Support nucleotide S-groups in macro rendering

Author: Copilot

packages/ketcher-core/__tests__/application/render/restruct/resgroup.test.ts

@@ -6,16 +6,19 @@ import {
   Render,
 } from 'application/render';
 import {
-  type Struct,
+  Atom,
   Bond,
   Pool,
   RGroupAttachmentPoint,
   SGroup,
+  SUPERATOM_CLASS,
+  Struct,
   Vec2,
 } from 'domain/entities';
 import { restruct } from '../../../mock-data';
 import { mockFn } from 'jest-mock-extended';
 import type { RenderOptions } from 'application/render/render.types';
+import { RenderStruct } from 'application/render/renderStruct';
 
 describe('resgroup should draw brackets with attachment points correctly', () => {
   const mockBonds = [
@@ -99,6 +102,7 @@ describe('resgroup should draw brackets with attachment points correctly', () =>
       y: 6.574988999717658,
       z: 0,
     });
+
     restruct.rgroupAttachmentPoints.set(0, reRGroupAttachmentPoint);
     const option = {
       microModeScale: 20,
@@ -125,7 +129,7 @@ describe('resgroup should draw brackets with attachment points correctly', () =>
     const bonds = new Pool();
     mockBonds.forEach((bond, i) => bonds.set(i, new Bond(bond)));
     restruct.molecule.bonds = bonds;
-    reSgroup.draw(restruct, sGroup);
+    reSgroup.draw(restruct as unknown as ReStruct, sGroup);
     expect(attachmentsSpy).toHaveBeenCalled();
   });
 
@@ -144,7 +148,7 @@ describe('resgroup should draw brackets with attachment points correctly', () =>
     restruct.rgroupAttachmentPoints.set(1, reRGroupAttachmentPoint);
     restruct.molecule.getRGroupAttachmentPointsByAtomId =
       mockFn().mockReturnValue([0, 1]);
-    reSgroup.draw(restruct, sGroup);
+    reSgroup.draw(restruct as unknown as ReStruct, sGroup);
     expect(attachmentsSpy).toHaveBeenCalled();
   });
 
@@ -169,3 +173,48 @@ describe('resgroup should draw brackets with attachment points correctly', () =>
     expect(attachmentsSpy).toHaveBeenCalled();
   });
 });
+
+describe('resgroup should draw nucleotide component S-groups', () => {
+  it('should draw nucleotide component brackets and class label', () => {
+    const option = {
+      microModeScale: 20,
+      width: 100,
+      height: 100,
+    } as RenderOptions;
+    const render = new Render(document as unknown as HTMLElement, option);
+    render.ctab = restruct as unknown as ReStruct;
+    restruct.render = render as any;
+
+    const sGroup = new SGroup('nucleotideComponent');
+    const reSgroup = new ReSGroup(sGroup);
+    sGroup.data.class = SUPERATOM_CLASS.BASE;
+    SGroup.addAtom(sGroup, 2, restruct.molecule as unknown as Struct);
+
+    reSgroup.draw(restruct as unknown as ReStruct, sGroup);
+
+    expect(
+      render.paper.canvas.querySelector('[data-label-text="Base"]'),
+    ).toBeTruthy();
+  });
+});
+
+describe('RenderStruct.prepareStruct in macromolecules mode', () => {
+  const isPolymerEditorTurnedOn = window.isPolymerEditorTurnedOn;
+
+  afterEach(() => {
+    window.isPolymerEditorTurnedOn = isPolymerEditorTurnedOn;
+  });
+
+  it('should preserve S-groups for macromolecules rendering', () => {
+    const struct = new Struct();
+    const atomId = struct.atoms.add(new Atom({ label: 'C' }));
+    const sGroup = new SGroup('GEN');
+    SGroup.addAtom(sGroup, atomId, struct);
+    sGroup.id = struct.sgroups.add(sGroup);
+    window.isPolymerEditorTurnedOn = true;
+
+    const preparedStruct = RenderStruct.prepareStruct(struct);
+
+    expect(preparedStruct.sgroups.size).toBe(1);
+  });
+});

