Backmerge: #2142 s groups that combine multiple molecules get lost wh…

…en saving as ket file (#2219) (#2225)

* Revert "#2142: s groups get lost when saving as ket file (#2191)"

This reverts commit 2892953.

* Fix S-Groups which combines multiple molecules getting lost when saving as ket file

* #2142 – updated indigo version to 1.10.0-rc.3

---------

Co-authored-by: Yulei Chen <yulei_chen@epam.com>

packages/ketcher-core/__tests__/domain/entities/pile.test.ts

@@ -0,0 +1,41 @@
+import { Pile } from 'domain/entities/pile'
+
+describe('unionIntersections', () => {
+  it('unions multiple sets which have intersections', () => {
+    const setA = new Pile([0, 1])
+    const setB = new Pile([1, 2, 3])
+    const setC = new Pile([2, 3])
+
+    const union = Pile.unionIntersections([setA, setB, setC])
+
+    expect(union).toHaveLength(1)
+    expect(union[0]).toEqual(new Pile([0, 1, 2, 3]))
+  })
+
+  it('does not union sets which have no intersections', () => {
+    const setA = new Pile([0, 1])
+    const setB = new Pile([2, 3])
+
+    const union = Pile.unionIntersections([setA, setB])
+
+    expect(union).toHaveLength(2)
+    expect(union[0]).toEqual(setA)
+    expect(union[1]).toEqual(setB)
+  })
+
+  // Combines above two situations
+  it('unions multiple sets which have intersections, and skips sets without intersections', () => {
+    const setA = new Pile([0, 1])
+    const setB = new Pile([1, 2, 3])
+    const setC = new Pile([2, 3])
+    const setD = new Pile([4, 5])
+    const setE = new Pile([6])
+
+    const union = Pile.unionIntersections([setA, setB, setC, setD, setE])
+
+    expect(union).toHaveLength(3)
+    expect(union[0]).toEqual(new Pile([0, 1, 2, 3]))
+    expect(union[1]).toEqual(setD)
+    expect(union[2]).toEqual(setE)
+  })
+})

packages/ketcher-core/__tests__/domain/serializers/ket/KetSerializer.test.ts

@@ -205,20 +205,6 @@ describe('serialize (ToKet)', () => {
     const plusKet = parsedPrepareContent.root.nodes[3]
     expect(structPlus).toEqual(plusKet)
   })
-  it('correct work with sgroups', () => {
-    const parsedSgroupStruct = JSON.parse(ket.serialize(moleculeSgroupStruct))
-    expect(parsedSgroupStruct.root.nodes[6].data.type).toEqual('GEN')
-    expect(parsedSgroupStruct.root.nodes[7].data.type).toEqual('MUL')
-    expect(parsedSgroupStruct.root.nodes[7].data.mul).toEqual(1)
-    expect(parsedSgroupStruct.root.nodes[8].data.type).toEqual('SRU')
-    expect(parsedSgroupStruct.root.nodes[8].data.subscript).toEqual('n')
-    expect(parsedSgroupStruct.root.nodes[8].data.connectivity).toEqual('HT')
-    expect(parsedSgroupStruct.root.nodes[9].data.type).toEqual('MUL')
-    expect(parsedSgroupStruct.root.nodes[9].data.mul).toEqual(1)
-    expect(parsedSgroupStruct.root.nodes[10].data.type).toEqual('SUP')
-    expect(parsedSgroupStruct.root.nodes[11].data.subscript).toEqual('n')
-    expect(parsedSgroupStruct.root.nodes[11].data.connectivity).toEqual('HT')
-  })
   it('moleculeToKet', () => {
     const spy = jest.spyOn(moleculeToKet, 'moleculeToKet')
     ket.serialize(moleculeContentStruct)
@@ -244,6 +230,19 @@ describe('serialize (ToKet)', () => {
     expect(
       spy.mock.results[1].value.bonds.filter((bond) => bond.type === 2).length
     ).toEqual(3)
+    // sgroups
+    ket.serialize(moleculeSgroupStruct)
+    expect(spy.mock.results[2].value.sgroups[0].type).toEqual('GEN')
+    expect(spy.mock.results[2].value.sgroups[1].type).toEqual('MUL')
+    expect(spy.mock.results[2].value.sgroups[1].mul).toEqual(1)
+    expect(spy.mock.results[2].value.sgroups[2].type).toEqual('SRU')
+    expect(spy.mock.results[2].value.sgroups[2].subscript).toEqual('n')
+    expect(spy.mock.results[2].value.sgroups[2].connectivity).toEqual('HT')
+    expect(spy.mock.results[2].value.sgroups[3].type).toEqual('MUL')
+    expect(spy.mock.results[2].value.sgroups[3].mul).toEqual(1)
+    expect(spy.mock.results[2].value.sgroups[4].type).toEqual('SUP')
+    expect(spy.mock.results[2].value.sgroups[5].subscript).toEqual('n')
+    expect(spy.mock.results[2].value.sgroups[5].connectivity).toEqual('HT')
   })
   it('rgroupToKet', () => {
     const spy = jest.spyOn(rgroupToKet, 'rgroupToKet')

