From ce018cbd9c62b02f9468506061b9bd339f16248a Mon Sep 17 00:00:00 2001
From: Roman Rodionov <roman_rodionov@epam.com>
Date: Wed, 3 Jul 2024 14:46:29 +0200
Subject: [PATCH] #4973 - Connection between molecule and monomer lost after
 opening and saving to ket

- fixed monomer atoms ids mapping during struct clone
---
 .../src/domain/entities/monomerMicromolecule.ts          | 9 +++++++--
 packages/ketcher-core/src/domain/entities/struct.ts      | 2 +-
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/packages/ketcher-core/src/domain/entities/monomerMicromolecule.ts b/packages/ketcher-core/src/domain/entities/monomerMicromolecule.ts
index bf402bc12f..81bd9be656 100644
--- 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
index b173ce5593..0b12554407 100644
--- 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);