#4824 - Cycled chain breaks sequence canvas and entire app

- fixed case with infinite loop in chains analysis if phosphate is first in cycled chain
epam · Jun 10, 2024 · f509957 · f509957
1 parent 388797b
commit f509957
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Showing 2 changed files with 25 additions and 11 deletions.
diff --git a/packages/ketcher-core/src/domain/entities/monomer-chains/Chain.ts b/packages/ketcher-core/src/domain/entities/monomer-chains/Chain.ts
@@ -20,13 +20,11 @@ import { LinkerSequenceNode } from 'domain/entities/LinkerSequenceNode';
 export class Chain {
   public subChains: BaseSubChain[] = [];
 
-  public firstMonomer: BaseMonomer | null;
+  public firstMonomer?: BaseMonomer;
 
   public isCyclic = false;
 
   constructor(firstMonomer?: BaseMonomer, isCyclic?: boolean) {
-    this.firstMonomer = null;
-
     if (firstMonomer) {
       this.firstMonomer = firstMonomer;
 
@@ -53,10 +51,16 @@ export class Chain {
 
     const nextMonomer = getNextMonomerInChain(monomer);
 
-    if (monomer instanceof Sugar && isValidNucleoside(monomer)) {
-      this.lastSubChain.add(Nucleoside.fromSugar(monomer));
-    } else if (monomer instanceof Sugar && isValidNucleotide(monomer)) {
-      this.lastSubChain.add(Nucleotide.fromSugar(monomer));
+    if (
+      monomer instanceof Sugar &&
+      isValidNucleoside(monomer, this.firstMonomer)
+    ) {
+      this.lastSubChain.add(Nucleoside.fromSugar(monomer, false));
+    } else if (
+      monomer instanceof Sugar &&
+      isValidNucleotide(monomer, this.firstMonomer)
+    ) {
+      this.lastSubChain.add(Nucleotide.fromSugar(monomer, false));
     } else if (monomer instanceof Peptide) {
       this.lastSubChain.add(new MonomerSequenceNode(monomer));
     } else if (

diff --git a/packages/ketcher-core/src/domain/helpers/monomers.ts b/packages/ketcher-core/src/domain/helpers/monomers.ts
@@ -86,22 +86,32 @@ export function isMonomerBeginningOfChain(
   );
 }
 
-export function isValidNucleotide(sugar: Sugar) {
+export function isValidNucleotide(
+  sugar: Sugar,
+  firstMonomerInCyclicChain?: BaseMonomer,
+) {
   const phosphate = getPhosphateFromSugar(sugar);
   const nextMonomerAfterPhosphate = getNextMonomerInChain(phosphate);
 
   return Boolean(
     getRnaBaseFromSugar(sugar) &&
       getPhosphateFromSugar(sugar) &&
-      nextMonomerAfterPhosphate,
+      nextMonomerAfterPhosphate &&
+      phosphate !== firstMonomerInCyclicChain,
   );
 }
 
-export function isValidNucleoside(sugar: Sugar) {
+export function isValidNucleoside(
+  sugar: Sugar,
+  firstMonomerInCyclicChain?: BaseMonomer,
+) {
   const phosphate = getPhosphateFromSugar(sugar);
   const nextMonomerAfterPhosphate = getNextMonomerInChain(phosphate);
 
   return (
-    getRnaBaseFromSugar(sugar) && (!phosphate || !nextMonomerAfterPhosphate)
+    getRnaBaseFromSugar(sugar) &&
+    (!phosphate ||
+      !nextMonomerAfterPhosphate ||
+      phosphate === firstMonomerInCyclicChain)
   );
 }