#4839 - System loses connections to molecule R2 if there is no R1 att…

…achment point

- fixed attachment point number searching for molecules

#4836 - Molecule changes position after saving and opening from file
- added moving molecules structures in macromode for opening/pasting from file, snake layout

#4840 - Paste from clipboard does not work for molecules in macro mode
- changed serialization method in macromolecules paste

packages/ketcher-core/src/application/editor/modes/BaseMode.ts

@@ -127,16 +127,15 @@ export abstract class BaseMode {
       }
     });
     const ketSerializer = new KetSerializer();
-    const { serializedMacromolecules } = ketSerializer.serializeMacromolecules(
+    const serializedKet = ketSerializer.serialize(
       new Struct(),
       drawingEntitiesManager,
     );
-    const clipboardItemString = JSON.stringify(serializedMacromolecules);
     if (isClipboardAPIAvailable()) {
-      navigator.clipboard.writeText(clipboardItemString);
+      navigator.clipboard.writeText(serializedKet);
     } else {
       legacyCopy(event.clipboardData, {
-        'text/plain': clipboardItemString,
+        'text/plain': serializedKet,
       });
       event.preventDefault();
     }
@@ -289,7 +288,7 @@ export abstract class BaseMode {
           ? new Vec2(monomer.position).add(offset)
           : new Vec2(monomer.position);
       }
-      monomer.moveAbsolute(position);
+      drawingEntitiesManager.moveMonomer(monomer, position);
       index++;
     });
   }

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

@@ -937,7 +937,12 @@ export class DrawingEntitiesManager {
     return { command, monomers };
   }
 
-  private rearrangeChainModelChange(monomer: BaseMonomer, newPosition: Vec2) {
+  public rearrangeChainModelChange(monomer: BaseMonomer, newPosition: Vec2) {
+    if (monomer.monomerItem.props.isMicromoleculeFragment) {
+      const offset = newPosition.sub(monomer.position);
+      this.moveChemAtomsPoint(monomer, offset);
+    }
+
     monomer.moveAbsolute(newPosition);
 
     return monomer;
@@ -1365,7 +1370,7 @@ export class DrawingEntitiesManager {
     const structCenter = this.getMacroStructureCenter();
     const offset = Vec2.diff(centerPointOfModel, structCenter);
     this.monomers.forEach((monomer: BaseMonomer) => {
-      monomer.moveAbsolute(new Vec2(monomer.position).add(offset));
+      this.moveMonomer(monomer, new Vec2(monomer.position).add(offset));
     });
     this.polymerBonds.forEach((bond: PolymerBond) => {
       const { x: startX, y: startY } = new Vec2(bond.position).add(offset);

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

@@ -36,32 +36,32 @@ export function polymerBondToDrawingEntity(
   const firstAttachmentPoint =
     connection.endpoint1.attachmentPointId ||
     getAttachmentPointLabel(
-      (firstMonomer.monomerItem.struct.sgroups
+      firstMonomer.monomerItem.struct.sgroups
         .get(0)
         ?.getAttachmentPoints()
-        .findIndex(
+        .find(
           (attachmentPoint, attachmentPointIndex) =>
             attachmentPoint.atomId ===
               atomIdMap.get(Number(connection.endpoint1.atomId)) &&
             !superatomMonomerToUsedAttachmentPoint
               .get(firstMonomer)
               ?.has(getAttachmentPointLabel(attachmentPointIndex + 1)),
-        ) as number) + 1,
+        )?.attachmentPointNumber as number,
     );
   const secondAttachmentPoint =
     connection.endpoint2.attachmentPointId ||
     getAttachmentPointLabel(
-      (secondMonomer.monomerItem.struct.sgroups
+      secondMonomer.monomerItem.struct.sgroups
         .get(0)
         ?.getAttachmentPoints()
-        .findIndex(
+        .find(
           (attachmentPoint, attachmentPointIndex) =>
             attachmentPoint.atomId ===
               atomIdMap.get(Number(connection.endpoint2.atomId)) &&
             !superatomMonomerToUsedAttachmentPoint
               .get(secondMonomer)
               ?.has(getAttachmentPointLabel(attachmentPointIndex + 1)),
-        ) as number) + 1,
+        )?.attachmentPointNumber as number,
     );
 
   if (