From f7e78c120da5ffac33c78b36088fba8654ee1416 Mon Sep 17 00:00:00 2001
From: Aleksei Proskurnov <proskurn@gmail.com>
Date: Fri, 31 Jan 2025 14:55:19 +0100
Subject: [PATCH] Two sense to antisense connection order problem

---
 .../monomer-chains/ChainsCollection.ts        | 113 ++++++++++++++----
 1 file changed, 91 insertions(+), 22 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 0339be368c..3a0125507d 100644
--- a/packages/ketcher-core/src/domain/entities/monomer-chains/ChainsCollection.ts
+++ b/packages/ketcher-core/src/domain/entities/monomer-chains/ChainsCollection.ts
@@ -104,7 +104,10 @@ export class ChainsCollection {
         });
       });
     });
+
     this.chains = [...reorderedChains.values()];
+
+    this.reorderChainsPutSenseChainOrderInAccordanceAntisenseConnection();
   }
 
   public add(chain: Chain) {
@@ -370,6 +373,90 @@ export class ChainsCollection {
     return undefined;
   }
 
+  private getComplimentaryChainIfNucleotide(node: SubChainNode) {
+    const monomerToChain = this.monomerToChain;
+
+    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 { complimentaryChain, complimentaryNode };
+  }
+
+  private reorderChainsPutSenseChainOrderInAccordanceAntisenseConnection() {
+    const handledChain = new Set<Chain>();
+    const reorderedSenseForSequentialAntisenseChains: Chain[] = new Array(
+      this.chains.length,
+    );
+    this.chains.forEach((chain) => {
+      if (!handledChain.has(chain)) {
+        reorderedSenseForSequentialAntisenseChains[handledChain.size] = chain;
+        handledChain.add(chain);
+      }
+
+      if (chain.isAntisense) {
+        return;
+      }
+
+      chain.forEachNode(({ node: sNode }) => {
+        const {
+          complimentaryChain: antisenseChain,
+          complimentaryNode: antisenseNode,
+        } = this.getComplimentaryChainIfNucleotide(sNode) ?? {};
+        if (!antisenseChain) {
+          return;
+        }
+
+        let isFindCur = false;
+        antisenseChain.forEachNode(({ node: aNode }) => {
+          if (aNode === antisenseNode) {
+            isFindCur = true;
+          }
+          if (!isFindCur) {
+            const { complimentaryChain: anotherSenseChain } =
+              this.getComplimentaryChainIfNucleotide(aNode) ?? {};
+            if (anotherSenseChain && !handledChain.has(anotherSenseChain)) {
+              const curChainIdx =
+                reorderedSenseForSequentialAntisenseChains.findIndex(
+                  (v) => v === chain,
+                );
+              let last = anotherSenseChain;
+              for (
+                let i = curChainIdx;
+                i < reorderedSenseForSequentialAntisenseChains.length;
+                i++
+              ) {
+                const tmp = reorderedSenseForSequentialAntisenseChains[i];
+                reorderedSenseForSequentialAntisenseChains[i] = last;
+                last = tmp;
+              }
+              handledChain.add(anotherSenseChain);
+            }
+          }
+        });
+      });
+    });
+    this.chains = [...reorderedSenseForSequentialAntisenseChains];
+  }
+
   // for example
   // 1 x x x
   //   |
@@ -385,32 +472,14 @@ export class ChainsCollection {
 
     const res: GrouppedChain[] = [{ group: 0, chain: c }];
     const handledChains = new Set<Chain>([c]);
-    const monomerToChain = this.monomerToChain;
 
     while (chains.length) {
       const { group, chain } = chains.pop() as GrouppedChain;
       chain.forEachNode(({ node }) => {
-        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 ||
-          handledChains.has(complimentaryChain)
-        ) {
+        const { complimentaryChain } =
+          this.getComplimentaryChainIfNucleotide(node) ?? {};
+
+        if (!complimentaryChain || handledChains.has(complimentaryChain)) {
           return;
         }