From 747d572e50ddf3163cd5a71af66ae0d173f6dca8 Mon Sep 17 00:00:00 2001
From: Roman Rodionov <roman_rodionov@epam.com>
Date: Mon, 10 Feb 2025 16:29:05 +0100
Subject: [PATCH] - fixed after rebase

---
 .../monomer-chains/ChainsCollection.ts        | 87 +++++++++++++------
 1 file changed, 60 insertions(+), 27 deletions(-)

diff --git a/packages/ketcher-core/src/domain/entities/monomer-chains/ChainsCollection.ts b/packages/ketcher-core/src/domain/entities/monomer-chains/ChainsCollection.ts
index ec7f36c787..22e403f70c 100644
--- a/packages/ketcher-core/src/domain/entities/monomer-chains/ChainsCollection.ts
+++ b/packages/ketcher-core/src/domain/entities/monomer-chains/ChainsCollection.ts
@@ -423,35 +423,51 @@ export class ChainsCollection {
     }
   }
 
-  private getComplimentaryChainIfNucleotide(node: SubChainNode) {
-    const monomerToChain = this.monomerToChain;
+  private getComplimentaryChainIfNucleotide(
+    node: SubChainNode,
+    monomerToChain: Map<BaseMonomer, Chain>,
+    monomerToNode: Map<BaseMonomer, SubChainNode>,
+  ) {
+    let complimentaryChain: Chain | undefined;
+    let complimentaryNode: SubChainNode | undefined;
+
+    for (const monomerToCheck of node.monomers) {
+      const { monomer, complimentaryMonomer } =
+        this.getFirstComplimentaryMonomer(monomerToCheck) || {};
+      const complimentaryNodeOrUndefined =
+        complimentaryMonomer && monomerToNode.get(complimentaryMonomer);
+      const complimentaryChainOrUndefined =
+        complimentaryMonomer && monomerToChain.get(complimentaryMonomer);
+
+      const isRnaMonomer =
+        isRnaBaseOrAmbiguousRnaBase(monomer) &&
+        Boolean(getSugarFromRnaBase(monomer));
+      const isRnaComplimentaryMonomer =
+        isRnaBaseOrAmbiguousRnaBase(complimentaryMonomer) &&
+        Boolean(getSugarFromRnaBase(complimentaryMonomer));
+
+      if (
+        !complimentaryNodeOrUndefined ||
+        !complimentaryChainOrUndefined ||
+        !(isRnaMonomer || isRnaComplimentaryMonomer)
+      ) {
+        continue;
+      }
 
-    const { monomer, complimentaryMonomer } =
-    this.getFirstAntisenseMonomerInNode(node) || {};
-    const complimentaryNode =
-      complimentaryMonomer && this.monomerToNode.get(complimentaryMonomer);
-    const complimentaryChain =
-      complimentaryMonomer && monomerToChain.get(complimentaryMonomer);
-
-    const isRnaMonomer =
-      isRnaBaseOrAmbiguousRnaBase(monomer) &&
-      Boolean(getSugarFromRnaBase(monomer));
-    const isRnaComplimentaryMonomer =
-      isRnaBaseOrAmbiguousRnaBase(complimentaryMonomer) &&
-      Boolean(getSugarFromRnaBase(complimentaryMonomer));
-
-    if (
-      !complimentaryNode ||
-      !complimentaryChain ||
-      !(isRnaMonomer || isRnaComplimentaryMonomer)
-    ) {
-      return null;
+      // return first found complimentary chain and node
+      return {
+        complimentaryChain: complimentaryChainOrUndefined,
+        complimentaryNode: complimentaryNodeOrUndefined,
+      };
     }
+
     return { complimentaryChain, complimentaryNode };
   }
 
   private reorderChainsPutSenseChainOrderInAccordanceAntisenseConnection() {
     const handledChain = new Set<Chain>();
+    const monomerToChain = this.monomerToChain;
+    const monomerToNode = this.monomerToNode;
     const reorderedSenseForSequentialAntisenseChains: Chain[] = new Array(
       this.chains.length,
     );
@@ -469,7 +485,12 @@ export class ChainsCollection {
         const {
           complimentaryChain: antisenseChain,
           complimentaryNode: antisenseNode,
-        } = this.getComplimentaryChainIfNucleotide(sNode) ?? {};
+        } =
+          this.getComplimentaryChainIfNucleotide(
+            sNode,
+            monomerToChain,
+            monomerToNode,
+          ) ?? {};
         if (!antisenseChain) {
           return;
         }
@@ -481,7 +502,11 @@ export class ChainsCollection {
           }
           if (!isFindCur) {
             const { complimentaryChain: anotherSenseChain } =
-            this.getComplimentaryChainIfNucleotide(aNode) ?? {};
+              this.getComplimentaryChainIfNucleotide(
+                aNode,
+                monomerToChain,
+                monomerToNode,
+              ) ?? {};
             if (anotherSenseChain && !handledChain.has(anotherSenseChain)) {
               const curChainIdx =
                 reorderedSenseForSequentialAntisenseChains.findIndex(
@@ -518,7 +543,6 @@ export class ChainsCollection {
   // in the picture we have 5 chains, if we pass number 1 it return 1, 2 and 3, if pass 5, return 4, 5
   public getAllChainsWithConnectionInBlock(c: Chain) {
     const chains: GrouppedChain[] = [{ group: 0, chain: c }];
-    const monomerToNode = this.monomerToNode;
     const cycledComplimentaryChains = new Set<Chain>(
       this.findCycledComplimentaryChains(c, c),
     );
@@ -526,15 +550,24 @@ export class ChainsCollection {
     const res: GrouppedChain[] = [{ group: 0, chain: c }];
     const handledChains = new Set<Chain>([c]);
     const monomerToChain = this.monomerToChain;
+    const monomerToNode = this.monomerToNode;
 
     while (chains.length) {
       const { group, chain } = chains.pop() as GrouppedChain;
 
       chain.forEachNode(({ node }) => {
         const { complimentaryChain } =
-        this.getComplimentaryChainIfNucleotide(node) ?? {};
+          this.getComplimentaryChainIfNucleotide(
+            node,
+            monomerToChain,
+            monomerToNode,
+          ) ?? {};
 
-        if (!complimentaryChain || handledChains.has(complimentaryChain) || cycledComplimentaryChains.has(complimentaryChain)) {
+        if (
+          !complimentaryChain ||
+          handledChains.has(complimentaryChain) ||
+          cycledComplimentaryChains.has(complimentaryChain)
+        ) {
           return;
         }