Backmerge: #4879 - Ketcher part: Save to mol for micro and macro stru…

…ctures connected through attachment points works wrong (#4970)

- added removing the leavingGroup atom from structure before serialisation if there is connection to monomer

* #4973 - Connection between molecule and monomer lost after opening and saving to ket

- fixed monomer atoms ids mapping during struct clone
- fixed removeLeavingGroupsFromConnectedAtoms

ketcher-autotests/tests/test-data/KET/structure-with-two-attachment-points-expected.ket

@@ -81,17 +81,15 @@
                     13.044183315187814,
                     -7.56543102512855,
                     0
-                ],
-                "selected": true
+                ]
             },
             {
                 "label": "H",
                 "location": [
                     14.29031242217327,
                     -6.319190021917031,
                     0
-                ],
-                "selected": true
+                ]
             }
         ],
         "bonds": [

ketcher-autotests/tests/test-data/Molfiles-V3000/chem-connected-to-micro-structure-expected.mol

@@ -1,18 +1,17 @@
 
-  -INDIGO-06142409592D
+  -INDIGO-07032413592D
 
   0  0  0  0  0  0  0  0  0  0  0 V3000
 M  V30 BEGIN CTAB
-M  V30 COUNTS 8 8 1 0 0
+M  V30 COUNTS 7 7 1 0 0
 M  V30 BEGIN ATOM
 M  V30 1 C 10.569 -8.0 0.0 0
 M  V30 2 C 12.2993 -7.99959 0.0 0
 M  V30 3 C 11.4358 -7.49997 0.0 0
 M  V30 4 C 12.2993 -9.00053 0.0 0
 M  V30 5 C 10.569 -9.00502 0.0 0
 M  V30 6 C 11.438 -9.50003 0.0 0
-M  V30 7 H 11.4364 -6.49997 0.0 0
-M  V30 8 A6OH 14.9592 -7.2 0.0 0 CLASS=LINKER ATTCHORD=(2 3 Br)
+M  V30 7 A6OH 14.9592 -7.2 0.0 0 CLASS=LINKER ATTCHORD=(2 3 Br)
 M  V30 END ATOM
 M  V30 BEGIN BOND
 M  V30 1 2 3 1
@@ -22,13 +21,12 @@ M  V30 4 1 6 4
 M  V30 5 2 4 2
 M  V30 6 1 2 3
 M  V30 7 1 3 7
-M  V30 8 1 3 8
 M  V30 END BOND
 M  V30 BEGIN SGROUP
-M  V30 1 SUP 1 ATOMS=(7 3 1 5 6 4 2 7) BRKXYZ=(9 0.000000 0.000000 0.000000 0-
-M  V30 .000000 0.000000 0.000000 0.000000 0.000000 0.000000) BRKXYZ=(9 0.0000-
-M  V30 00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.00-
-M  V30 0000) ESTATE=E SAP=(3 3 7 1)
+M  V30 1 SUP 1 ATOMS=(6 3 1 5 6 4 2) BRKXYZ=(9 0.000000 0.000000 0.000000 0.0-
+M  V30 00000 0.000000 0.000000 0.000000 0.000000 0.000000) BRKXYZ=(9 0.000000-
+M  V30  0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.0000-
+M  V30 00) ESTATE=E SAP=(3 3 0 1)
 M  V30 END SGROUP
 M  V30 END CTAB
 M  V30 BEGIN TEMPLATE

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

@@ -399,7 +399,7 @@ export abstract class BaseMonomer extends DrawingEntity {
         },
       );
 
-      if (bondsToLeavingGroupAtom.size !== 1) {
+      if (bondsToLeavingGroupAtom.size > 1) {
         return;
       }
 
@@ -456,7 +456,7 @@ export abstract class BaseMonomer extends DrawingEntity {
         },
       );
 
-      if (bondsToLeavingGroupAtom.size !== 1) {
+      if (bondsToLeavingGroupAtom.size > 1) {
         return;
       }
 

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;
   }

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

@@ -112,7 +112,7 @@ export class SGroup {
       mul: 1, // multiplication count for MUL group
       connectivity: 'ht', // head-to-head, head-to-tail or either-unknown
       name: '',
-      subscript: 'n',
+      subscript: '',
       expanded: undefined,
       // data s-group fields
       attached: false,

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);

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

@@ -14,7 +14,13 @@
  * limitations under the License.
  ***************************************************************************/
 
