomers,
 }: SelectedMonomersContextMenuType) => {
   const editor = useAppSelector(selectEditor);
-  const isAntisenseCreationDisabled = selectedMonomers?.some(
-    (selectedMonomer: BaseMonomer) => {
-      const rnaBaseForSugar =
-        selectedMonomer instanceof Sugar &&
-        getRnaBaseFromSugar(selectedMonomer);
-
-      return (
-        (selectedMonomer instanceof RNABase &&
-          (selectedMonomer.hydrogenBonds.length > 0 ||
-            selectedMonomer.covalentBonds.length > 1)) ||
-        (isRnaBaseOrAmbiguousRnaBase(selectedMonomer) &&
-          !isSenseBase(selectedMonomer)) ||
-        (rnaBaseForSugar &&
-          (rnaBaseForSugar.hydrogenBonds.length > 0 ||
-            !isSenseBase(rnaBaseForSugar)))
-      );
-    },
-  );
 
   const menuItems = [
     {
@@ -122,7 +32,7 @@ export const SelectedMonomersContextMenu = ({
       name: 'create_antisense_chain',
       title: 'Create Antisense Strand',
       separator: true,
-      disabled: isAntisenseCreationDisabled,
+      disabled: isAntisenseCreationDisabled(selectedMonomers),
       hidden: ({ props }: { props?: { selectedMonomers?: BaseMonomer[] } }) => {
         return !props?.selectedMonomers?.some((selectedMonomer) => {
           return (

packages/ketcher-macromolecules/src/components/contextMenu/SelectedMonomersContextMenu/helpers.ts

@@ -0,0 +1,100 @@
+import {
+  AmbiguousMonomer,
+  BaseMonomer,
+  getRnaBaseFromSugar,
+  isRnaBaseOrAmbiguousRnaBase,
+  KetAmbiguousMonomerTemplateSubType,
+  RNABase,
+  Sugar,
+} from 'ketcher-core';
+
+const getMonomersCode = (monomers: BaseMonomer[]) => {
+  return monomers
+    .map((monomer) => monomer.monomerItem.props.MonomerNaturalAnalogCode)
+    .sort()
+    .join('');
+};
+
+export const isSenseBase = (monomer: BaseMonomer | AmbiguousMonomer) => {
+  const { monomerItem } = monomer;
+  const isNaturalAnalogue =
+    monomerItem.props.MonomerNaturalAnalogCode === 'A' ||
+    monomerItem.props.MonomerNaturalAnalogCode === 'C' ||
+    monomerItem.props.MonomerNaturalAnalogCode === 'G' ||
+    monomerItem.props.MonomerNaturalAnalogCode === 'T' ||
+    monomerItem.props.MonomerNaturalAnalogCode === 'U';
+  if (isNaturalAnalogue) {
+    return true;
+  }
+  if (!monomer.monomerItem.isAmbiguous) {
+    return false;
+  }
+
+  if (
+    (monomer as AmbiguousMonomer).subtype ===
+    KetAmbiguousMonomerTemplateSubType.MIXTURE
+  ) {
+    return false;
+  }
+
+  const N1 = 'ACGT';
+  const N2 = 'ACGU';
+  const B1 = 'CGT';
+  const B2 = 'CGU';
+  const D1 = 'AGT';
+  const D2 = 'AGU';
+  const H1 = 'ACT';
+  const H2 = 'ACU';
+  const K1 = 'GT';
+  const K2 = 'GU';
+  const W1 = 'AT';
+  const W2 = 'AU';
+  const Y1 = 'CT';
+  const Y2 = 'CU';
+  const M = 'AC';
+  const R = 'AG';
+  const S = 'CG';
+  const V = 'ACG';
+  const ambigues = [
+    N1,
+    N2,
+    B1,
+    B2,
+    D1,
+    D2,
+    H1,
+    H2,
+    K1,
+    K2,
+    W1,
+    W2,
+    Y1,
+    Y2,
+    M,
+    R,
+    S,
+    V,
+  ];
+  const code = getMonomersCode((monomer as AmbiguousMonomer).monomers);
+  return ambigues.some((v) => v === code);
+};
+
+export const isAntisenseCreationDisabled = (
+  selectedMonomers: BaseMonomer[],
+) => {
+  return selectedMonomers?.some((selectedMonomer: BaseMonomer) => {
+    const rnaBaseForSugar =
+      selectedMonomer instanceof Sugar && getRnaBaseFromSugar(selectedMonomer);
+
+    return (
+      (selectedMonomer instanceof RNABase &&
+        (selectedMonomer.hydrogenBonds.length > 0 ||
+          selectedMonomer.covalentBonds.length > 1)) ||
+      (isRnaBaseOrAmbiguousRnaBase(selectedMonomer) &&
+        !isSenseBase(selectedMonomer)) ||
+      (rnaBaseForSugar &&
+        (rnaBaseForSugar.hydrogenBonds.length > 0 ||
+          !isSenseBase(rnaBaseForSugar)))
+    );
+  });
+};

packages/ketcher-macromolecules/src/components/contextMenu/SequenceItemContextMenu/SequenceItemContextMenu.tsx

