#4693 - Incorrect bond alignment to tBu S-group (#4741)

- fixed position calculation for external bonds to sgroups without attachment points
epam · Jun 4, 2024 · d00edaa · d00edaa
1 parent 7e7f117
commit d00edaa
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Showing 2 changed files with 34 additions and 8 deletions.
diff --git a/packages/ketcher-core/src/application/render/restruct/rebond.ts b/packages/ketcher-core/src/application/render/restruct/rebond.ts
@@ -19,6 +19,7 @@ import {
   Bond,
   FunctionalGroup,
   HalfBond,
+  SGroup,
   Struct,
   Vec2,
 } from 'domain/entities';
@@ -58,19 +59,27 @@ class ReBond extends ReObject {
     return true;
   }
 
+  private static getAtomPositionForBond(
+    struct: Struct,
+    atomId: number,
+    sgroup?: SGroup,
+  ) {
+    return sgroup instanceof MonomerMicromolecule
+      ? (sgroup.getAttachmentAtomId() as number)
+      : sgroup?.isContracted()
+      ? sgroup?.getContractedPosition(struct).atomId
+      : atomId;
+  }
+
   static bondRecalc(bond: ReBond, restruct: ReStruct, options: any): void {
     const render = restruct.render;
     const sgroup1 = restruct.molecule.getGroupFromAtomId(bond.b.begin);
     const sgroup2 = restruct.molecule.getGroupFromAtomId(bond.b.end);
     const beginAtom = restruct.atoms.get(
-      sgroup1 instanceof MonomerMicromolecule
-        ? (sgroup1.getAttachmentAtomId() as number)
-        : bond.b.begin,
+      ReBond.getAtomPositionForBond(restruct.molecule, bond.b.begin, sgroup1),
     );
     const endAtom = restruct.atoms.get(
-      sgroup2 instanceof MonomerMicromolecule
-        ? (sgroup2.getAttachmentAtomId() as number)
-        : bond.b.end,
+      ReBond.getAtomPositionForBond(restruct.molecule, bond.b.end, sgroup2),
     );
 
     if (

diff --git a/packages/ketcher-core/src/domain/entities/sgroup.ts b/packages/ketcher-core/src/domain/entities/sgroup.ts
@@ -26,6 +26,7 @@ import { FunctionalGroup, Pool, SGroupAttachmentPoint } from 'domain/entities';
 import { ReSGroup } from 'application/render';
 import { SgContexts } from 'application/editor/shared/constants';
 import assert from 'assert';
+import { isNumber } from 'lodash';
 
 export class SGroupBracketParams {
   readonly c: Vec2;
@@ -329,9 +330,25 @@ export class SGroup {
   } {
     let atomId = this.attachmentPoints[0]?.atomId;
     let representAtom = struct.atoms.get(atomId);
+    // if there is no attachment points in sgroup - use first externally connected atom if exist or just first atom
     if (!representAtom) {
-      atomId = this.atoms[0];
-      representAtom = struct.atoms.get(this.atoms[0]);
+      let externalConnectionAtom;
+      struct.bonds.forEach((bond) => {
+        const isBeginAtomInCurrentSgroup =
+          this.atoms.indexOf(bond.begin) !== -1;
+        const isEndAtomInCurrentSgroup = this.atoms.indexOf(bond.end) !== -1;
+
+        if (isBeginAtomInCurrentSgroup && !isEndAtomInCurrentSgroup) {
+          externalConnectionAtom = bond.begin;
+        } else if (isEndAtomInCurrentSgroup && !isBeginAtomInCurrentSgroup) {
+          externalConnectionAtom = bond.end;
+        }
+      });
+
+      atomId = isNumber(externalConnectionAtom)
+        ? externalConnectionAtom
+        : this.atoms[0];
+      representAtom = struct.atoms.get(atomId);
     }
     assert(representAtom != null);
     return { atomId, position: representAtom.pp };