6021 connection between molecule and monomer does not affect an amoun…

…t of implicit hydrogens (#6229) * 6021-connection-between-molecule-and-monomer-does-not-affect-an-amount-of-implicit-hydrogens * add type check * update test --------- Co-authored-by: Andrey Menshikov <[email protected]>
epam · Dec 30, 2024 · 06b5dc5 · 06b5dc5
1 parent 76dd6d2
commit 06b5dc5
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Showing 9 changed files with 42 additions and 27 deletions.
diff --git a/.../13-Connect-with-hydrogen-bond-ambiguous-base-and-atom-BrH-1-chromium-linux.png b/.../13-Connect-with-hydrogen-bond-ambiguous-base-and-atom-BrH-1-chromium-linux.png
diff --git a/...-Connect-with-hydrogen-bond-ambiguous-peptide-and-atom-BrH-1-chromium-linux.png b/...-Connect-with-hydrogen-bond-ambiguous-peptide-and-atom-BrH-1-chromium-linux.png
diff --git a/...napshots/13-Connect-with-hydrogen-bond-base-A-and-atom-BrH-1-chromium-linux.png b/...napshots/13-Connect-with-hydrogen-bond-base-A-and-atom-BrH-1-chromium-linux.png
diff --git a/...-Connect-with-hydrogen-bond-nucleotide-5hMedC-and-atom-BrH-1-chromium-linux.png b/...-Connect-with-hydrogen-bond-nucleotide-5hMedC-and-atom-BrH-1-chromium-linux.png
diff --git a/...shots/13-Connect-with-hydrogen-bond-peptide-A-and-atom-BrH-1-chromium-linux.png b/...shots/13-Connect-with-hydrogen-bond-peptide-A-and-atom-BrH-1-chromium-linux.png
diff --git a/...with-hydrogen-bond-unresolved-monomer-Unknown-and-atom-BrH-1-chromium-linux.png b/...with-hydrogen-bond-unresolved-monomer-Unknown-and-atom-BrH-1-chromium-linux.png
diff --git a/packages/ketcher-core/src/application/render/renderers/RenderersManager.ts b/packages/ketcher-core/src/application/render/renderers/RenderersManager.ts
@@ -345,6 +345,7 @@ export class RenderersManager {
 
   public addMonomerToAtomBond(bond: MonomerToAtomBond) {
     const bondRenderer = new MonomerToAtomBondRenderer(bond);
+    this.redrawDrawingEntity(bond.atom);
 
     bondRenderer.show();
     bond.monomer.renderer?.redrawAttachmentPoints();
@@ -353,6 +354,7 @@ export class RenderersManager {
 
   public deleteMonomerToAtomBond(bond: MonomerToAtomBond) {
     bond.renderer?.remove();
+    this.redrawDrawingEntity(bond.atom);
   }
 
   public runPostRenderMethods() {

diff --git a/packages/ketcher-core/src/domain/entities/CoreAtom.ts b/packages/ketcher-core/src/domain/entities/CoreAtom.ts
@@ -6,6 +6,7 @@ import { BaseRenderer } from 'application/render';
 import { AtomLabel, Elements } from 'domain/constants';
 import { AtomRenderer } from 'application/render/renderers/AtomRenderer';
 import { isNumber } from 'lodash';
+import { MonomerToAtomBond } from './MonomerToAtomBond';
 
 export interface AtomProperties {
   charge?: number | null;
@@ -15,7 +16,7 @@ export interface AtomProperties {
   alias?: string | null;
 }
 export class Atom extends DrawingEntity {
-  public bonds: Bond[] = [];
+  public bonds: Array<Bond | MonomerToAtomBond> = [];
   public renderer: AtomRenderer | undefined = undefined;
   constructor(
     position: Vec2,
@@ -31,8 +32,14 @@ export class Atom extends DrawingEntity {
     return this.position;
   }
 
-  public addBond(bond: Bond) {
-    this.bonds.push(bond);
+  public addBond(bond: Bond | MonomerToAtomBond) {
+    if (!this.bonds.includes(bond)) {
+      this.bonds.push(bond);
+    }
+  }
+
+  public deleteBond(bondId: number) {
+    this.bonds = this.bonds.filter((bond) => bond.id !== bondId);
   }
 
   public setRenderer(renderer: AtomRenderer) {
@@ -48,26 +55,31 @@ export class Atom extends DrawingEntity {
     let connectionsAmount = 0;
 
     for (let i = 0; i < this.bonds.length; i++) {
-      switch (this.bonds[i].type) {
-        case BondType.Single:
-          connectionsAmount += 1;
-          break;
-        case BondType.Double:
-          connectionsAmount += 2;
-          break;
-        case BondType.Triple:
-          connectionsAmount += 3;
-          break;
-        case BondType.Dative:
-        case BondType.Hydrogen:
-          break;
-        case BondType.Aromatic:
-          if (this.bonds.length === 1) {
+      const bond = this.bonds[i];
+      if (bond instanceof MonomerToAtomBond) {
+        connectionsAmount += 1;
+      } else {
+        switch (bond.type) {
+          case BondType.Single:
+            connectionsAmount += 1;
+            break;
+          case BondType.Double:
+            connectionsAmount += 2;
+            break;
+          case BondType.Triple:
+            connectionsAmount += 3;
+            break;
+          case BondType.Dative:
+          case BondType.Hydrogen:
+            break;
+          case BondType.Aromatic:
+            if (this.bonds.length === 1) {
+              return -1;
+            }
+            return this.bonds.length;
+          default:
             return -1;
-          }
-          return this.bonds.length;
-        default:
-          return -1;
+        }
       }
     }
 

diff --git a/packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts b/packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts
@@ -2447,8 +2447,9 @@ export class DrawingEntitiesManager {
         if (bond.selected) {
           return;
         }
-
-        command.merge(this.deleteBond(bond));
+        if (bond instanceof Bond) {
+          command.merge(this.deleteBond(bond));
+        }
       });
 
       this.monomerToAtomBonds.forEach((monomerToAtomBond) => {
@@ -2553,12 +2554,12 @@ export class DrawingEntitiesManager {
     if (_monomerToAtomBond) {
       this.monomerToAtomBonds.set(_monomerToAtomBond.id, _monomerToAtomBond);
       monomer.setBond(attachmentPoint, _monomerToAtomBond);
-
+      atom.addBond(_monomerToAtomBond);
       return _monomerToAtomBond;
     }
 
     const monomerToAtomBond = new MonomerToAtomBond(monomer, atom);
-
+    atom.addBond(monomerToAtomBond);
     this.monomerToAtomBonds.set(monomerToAtomBond.id, monomerToAtomBond);
 
     monomerToAtomBond.moveToLinkedEntities();
@@ -2579,7 +2580,7 @@ export class DrawingEntitiesManager {
       monomerAtomBond.monomer.unsetBond(attachmentPointName);
     }
     this.monomerToAtomBonds.delete(monomerAtomBond.id);
-
+    monomerAtomBond.atom.deleteBond(monomerAtomBond.id);
     return monomerAtomBond;
   }