#5359 - Display molecules in macro mode: basic structures with atoms …

…and bonds (#5636)

- fixed monomer to atom bonds repositioning issue after switching between modes if there are more than one molecule

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

@@ -22,13 +22,13 @@ import {
   getAttachmentPointLabel,
   getAttachmentPointNumberFromLabel,
 } from 'domain/helpers/attachmentPointCalculations';
-import { isNumber } from 'lodash';
+import { invert, isNumber } from 'lodash';
 import { IKetAttachmentPoint } from 'application/formatters';
 import { MonomerToAtomBond } from 'domain/entities/MonomerToAtomBond';
 import { CoreEditor } from 'application/editor/Editor';
-import { isMonomerSgroupWithAttachmentPoints } from '../../utilities/monomers';
 import { Atom } from 'domain/entities/CoreAtom';
 import { AtomLabel } from 'domain/constants';
+import { isMonomerSgroupWithAttachmentPoints } from '../../utilities/monomers';
 
 export class MacromoleculesConverter {
   private static convertMonomerToMonomerMicromolecule(
@@ -373,9 +373,12 @@ export class MacromoleculesConverter {
   public static findAtomByMicromoleculeAtomId(
     drawingEntitiesManager: DrawingEntitiesManager,
     atomId: number,
+    monomer?: BaseMonomer,
   ) {
     return [...drawingEntitiesManager.atoms.values()].find(
-      (atom) => atom.atomIdInMicroMode === atomId,
+      (atom) =>
+        atom.atomIdInMicroMode === atomId &&
+        (!monomer || monomer === atom.monomer),
     );
   }
 
@@ -402,6 +405,7 @@ export class MacromoleculesConverter {
 
     let fragmentNumber = 1;
     const fragmentIdToAtomIdMap = new Map<number, Map<number, number>>();
+    const globalAtomIdToMonomerMap = new Map<number, BaseMonomer>();
 
     fragments.forEach((_fragment) => {
       const atomIdMap = new Map<number, number>();
@@ -412,26 +416,20 @@ export class MacromoleculesConverter {
         drawingEntitiesManager,
       );
       const monomer = monomerAddCommand.operations[0].monomer as BaseMonomer;
+      const atomIdMapObject = Object.fromEntries(atomIdMap.entries());
+      const localAtomIdToGlobalAtomId = invert(atomIdMapObject);
+      const atomsMap = new Map<number, Atom>();
 
       _fragment.forEach((fragmentId) => {
         fragmentIdToMonomer.set(fragmentId as number, monomer);
         fragmentIdToAtomIdMap.set(fragmentId, atomIdMap);
       });
       command.merge(monomerAddCommand);
-      fragmentNumber++;
-    });
-    const superatomAttachmentPointToBond = new Map<
-      SGroupAttachmentPoint,
-      Bond
-    >();
 
-    drawingEntitiesManager.monomers.forEach((monomer) => {
       if (
         monomer.monomerItem.props.isMicromoleculeFragment &&
         !isMonomerSgroupWithAttachmentPoints(monomer)
       ) {
-        const atomsMap: { [atomId: number]: Atom } = {};
-
         monomer.monomerItem.struct.atoms.forEach((atom, atomId) => {
           const atomAddCommand = drawingEntitiesManager.addAtom(
             atom.pp,
@@ -440,23 +438,41 @@ export class MacromoleculesConverter {
             atom.label as AtomLabel,
           );
 
-          atomsMap[atomId] = atomAddCommand.operations[0].atom as Atom;
           command.merge(atomAddCommand);
+          atomsMap.set(atomId, atomAddCommand.operations[0].atom as Atom);
+          globalAtomIdToMonomerMap.set(
+            Number(localAtomIdToGlobalAtomId[atomId]),
+            monomer,
+          );
         });
 
         monomer.monomerItem.struct.bonds.forEach((bond) => {
+          const firstAtom = atomsMap.get(bond.begin);
+          const secondAtom = atomsMap.get(bond.end);
+
+          if (!firstAtom || !secondAtom) {
+            return;
+          }
+
           command.merge(
             drawingEntitiesManager.addBond(
-              atomsMap[bond.begin],
-              atomsMap[bond.end],
+              firstAtom,
+              secondAtom,
               bond.type,
               bond.stereo,
             ),
           );
         });
       }
+
+      fragmentNumber++;
     });
 
+    const superatomAttachmentPointToBond = new Map<
+      SGroupAttachmentPoint,
+      Bond
+    >();
+
     struct.bonds.forEach((bond) => {
       const beginAtom = struct.atoms.get(bond.begin);
       const endAtom = struct.atoms.get(bond.end);
@@ -500,6 +516,7 @@ export class MacromoleculesConverter {
         MacromoleculesConverter.findAtomByMicromoleculeAtomId(
           drawingEntitiesManager,
           atomIdInMicromolecules,
+          globalAtomIdToMonomerMap.get(moleculeAtomId),
         );
 
       if (

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

@@ -516,7 +516,7 @@ export class KetSerializer implements Serializer<Struct> {
         deserializedMicromolecules,
         drawingEntitiesManager,
       );
-    const atomIdsMap = new Map<number, number>();
+    const localAtomIdToGlobalAtomId = new Map<number, number>();
 
     command.merge(structToDrawingEntitiesConversionResult.modelChanges);
 
@@ -528,8 +528,8 @@ export class KetSerializer implements Serializer<Struct> {
 
     structToDrawingEntitiesConversionResult.fragmentIdToAtomIdMap.forEach(
       (_atomIdsMap) => {
-        _atomIdsMap.forEach((atomId, oldAtomId) => {
-          atomIdsMap.set(oldAtomId, atomId);
+        _atomIdsMap.forEach((globalAtomId, localAtomId) => {
+          localAtomIdToGlobalAtomId.set(localAtomId, globalAtomId);
         });
       },
     );
@@ -569,11 +569,16 @@ export class KetSerializer implements Serializer<Struct> {
             (firstMonomer.monomerItem.props.isMicromoleculeFragment ||
               secondMonomer.monomerItem.props.isMicromoleculeFragment)
           ) {
+            const atomId = Number(
+              connection.endpoint1.atomId || connection.endpoint2.atomId,
+            );
+
             const atom = MacromoleculesConverter.findAtomByMicromoleculeAtomId(
               drawingEntitiesManager,
-              Number(
-                connection.endpoint1.atomId || connection.endpoint2.atomId,
-              ),
+              atomId,
+              firstMonomer.monomerItem.props.isMicromoleculeFragment
+                ? firstMonomer
+                : secondMonomer,
             );
             const attachmentPointName =
               connection.endpoint1.attachmentPointId ||
@@ -597,7 +602,7 @@ export class KetSerializer implements Serializer<Struct> {
             const bondAdditionCommand = polymerBondToDrawingEntity(
               connection,
               drawingEntitiesManager,
-              atomIdsMap,
+              localAtomIdToGlobalAtomId,
               superatomMonomerToUsedAttachmentPoint,
               firstMonomer,
               secondMonomer,