#5335 - The application crashes when selecting Enhanced Stereochemist…

…ry from the right-click menu (#5342) (#5348) - added set stereo labels to atoms to setMolecule
epam · Aug 23, 2024 · b5a9b01 · b5a9b01
1 parent db13a9c
commit b5a9b01
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Showing 4 changed files with 25 additions and 23 deletions.
diff --git a/packages/ketcher-core/src/application/render/restruct/rergroup.js b/packages/ketcher-core/src/application/render/restruct/rergroup.js
@@ -14,8 +14,8 @@
  * limitations under the License.
  ***************************************************************************/
 
-import { Box2Abs, Vec2 } from 'domain/entities';
-
+import { Box2Abs } from 'domain/entities/box2Abs';
+import { Vec2 } from 'domain/entities/vec2';
 import { LayerMap } from './generalEnumTypes';
 import ReObject from './reobject';
 import { Scale } from 'domain/helpers';

diff --git a/packages/ketcher-core/src/application/utils.ts b/packages/ketcher-core/src/application/utils.ts
@@ -57,6 +57,7 @@ export async function prepareStructToRender(
   struct.initHalfBonds();
   struct.initNeighbors();
   struct.setImplicitHydrogen();
+  struct.setStereoLabelsToAtoms();
   struct.markFragments();
 
   return struct;

diff --git a/packages/ketcher-core/src/domain/entities/struct.ts b/packages/ketcher-core/src/domain/entities/struct.ts
@@ -16,7 +16,7 @@
 
 import assert from 'assert';
 import { Atom, radicalElectrons } from './atom';
-import { EditorSelection } from 'application/editor';
+import { EditorSelection, getStereoAtomsMap } from 'application/editor';
 import { Bond } from './bond';
 import { Box2Abs } from './box2Abs';
 import { Elements } from 'domain/constants';
@@ -1073,6 +1073,26 @@ export class Struct {
     }
   }
 
+  public setStereoLabelsToAtoms() {
+    const stereAtomsMap = getStereoAtomsMap(
+      this,
+      Array.from(this.bonds.values()),
+    );
+
+    this.atoms.forEach((atom, id) => {
+      if (this?.atomGetNeighbors(id)?.length === 0) {
+        atom.stereoLabel = null;
+        atom.stereoParity = 0;
+      } else {
+        const stereoProp = stereAtomsMap.get(id);
+        if (stereoProp) {
+          atom.stereoLabel = stereoProp.stereoLabel;
+          atom.stereoParity = stereoProp.stereoParity;
+        }
+      }
+    });
+  }
+
   atomGetNeighbors(aid: number): Array<Neighbor> | undefined {
     return this.atoms.get(aid)?.neighbors.map((nei) => {
       const hb = this.halfBonds.get(nei)!;

diff --git a/packages/ketcher-react/src/script/ui/state/shared.ts b/packages/ketcher-react/src/script/ui/state/shared.ts
@@ -18,7 +18,6 @@ import {
   FormatterFactory,
   Pile,
   SGroup,
-  getStereoAtomsMap,
   identifyStructFormat,
   Struct,
   SupportedFormat,
@@ -186,25 +185,7 @@ export function load(struct: Struct, options?) {
 
       parsedStruct.findConnectedComponents();
       parsedStruct.setImplicitHydrogen();
-
-      const stereAtomsMap = getStereoAtomsMap(
-        parsedStruct,
-        Array.from(parsedStruct.bonds.values()),
-      );
-
-      parsedStruct.atoms.forEach((atom, id) => {
-        if (parsedStruct?.atomGetNeighbors(id)?.length === 0) {
-          atom.stereoLabel = null;
-          atom.stereoParity = 0;
-        } else {
-          const stereoProp = stereAtomsMap.get(id);
-          if (stereoProp) {
-            atom.stereoLabel = stereoProp.stereoLabel;
-            atom.stereoParity = stereoProp.stereoParity;
-          }
-        }
-      });
-
+      parsedStruct.setStereoLabelsToAtoms();
       parsedStruct.markFragments();
 
       if (fragment) {