#4973 - Connection between molecule and monomer lost after opening an…

…d saving to ket (#4980) - fixed monomer atoms ids mapping during struct clone - fixed removeLeavingGroupsFromConnectedAtoms
epam · Jul 4, 2024 · 46d3f1f · 46d3f1f
1 parent 98d6c08
commit 46d3f1f
Show file tree

Hide file tree

Showing 3 changed files with 19 additions and 5 deletions.
diff --git a/packages/ketcher-core/src/domain/entities/monomerMicromolecule.ts b/packages/ketcher-core/src/domain/entities/monomerMicromolecule.ts
@@ -30,13 +30,18 @@ export class MonomerMicromolecule extends SGroup {
     return { position: this.pp, atomId: sgroupContractedPosition.atomId };
   }
 
-  public static clone(monomerMicromolecule: MonomerMicromolecule) {
+  public static clone(
+    monomerMicromolecule: MonomerMicromolecule,
+    atomIdMap?: Map<number, number>,
+  ) {
     const monomerMicromoleculeClone = new MonomerMicromolecule(
       monomerMicromolecule.type,
       monomerMicromolecule.monomer,
     );
     monomerMicromoleculeClone.pp = monomerMicromolecule.pp;
-    monomerMicromoleculeClone.atoms = monomerMicromolecule.atoms;
+    monomerMicromoleculeClone.atoms = atomIdMap
+      ? monomerMicromolecule.atoms.map((elem) => atomIdMap.get(elem))
+      : monomerMicromolecule.atoms;
 
     return monomerMicromoleculeClone;
   }

diff --git a/packages/ketcher-core/src/domain/entities/struct.ts b/packages/ketcher-core/src/domain/entities/struct.ts
@@ -293,7 +293,7 @@ export class Struct {
 
       sg =
         oldSgroup instanceof MonomerMicromolecule
-          ? MonomerMicromolecule.clone(oldSgroup)
+          ? MonomerMicromolecule.clone(oldSgroup, aidMap!)
           : SGroup.clone(sg, aidMap!);
 
       const id = cp.sgroups.add(sg);

diff --git a/packages/ketcher-core/src/domain/serializers/ket/ketSerializer.ts b/packages/ketcher-core/src/domain/serializers/ket/ketSerializer.ts
@@ -644,6 +644,10 @@ export class KetSerializer implements Serializer<Struct> {
 
     struct.sgroups.forEach((sgroup) => {
       const attachmentPoints = sgroup.getAttachmentPoints();
+      const attachmentPointsToReplace: Map<
+        SGroupAttachmentPoint,
+        SGroupAttachmentPoint
+      > = new Map();
       attachmentPoints.forEach((attachmentPoint) => {
         if (
           isNumber(attachmentPoint.leaveAtomId) &&
@@ -655,14 +659,19 @@ export class KetSerializer implements Serializer<Struct> {
             attachmentPoint.attachmentId,
             attachmentPoint.attachmentPointNumber,
           );
-          sgroup.removeAttachmentPoint(attachmentPoint);
-          sgroup.addAttachmentPoint(attachmentPointClone);
+          attachmentPointsToReplace.set(attachmentPoint, attachmentPointClone);
           sgroup.atoms.splice(
             sgroup.atoms.indexOf(attachmentPoint.leaveAtomId),
             1,
           );
         }
       });
+      attachmentPointsToReplace.forEach(
+        (attachmentPointToAdd, attachmentPointToDelete) => {
+          sgroup.removeAttachmentPoint(attachmentPointToDelete);
+          sgroup.addAttachmentPoint(attachmentPointToAdd);
+        },
+      );
     });
 
     return struct;