packages/ketcher-core/__tests__/domain/serializers/ket/KetSerializer.test.ts

@@ -15,6 +15,8 @@ import {
   RxnArrow,
   RxnPlus,
   SimpleObject,
+  SGroup,
+  Struct,
   Text,
   Vec2,
 } from 'domain/entities';
@@ -267,6 +269,24 @@ describe('serialize (ToKet)', () => {
     expect(spy.mock.results[2].value.sgroups[5].subscript).toEqual('n');
     expect(spy.mock.results[2].value.sgroups[5].connectivity).toEqual('HT');
   });
+  it('serializes and deserializes nucleotide component S-groups', () => {
+    const struct = new Struct();
+    const sgroup = new SGroup('nucleotideComponent');
+    sgroup.atoms = [0];
+    sgroup.data.class = 'BASE';
+    struct.sgroups.add(sgroup);
+
+    const serialized = moleculeToKet.moleculeToKet(struct);
+    expect(serialized.sgroups[0]).toEqual({
+      type: 'nucleotideComponent',
+      atoms: [0],
+      class: 'BASE',
+    });
+
+    const deserialized = moleculeToStruct.sgroupToStruct(serialized.sgroups[0]);
+    expect(deserialized.type).toEqual('nucleotideComponent');
+    expect(deserialized.data.class).toEqual('BASE');
+  });
   it('rgroupToKet', () => {
     const spy = jest.spyOn(rgroupToKet, 'rgroupToKet');
     const result = JSON.parse(ket.serialize(contentRgroupStruct)).rg14;

packages/ketcher-core/src/application/render/renderStruct.ts

@@ -23,6 +23,9 @@ export class RenderStruct {
     if (struct.sgroups.size > 0) {
       const newStruct = struct.clone();
       convertAllSGroupAttachmentPointsToRGroupAttachmentPoints(newStruct);
+      if (window.isPolymerEditorTurnedOn) {
+        return newStruct;
+      }
       if (!newStruct.sgroups.get(0)?.isSuperatomWithoutLabel) {
         newStruct.sgroups.delete(0);
       }

packages/ketcher-core/src/application/render/restruct/resgroup.ts

@@ -148,6 +148,14 @@ class ReSGroup extends ReObject {
           SGroupdrawBracketsOptions.superatomClass = sgroup.data.class;
           break;
         }
+        case 'nucleotideComponent': {
+          SGroupdrawBracketsOptions.lowerIndexText =
+            SUPERATOM_CLASS_TEXT[sgroup.data.class];
+          SGroupdrawBracketsOptions.upperIndexText = null;
+          SGroupdrawBracketsOptions.indexAttribute = { 'font-style': 'italic' };
+          SGroupdrawBracketsOptions.superatomClass = sgroup.data.class;
+          break;
+        }
         case 'DAT': {
           set = drawGroupDat(remol, sgroup);
           break;
@@ -166,6 +174,7 @@ class ReSGroup extends ReObject {
         'GEN',
         'COP',
         'queryComponent',
+        'nucleotideComponent',
       ];
       if (
         sgroupTypesWithBrackets.includes(sgroup.type) &&

packages/ketcher-core/src/domain/serializers/ket/fromKet/moleculeToStruct.ts

@@ -164,6 +164,10 @@ export function sgroupToStruct(source) {
       );
       break;
     }
+    case 'nucleotideComponent': {
+      ifDef(sgroup.data, 'class', source.class);
+      break;
+    }
     case 'DAT': {
       ifDef(sgroup.data, 'absolute', source.placement);
       ifDef(sgroup.data, 'attached', source.display);

packages/ketcher-core/src/domain/serializers/ket/schema.json

@@ -508,7 +508,16 @@
           },
           "type": {
             "type": "string",
-            "enum": ["GEN", "MUL", "SRU", "SUP", "DAT", "queryComponent", "COP"]
+            "enum": [
+              "GEN",
+              "MUL",
+              "SRU",
+              "SUP",
+              "DAT",
+              "queryComponent",
+              "nucleotideComponent",
+              "COP"
+            ]
           }
         },
         "if": {

packages/ketcher-core/src/domain/serializers/ket/toKet/moleculeToKet.ts

@@ -216,6 +216,10 @@ function sgroupToKet(struct: Struct, source: SGroup) {
       );
       break;
     }
+    case 'nucleotideComponent': {
+      ifDef(result, 'class', source.data.class);
+      break;
+    }
     case 'DAT': {
       const data = source.data;
       ifDef(result, 'placement', data.absolute, true);