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

@@ -48,4 +48,45 @@ export class Pile<TValue = any> extends Set<TValue> {
 
     return union
   }
+
+  intersection(setB: Pile): Pile<TValue> {
+    const thisSet = new Pile(this)
+    return new Pile([...thisSet].filter((item) => setB.has(item)))
+  }
+
+  /**
+   * Union multiple sets which have intersections
+   * @example ```
+   * const setA = new Pile([0, 1])
+   * const setB = new Pile([1, 2])
+   * const setC = new Pile([2, 3])
+   * const setD = new Pile([4, 5])
+   * console.log(Pile.unionMultiple([setA, setB, setC, setD]))
+   * // [{0, 1, 2, 3}, {4, 5}]
+   * ```
+   */
+  static unionIntersections<T>(sets: Array<Pile<T>>): Array<Pile<T>> {
+    let unionized = false
+
+    // Union two of sets
+    const setsToReturn = sets.reduce((prevSets, curSet) => {
+      let isCurSetMerged = false
+
+      const newSets = prevSets.map((set) => {
+        const intersec = set.intersection(curSet)
+        if (intersec.size > 0) {
+          unionized = true
+          isCurSetMerged = true
+          return set.union(curSet)
+        }
+        return set
+      })
+
+      if (!isCurSetMerged) newSets.push(curSet)
+      return newSets
+    }, new Array<Pile<T>>())
+
+    // Recursively union two of sets === union all sets
+    return unionized ? Pile.unionIntersections(setsToReturn) : setsToReturn
+  }
 }

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

@@ -49,6 +49,7 @@ export function moleculeToStruct(ketItem: any): Struct {
   struct.initHalfBonds()
   struct.initNeighbors()
   struct.markFragments()
+  struct.bindSGroupsToFunctionalGroups()
 
   return struct
 }

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

@@ -19,8 +19,8 @@ import { arrowToKet, plusToKet } from './toKet/rxnToKet'
 
 import { Serializer } from '../serializers.types'
 import { headerToKet } from './toKet/headerToKet'
-import { moleculeToKet, sgroupToKet } from './toKet/moleculeToKet'
-import { moleculeToStruct, sgroupToStruct } from './fromKet/moleculeToStruct'
+import { moleculeToKet } from './toKet/moleculeToKet'
+import { moleculeToStruct } from './fromKet/moleculeToStruct'
 import { prepareStructForKet } from './toKet/prepare'
 import { rgroupToKet } from './toKet/rgroupToKet'
 import { rgroupToStruct } from './fromKet/rgroupToStruct'
@@ -64,10 +64,6 @@ function parseNode(node: any, struct: any) {
       textToStruct(node, struct)
       break
     }
-    case 'sgroup': {
-      struct.sgroups.add(sgroupToStruct(node.data))
-      break
-    }
     default:
       break
   }
@@ -85,7 +81,6 @@ export class KetSerializer implements Serializer<Struct> {
       else if (nodes[i].$ref) parseNode(ket[nodes[i].$ref], resultingStruct)
     })
     resultingStruct.name = ket.header ? ket.header.moleculeName : null
-    resultingStruct.bindSGroupsToFunctionalGroups()
 
     return resultingStruct
   }
@@ -107,13 +102,13 @@ export class KetSerializer implements Serializer<Struct> {
       switch (item.type) {
         case 'molecule': {
           result.root.nodes.push({ $ref: `mol${moleculeId}` })
-          result[`mol${moleculeId++}`] = moleculeToKet(item.fragment)
+          result[`mol${moleculeId++}`] = moleculeToKet(item.fragment!)
           break
         }
         case 'rgroup': {
           result.root.nodes.push({ $ref: `rg${item.data!.rgnumber}` })
           result[`rg${item.data!.rgnumber}`] = rgroupToKet(
-            item.fragment,
+            item.fragment!,
             item.data
           )
           break
@@ -134,13 +129,6 @@ export class KetSerializer implements Serializer<Struct> {
           result.root.nodes.push(textToKet(item))
           break
         }
-        case 'sgroup': {
-          result.root.nodes.push({
-            type: item.type,
-            data: sgroupToKet(struct, item.data)
-          })
-          break
-        }
         default:
           break
       }