@@ -11,6 +11,11 @@ import {
   BaseSequenceItemRenderer,
   ModeTypes,
   NodesSelection,
+  getRnaBaseFromSugar,
+  getSugarFromRnaBase,
+  BaseMonomer,
+  RNABase,
+  Sugar,
 } from 'ketcher-core';
 import { setSelectedTabIndex } from 'state/library';
 import {
@@ -23,6 +28,7 @@ import {
 } from 'state/rna-builder';
 import { generateSequenceContextMenuProps } from 'components/contextMenu/SequenceItemContextMenu/helpers';
 import { ContextMenu } from 'components/contextMenu/ContextMenu';
+import { isAntisenseCreationDisabled } from 'components/contextMenu/SelectedMonomersContextMenu/helpers';
 import { LIBRARY_TAB_INDEX } from 'src/constants';
 
 type SequenceItemContextMenuType = {
@@ -31,6 +37,8 @@ type SequenceItemContextMenuType = {
 
 export enum SequenceItemContextMenuNames {
   title = 'sequence_menu_title',
+  createRnaAntisenseStrand = 'create_rna_antisense_strand',
+  createDnaAntisenseStrand = 'create_dna_antisense_strand',
   modifyInRnaBuilder = 'modify_in_rna_builder',
   editSequence = 'edit_sequence',
   startNewSequence = 'start_new_sequence',
@@ -42,11 +50,46 @@ export const SequenceItemContextMenu = ({
   const editor = useAppSelector(selectEditor);
   const dispatch = useAppDispatch();
   const menuProps = generateSequenceContextMenuProps(selections);
+  const extractedBaseMonomers: BaseMonomer[] =
+    selections?.[0]
+      ?.flatMap((item) => {
+        const node = item.node as {
+          sugar?: BaseMonomer;
+          rnaBase?: BaseMonomer;
+          phosphate?: BaseMonomer;
+          monomer?: BaseMonomer;
+        };
+        return node
+          ? [node.sugar, node.rnaBase, node.phosphate, node.monomer]
+          : [];
+      })
+      .filter(
+        (baseMonomer): baseMonomer is BaseMonomer => baseMonomer !== undefined,
+      ) || [];
+
   const isSequenceEditInRNABuilderMode = useAppSelector(
     selectIsSequenceEditInRNABuilderMode,
   );
   const isSequenceMode = useLayoutMode() === ModeTypes.sequence;
 
+  const isAntisenseOptionHidden = ({
+    props,
+  }: {
+    props?: { sequenceItemRenderer?: BaseSequenceItemRenderer };
+  }) => {
+    return (
+      !props?.sequenceItemRenderer ||
+      !extractedBaseMonomers?.some((selectedMonomer) => {
+        return (
+          (selectedMonomer instanceof RNABase &&
+            getSugarFromRnaBase(selectedMonomer)) ||
+          (selectedMonomer instanceof Sugar &&
+            getRnaBaseFromSugar(selectedMonomer))
+        );
+      })
+    );
+  };
+
   const menuItems = [
     {
       name: SequenceItemContextMenuNames.title,
@@ -64,6 +107,18 @@ export const SequenceItemContextMenu = ({
         );
       },
     },
+    {
+      name: SequenceItemContextMenuNames.createRnaAntisenseStrand,
+      title: 'Create RNA antisense strand',
+      disabled: isAntisenseCreationDisabled(extractedBaseMonomers),
+      hidden: isAntisenseOptionHidden,
+    },
+    {
+      name: SequenceItemContextMenuNames.createDnaAntisenseStrand,
+      title: 'Create DNA antisense strand',
+      disabled: true,
+      hidden: isAntisenseOptionHidden,
+    },
     {
       name: SequenceItemContextMenuNames.modifyInRnaBuilder,
       title: 'Modify in RNA Builder...',
@@ -128,6 +183,12 @@ export const SequenceItemContextMenu = ({
       case SequenceItemContextMenuNames.editSequence:
         editor.events.editSequence.dispatch(props.sequenceItemRenderer);
         break;
+      case SequenceItemContextMenuNames.createRnaAntisenseStrand:
+        editor.events.createAntisenseChain.dispatch();
+        break;
+      case SequenceItemContextMenuNames.createDnaAntisenseStrand:
+        // TODO: implement createDnaAntisenseStrand
+        break;
       default:
         break;
     }