#3949 - Parameter "sgroups" does not appear in .ket file if a S-Group…

… is applied to structure along with molecule (#3975)

- fixed serialization/deserialization in case when one sgroup contains several fragments

---------

Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>

ketcher-autotests/tests/Structure-Creating-&-Editing/SMARTS-attributes/Reaction-queries-attributes/reaction-queries-attributes.spec.ts

@@ -105,7 +105,6 @@ test.describe('Checking reaction queries attributes in SMARTS format', () => {
   });
 
   test('Checking SMARTS with S-Group with two elements', async ({ page }) => {
-    test.fail();
     /**
      * Test case: https://github.com/epam/Indigo/issues/1316
      */

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

@@ -250,6 +250,46 @@ export class MacromoleculesConverter {
     return attachmentPointLabel;
   }
 
+  // This method returns array of arrays of fragmentIds grouped by sgroup
+  // It needs to serialize/deserialize several molecules grouped by sgroup as a single molecule
+  public static getFragmentsGroupedBySgroup(struct: Struct) {
+    const groupedFragments: number[][] = [];
+    struct.frags.forEach((_fragment, fragmentId) => {
+      const isAlreadyGrouped = groupedFragments.find((fragmentsGroup) =>
+        fragmentsGroup.includes(fragmentId),
+      );
+      if (isAlreadyGrouped) {
+        return;
+      }
+
+      // Find all sgroups related to fragment
+      const fragmentSgroups = new Set<SGroup>();
+      struct.atoms.forEach((atom, atomId) => {
+        if (atom.fragment !== fragmentId) return;
+        const sgroup = struct.getGroupFromAtomId(atomId);
+        if (sgroup) {
+          fragmentSgroups.add(sgroup);
+        }
+      });
+
+      // Add new group of fragments with fragments related to one sgroup
+      const lastFragmentGroupIndex = groupedFragments.push([fragmentId]) - 1;
+      fragmentSgroups.forEach((sgroup) => {
+        sgroup.atoms.forEach((aid) => {
+          const atomFragmentId = struct.atoms.get(aid)?.fragment;
+          if (
+            atomFragmentId &&
+            !groupedFragments[lastFragmentGroupIndex].includes(atomFragmentId)
+          ) {
+            groupedFragments[lastFragmentGroupIndex].push(atomFragmentId);
+          }
+        });
+      });
+    });
+
+    return groupedFragments;
+  }
+
   public static convertStructToDrawingEntities(
     struct: Struct,
     drawingEntitiesManager: DrawingEntitiesManager,
@@ -268,9 +308,11 @@ export class MacromoleculesConverter {
         );
       }
     });
+    const fragments = this.getFragmentsGroupedBySgroup(struct);
+
     let fragmentNumber = 1;
-    struct.frags.forEach((_fragment, fragmentId) => {
-      const fragmentStruct = struct.getFragment(fragmentId, false);
+    fragments.forEach((_fragment, fragmentId) => {
+      const fragmentStruct = struct.getFragment(_fragment, false);
       const monomerAddCommand = this.convertFragmentToChem(
         fragmentNumber,
         fragmentStruct,

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

@@ -171,17 +171,17 @@ export class Struct {
     return this.clone(atomSet);
   }
 
-  getFragmentIds(fid: number): Pile<number> {
+  getFragmentIds(_fid: number | number[]): Pile<number> {
     const atomSet = new Pile<number>();
-
+    const fid = Array.isArray(_fid) ? _fid : [_fid];
     this.atoms.forEach((atom, aid) => {
-      if (atom.fragment === fid) atomSet.add(aid);
+      if (fid.includes(atom.fragment)) atomSet.add(aid);
     });
 
     return atomSet;
   }
 
-  getFragment(fid: number, copyNonFragmentObjects = true): Struct {
+  getFragment(fid: number | number[], copyNonFragmentObjects = true): Struct {
     return this.clone(
       this.getFragmentIds(fid),
       null,

packages/ketcher-core/src/domain/serializers/ket/ketSerializer.ts

@@ -379,9 +379,12 @@ export class KetSerializer implements Serializer<Struct> {
     );
 
     let fragmentNumber = 1;
-    deserializedMicromolecules.frags.forEach((_fragment, fragmentId) => {
+    const fragments = MacromoleculesConverter.getFragmentsGroupedBySgroup(
+      deserializedMicromolecules,
+    );
+    fragments.forEach((_fragment) => {
       const fragmentStruct = deserializedMicromolecules.getFragment(
-        fragmentId,
+        _fragment,
         false,
       );
       const fragmentBbox = fragmentStruct.getCoordBoundingBox();