#4607 - Inconsistent display of a separate phosphate in the sequence …

…representation in the Sequence mode (#4766) - correct isValidNucleoside() and isValidNucleotide() - correct the definition of individual phosphate and linker
epam · Jun 14, 2024 · 22ad484 · 22ad484
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commit 22ad484
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Showing 10 changed files with 51 additions and 26 deletions.
diff --git a/...fy-it--2b33a-f-connection-between-Phosphate-and-RNA-to-SVG-2-chromium-linux.png b/...fy-it--2b33a-f-connection-between-Phosphate-and-RNA-to-SVG-2-chromium-linux.png
diff --git a/...fy-it--3c572-f-connection-between-Phosphate-and-RNA-to-SVG-1-chromium-linux.png b/...fy-it--3c572-f-connection-between-Phosphate-and-RNA-to-SVG-1-chromium-linux.png
diff --git a/...fy-it--5a557-f-connection-between-Phosphate-and-RNA-to-SVG-2-chromium-linux.png b/...fy-it--5a557-f-connection-between-Phosphate-and-RNA-to-SVG-2-chromium-linux.png
diff --git a/...fy-it--64708-f-connection-between-Phosphate-and-RNA-to-SVG-1-chromium-linux.png b/...fy-it--64708-f-connection-between-Phosphate-and-RNA-to-SVG-1-chromium-linux.png
diff --git a/...fy-it--ad04e-f-connection-between-Phosphate-and-RNA-to-SVG-2-chromium-linux.png b/...fy-it--ad04e-f-connection-between-Phosphate-and-RNA-to-SVG-2-chromium-linux.png
diff --git a/...fy-it--f0889-f-connection-between-Phosphate-and-RNA-to-SVG-1-chromium-linux.png b/...fy-it--f0889-f-connection-between-Phosphate-and-RNA-to-SVG-1-chromium-linux.png
diff --git a/...ce-Mode-Side-chain-connections-between-sugar-and-phosphate-2-chromium-linux.png b/...ce-Mode-Side-chain-connections-between-sugar-and-phosphate-2-chromium-linux.png
diff --git a/...ed-nuc-b031d-types-of-connection-between-Phosphate-and-RNA-1-chromium-linux.png b/...ed-nuc-b031d-types-of-connection-between-Phosphate-and-RNA-1-chromium-linux.png
diff --git a/packages/ketcher-core/src/domain/entities/monomer-chains/Chain.ts b/packages/ketcher-core/src/domain/entities/monomer-chains/Chain.ts
@@ -51,24 +51,36 @@ export class Chain {
   public add(monomer: BaseMonomer) {
     this.createSubChainIfNeed(monomer);
 
-    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));
-    } else if (monomer instanceof Peptide) {
+    if (monomer instanceof Sugar) {
+      if (isValidNucleoside(monomer)) {
+        this.lastSubChain.add(Nucleoside.fromSugar(monomer));
+        return;
+      }
+      if (isValidNucleotide(monomer)) {
+        this.lastSubChain.add(Nucleotide.fromSugar(monomer));
+        return;
+      }
+    }
+    if (monomer instanceof Peptide) {
       this.lastSubChain.add(new MonomerSequenceNode(monomer));
-    } else if (
+      return;
+    }
+    const nextMonomer = getNextMonomerInChain(monomer);
+    const isNextMonomerNucleosideOrNucleotideOrPeptide = () => {
+      const isNucleosideOrNucleotide =
+        nextMonomer instanceof Sugar &&
+        (isValidNucleotide(nextMonomer) || isValidNucleoside(nextMonomer));
+      return isNucleosideOrNucleotide || nextMonomer instanceof Peptide;
+    };
+    if (
       monomer instanceof Phosphate &&
-      (this.lastNode instanceof Nucleoside ||
-        (nextMonomer instanceof Sugar &&
-          (isValidNucleotide(nextMonomer) || isValidNucleotide(nextMonomer))))
+      (!this.lastNode || this.lastNode instanceof Nucleoside) &&
+      (!nextMonomer || isNextMonomerNucleosideOrNucleotideOrPeptide())
     ) {
       this.lastSubChain.add(new MonomerSequenceNode(monomer));
-    } else {
-      this.lastSubChain.add(new LinkerSequenceNode(monomer));
+      return;
     }
+    this.lastSubChain.add(new LinkerSequenceNode(monomer));
   }
 
   public addNode(node: SubChainNode) {
@@ -105,7 +117,12 @@ export class Chain {
     return nodes;
   }
 
-  public get lastNode() {
+  public get lastNode():
+    | EmptySequenceNode
+    | MonomerSequenceNode
+    | Nucleoside
+    | Nucleotide
+    | undefined {
     return this.lastSubChain?.lastNode;
   }
 

diff --git a/packages/ketcher-core/src/domain/helpers/monomers.ts b/packages/ketcher-core/src/domain/helpers/monomers.ts
@@ -86,22 +86,30 @@ export function isMonomerBeginningOfChain(
   );
 }
 
-export function isValidNucleotide(sugar: Sugar) {
+export function isValidNucleotide(sugar: Sugar): boolean {
+  if (!getRnaBaseFromSugar(sugar)) {
+    return false;
+  }
+
   const phosphate = getPhosphateFromSugar(sugar);
-  const nextMonomerAfterPhosphate = getNextMonomerInChain(phosphate);
+  if (!phosphate) {
+    return false;
+  }
 
-  return Boolean(
-    getRnaBaseFromSugar(sugar) &&
-      getPhosphateFromSugar(sugar) &&
-      nextMonomerAfterPhosphate,
-  );
+  const nextMonomerAfterPhosphate = getNextMonomerInChain(phosphate);
+  return !!nextMonomerAfterPhosphate;
 }
 
-export function isValidNucleoside(sugar: Sugar) {
+export function isValidNucleoside(sugar: Sugar): boolean {
+  if (!getRnaBaseFromSugar(sugar)) {
+    return false;
+  }
+
   const phosphate = getPhosphateFromSugar(sugar);
-  const nextMonomerAfterPhosphate = getNextMonomerInChain(phosphate);
+  if (!phosphate) {
+    return true;
+  }
 
-  return (
-    getRnaBaseFromSugar(sugar) && (!phosphate || !nextMonomerAfterPhosphate)
-  );
+  const nextMonomerAfterPhosphate = getNextMonomerInChain(phosphate);
+  return !nextMonomerAfterPhosphate;
 }