-import { Struct, Vec2 } from 'domain/entities';
+import {
+  Atom,
+  Bond,
+  SGroupAttachmentPoint,
+  Struct,
+  Vec2,
+} from 'domain/entities';
 import { arrowToKet, plusToKet } from './toKet/rxnToKet';
 import { Serializer } from '../serializers.types';
 import { headerToKet } from './toKet/headerToKet';
@@ -625,11 +631,62 @@ export class KetSerializer implements Serializer<Struct> {
     };
   }
 
+  public static removeLeavingGroupsFromConnectedAtoms(_struct: Struct) {
+    const struct = _struct.clone();
+
+    struct.atoms.forEach((_atom, atomId) => {
+      if (Atom.isHiddenLeavingGroupAtom(struct, atomId)) {
+        struct.atoms.delete(atomId);
+      }
+    });
+
+    struct.bonds.forEach((bond, bondId) => {
+      if (Bond.isBondToHiddenLeavingGroup(struct, bond)) {
+        struct.bonds.delete(bondId);
+      }
+    });
+
+    struct.sgroups.forEach((sgroup) => {
+      const attachmentPoints = sgroup.getAttachmentPoints();
+      const attachmentPointsToReplace: Map<
+        SGroupAttachmentPoint,
+        SGroupAttachmentPoint
+      > = new Map();
+      attachmentPoints.forEach((attachmentPoint) => {
+        if (
+          isNumber(attachmentPoint.leaveAtomId) &&
+          Atom.isHiddenLeavingGroupAtom(struct, attachmentPoint.leaveAtomId)
+        ) {
+          const attachmentPointClone = new SGroupAttachmentPoint(
+            attachmentPoint.atomId,
+            undefined,
+            attachmentPoint.attachmentId,
+            attachmentPoint.attachmentPointNumber,
+          );
+          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;
+  }
+
   serialize(
-    struct: Struct,
+    _struct: Struct,
     drawingEntitiesManager = new DrawingEntitiesManager(),
     selection?: EditorSelection,
   ) {
+    const struct = KetSerializer.removeLeavingGroupsFromConnectedAtoms(_struct);
     struct.enableInitiallySelected();
     const populatedStruct = populateStructWithSelection(struct, selection);
     MacromoleculesConverter.convertStructToDrawingEntities(

packages/ketcher-core/src/domain/serializers/mol/common.js

@@ -14,7 +14,7 @@
  * limitations under the License.
  ***************************************************************************/
 
-import { Pile, SGroup } from 'domain/entities';
+import { MonomerMicromolecule, Pile, SGroup } from 'domain/entities';
 
 import utils from './utils';
 import v2000 from './v2000';
@@ -202,9 +202,19 @@ function saveSupToMolfile(sgroup, mol, sgMap, atomMap, bondMap) {
   let lines = [];
   lines = lines.concat(makeAtomBondLines('SAL', idstr, sgroup.atoms, atomMap));
   lines = lines.concat(makeAtomBondLines('SBL', idstr, sgroup.bonds, bondMap));
-  if (sgroup.data.name && sgroup.data.name !== '') {
-    lines.push('M  SMT ' + idstr + ' ' + sgroup.data.name);
+
+  let sgroupName;
+
+  if (sgroup instanceof MonomerMicromolecule) {
+    sgroupName = sgroup.monomer.label;
+  } else if (sgroup.data.name && sgroup.data.name !== '') {
+    sgroupName = sgroup.data.name;
   }
+
+  if (sgroupName) {
+    lines.push('M  SMT ' + idstr + ' ' + sgroupName);
+  }
+
   return lines.join('\n');
 }
 

packages/ketcher-core/src/domain/serializers/mol/molSerializer.ts

@@ -19,6 +19,7 @@ import { Molfile } from './molfile';
 import { Serializer } from '../serializers.types';
 import { Struct } from 'domain/entities';
 import { KetcherLogger } from 'utilities';
+import { KetSerializer } from 'domain/serializers';
 
 export class MolSerializer implements Serializer<Struct> {
   static DefaultOptions: MolSerializerOptions = {
@@ -75,7 +76,9 @@ export class MolSerializer implements Serializer<Struct> {
     }
   }
 
-  serialize(struct: Struct): string {
+  serialize(_struct: Struct): string {
+    const struct = KetSerializer.removeLeavingGroupsFromConnectedAtoms(_struct);
+
     return new Molfile().saveMolecule(
       struct,
       this.options.ignoreErrors,