From 5016dee78a2b8d7f830d877bc7f313e26d340a33 Mon Sep 17 00:00:00 2001
From: Tim Alyakin <31693137+TimSPb89@users.noreply.github.com>
Date: Fri, 3 Feb 2023 12:58:13 +0300
Subject: [PATCH] #2033: Abbreviations: Atoms protrude beyond the expanded view
 (#2125)

* #2033 - Abbreviations: Atoms protrude beyond the expanded view for Functional Groups and Salts and Solvents

* #2033 - review fixes

* #2033 - review fix (replaced in with instanceof check)

* Revert "#2033 - review fix (replaced in with instanceof check)" to fix the build failure

This reverts commit 3b983e8a878d82312aa49915c19caa9acc5b1c51.
---
 .../application/render/restruct/resgroup.js   |  2 +-
 .../src/domain/entities/sgroup.ts             | 25 +++++++++++++++----
 2 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/packages/ketcher-core/src/application/render/restruct/resgroup.js b/packages/ketcher-core/src/application/render/restruct/resgroup.js
index 90468749d6..9483ee13cf 100644
--- a/packages/ketcher-core/src/application/render/restruct/resgroup.js
+++ b/packages/ketcher-core/src/application/render/restruct/resgroup.js
@@ -40,7 +40,7 @@ class ReSGroup extends ReObject {
     let set = this.render.paper.set()
     const atomSet = new Pile(sgroup.atoms)
     const crossBonds = SGroup.getCrossBonds(remol.molecule, atomSet)
-    SGroup.bracketPos(sgroup, remol.molecule, crossBonds)
+    SGroup.bracketPos(sgroup, remol.molecule, crossBonds, remol, this.render)
     const bracketBox = sgroup.bracketBox
     const d = sgroup.bracketDir
     sgroup.areas = [bracketBox]
diff --git a/packages/ketcher-core/src/domain/entities/sgroup.ts b/packages/ketcher-core/src/domain/entities/sgroup.ts
index cfd39b0a0a..7d3d90ecee 100644
--- a/packages/ketcher-core/src/domain/entities/sgroup.ts
+++ b/packages/ketcher-core/src/domain/entities/sgroup.ts
@@ -21,6 +21,7 @@ import { Pile } from './pile'
 import { Struct } from './struct'
 import { SaltsAndSolventsProvider } from '../helpers'
 import { Vec2 } from './vec2'
+import { ReStruct } from '../../application/render'
 
 export class SGroupBracketParams {
   readonly c: Vec2
@@ -335,7 +336,9 @@ export class SGroup {
   static bracketPos(
     sGroup,
     mol,
-    crossBondsPerAtom: { [key: number]: Array<Bond> }
+    crossBondsPerAtom: { [key: number]: Array<Bond> },
+    remol?: ReStruct,
+    render?
   ): void {
     const atoms = sGroup.atoms
     const crossBonds = crossBondsPerAtom
@@ -352,12 +355,24 @@ export class SGroup {
 
     let braketBox: Box2Abs | null = null
     const contentBoxes: Array<any> = []
+    const getAtom = (aid) => {
+      if (remol && render) {
+        return remol.atoms.get(aid)
+      }
+      return mol.atoms.get(aid)
+    }
     atoms.forEach((aid) => {
-      const atom = mol.atoms.get(aid)
-      const pos = new Vec2(atom.pp)
+      const atom = getAtom(aid)
       const ext = new Vec2(0.05 * 3, 0.05 * 3)
-      const bba = new Box2Abs(pos, pos).extend(ext, ext)
-      contentBoxes.push(bba)
+      let position
+      let structBoundingBox
+      if ('getVBoxObj' in atom && render) {
+        structBoundingBox = atom.getVBoxObj(render)
+      } else {
+        position = new Vec2(atom.pp)
+        structBoundingBox = new Box2Abs(position, position)
+      }
+      contentBoxes.push(structBoundingBox.extend(ext, ext))
     })
     contentBoxes.forEach((bba) => {
       let bbb: Box2Abs | null = null