#3475 - corrected logic for all types of monomers

epam · Nov 8, 2023 · 0a42c9f · 0a42c9f
1 parent ab84cf9
commit 0a42c9f
Show file tree

Hide file tree

Showing 6 changed files with 33 additions and 31 deletions.
diff --git a/packages/ketcher-core/src/domain/entities/BaseMonomer.ts b/packages/ketcher-core/src/domain/entities/BaseMonomer.ts
@@ -138,6 +138,10 @@ export abstract class BaseMonomer extends DrawingEntity {
     return Boolean(this.firstFreeAttachmentPoint);
   }
 
+  public isAttachmentPointExistAndFree(attachmentPoint: AttachmentPointName){
+        return this.hasAttachmentPoint(attachmentPoint) && !this.isAttachmentPointUsed(attachmentPoint)
+  }
+
   public setRenderer(renderer: BaseMonomerRenderer) {
     super.setBaseRenderer(renderer as BaseRenderer);
     this.renderer = renderer;

diff --git a/packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts b/packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts
@@ -349,17 +349,12 @@ export class DrawingEntitiesManager {
     const command = new Command();
     monomer.turnOnHover();
     monomer.turnOnAttachmentPointsVisibility();
-    const availableAttachmentPointForBondEnd =
-      monomer.availableAttachmentPointForBondEnd;
-    if (availableAttachmentPointForBondEnd) {
-      monomer.setPotentialBond(availableAttachmentPointForBondEnd, bond);
-    }
     bond.firstMonomer.removePotentialBonds();
     monomer.removePotentialBonds();
-    const firstValidAttPoint = monomer.getValidSourcePoint(bond.firstMonomer);
-    const secondValidAttPonint = monomer.getValidTargetPoint(bond.firstMonomer);
-    bond.firstMonomer.setPotentialBond(secondValidAttPonint, bond);
-    monomer.setPotentialBond(firstValidAttPoint, bond);
+    const firstMonomerValidSourcePoint = bond.firstMonomer.getValidSourcePoint(monomer);
+    const secondMonomerValidTargetPoint = monomer.getValidTargetPoint(bond.firstMonomer);
+    bond.firstMonomer.setPotentialBond(firstMonomerValidSourcePoint, bond);
+    monomer.setPotentialBond(secondMonomerValidTargetPoint, bond);
     const connectFirstMonomerOperation = new MonomerHoverOperation(
       bond.firstMonomer,
       true,

diff --git a/packages/ketcher-core/src/domain/entities/Peptide.ts b/packages/ketcher-core/src/domain/entities/Peptide.ts
@@ -1,23 +1,30 @@
 import { BaseMonomer } from './BaseMonomer';
 
 export class Peptide extends BaseMonomer {
+
   public getValidSourcePoint(monomer: BaseMonomer) {
-    if (
-      monomer.hasAttachmentPoint('R1') &&
-      !monomer.isAttachmentPointUsed('R1')
-    ) {
-      return this.R1AttachmentPoint;
-    }
-    return this.R2AttachmentPoint;
+
+        if (monomer.isAttachmentPointExistAndFree('R1') && this.isAttachmentPointExistAndFree('R2')) {
+
+          return 'R2';
+
+        }
+        if (this.isAttachmentPointExistAndFree('R1') && monomer.isAttachmentPointExistAndFree('R2') ) {
+          return 'R1';
+        }
+
+    return this.firstFreeAttachmentPoint;
   }
 
   public getValidTargetPoint(monomer: BaseMonomer) {
-    if (
-      monomer.hasAttachmentPoint('R2') &&
-      !monomer.isAttachmentPointUsed('R2')
-    ) {
-      return this.R2AttachmentPoint;
-    }
-    return this.R1AttachmentPoint;
+
+      if (this.isAttachmentPointExistAndFree('R1') && monomer.isAttachmentPointExistAndFree('R2') ) {
+        return 'R1';
+      }
+        if (monomer.isAttachmentPointExistAndFree('R1') && this.isAttachmentPointExistAndFree('R2')) {
+          return 'R2';
+        }
+
+    return this.firstFreeAttachmentPoint;
   }
 }
diff --git a/packages/ketcher-core/src/domain/entities/Phosphate.ts b/packages/ketcher-core/src/domain/entities/Phosphate.ts
@@ -25,7 +25,7 @@ export class Phosphate extends BaseMonomer {
       this.hasAttachmentPoint('R2') &&
       !this.isAttachmentPointUsed('R2')
     ) {
-      return 'R1';
+      return 'R2';
     }
     return this.firstFreeAttachmentPoint;
   }

diff --git a/packages/ketcher-core/src/domain/entities/RNABase.ts b/packages/ketcher-core/src/domain/entities/RNABase.ts
@@ -1,15 +1,11 @@
 import { BaseMonomer } from 'domain/entities/BaseMonomer';
-import { Sugar } from './Sugar';
 
 export class RNABase extends BaseMonomer {
   public getValidSourcePoint(monomer: BaseMonomer) {
     return monomer.firstFreeAttachmentPoint;
   }
 
   public getValidTargetPoint(monomer: BaseMonomer) {
-    if (monomer instanceof Sugar) {
-      return 'R3';
-    }
-    return this.firstFreeAttachmentPoint;
+    return monomer.firstFreeAttachmentPoint;
   }
 }
diff --git a/packages/ketcher-core/src/domain/entities/Sugar.ts b/packages/ketcher-core/src/domain/entities/Sugar.ts
@@ -27,14 +27,14 @@ export class Sugar extends BaseMonomer {
       this.hasAttachmentPoint('R3') &&
       !this.isAttachmentPointUsed('R3')
     ) {
-      return 'R1';
+      return 'R3';
     }
     if (
       monomer instanceof Phosphate &&
       this.hasAttachmentPoint('R1') &&
       !this.isAttachmentPointUsed('R1')
     ) {
-      return 'R2';
+      return 'R1';
     }
     return this.firstFreeAttachmentPoint;
   }