#6086 - Unable to create antisense chains for ambiguous monomers from…

… the library (#6113)

- added antisense creation for chains with ambiguous bases

packages/ketcher-core/src/domain/constants/monomers.ts

@@ -22,6 +22,20 @@ export enum RnaDnaNaturalAnaloguesEnum {
   URACIL = 'U',
 }
 
+export enum StandardAmbiguousRnaBase {
+  N = 'N',
+  B = 'B',
+  V = 'V',
+  D = 'D',
+  H = 'H',
+  K = 'K',
+  M = 'M',
+  W = 'W',
+  Y = 'Y',
+  R = 'R',
+  S = 'S',
+}
+
 export const rnaDnaNaturalAnalogues = [
   RnaDnaNaturalAnaloguesEnum.ADENINE,
   RnaDnaNaturalAnaloguesEnum.THYMINE,

packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts

@@ -89,6 +89,7 @@ import { MACROMOLECULES_BOND_TYPES } from 'application/editor/tools/Bond';
 import {
   RNA_DNA_NON_MODIFIED_PART,
   RnaDnaNaturalAnaloguesEnum,
+  StandardAmbiguousRnaBase,
 } from 'domain/constants/monomers';
 import { isNumber } from 'lodash';
 import { Chain } from 'domain/entities/monomer-chains/Chain';
@@ -2621,6 +2622,17 @@ export class DrawingEntitiesManager {
       [RnaDnaNaturalAnaloguesEnum.GUANINE]: RnaDnaNaturalAnaloguesEnum.CYTOSINE,
       [RnaDnaNaturalAnaloguesEnum.THYMINE]: RnaDnaNaturalAnaloguesEnum.ADENINE,
       [RnaDnaNaturalAnaloguesEnum.URACIL]: RnaDnaNaturalAnaloguesEnum.ADENINE,
+      [StandardAmbiguousRnaBase.N]: StandardAmbiguousRnaBase.N,
+      [StandardAmbiguousRnaBase.B]: StandardAmbiguousRnaBase.V,
+      [StandardAmbiguousRnaBase.D]: StandardAmbiguousRnaBase.H,
+      [StandardAmbiguousRnaBase.H]: StandardAmbiguousRnaBase.D,
+      [StandardAmbiguousRnaBase.K]: StandardAmbiguousRnaBase.M,
+      [StandardAmbiguousRnaBase.W]: StandardAmbiguousRnaBase.W,
+      [StandardAmbiguousRnaBase.Y]: StandardAmbiguousRnaBase.R,
+      [StandardAmbiguousRnaBase.M]: StandardAmbiguousRnaBase.K,
+      [StandardAmbiguousRnaBase.R]: StandardAmbiguousRnaBase.Y,
+      [StandardAmbiguousRnaBase.S]: StandardAmbiguousRnaBase.S,
+      [StandardAmbiguousRnaBase.V]: StandardAmbiguousRnaBase.B,
     };
   }
 
@@ -2683,15 +2695,15 @@ export class DrawingEntitiesManager {
           complimentaryChainWithData.complimentaryChain.monomers.some(
             (monomer) => {
               return (
-                (monomer instanceof RNABase &&
+                (isRnaBaseOrAmbiguousRnaBase(monomer) &&
                   Boolean(getSugarFromRnaBase(monomer)) &&
                   monomer.hydrogenBonds.length > 0) ||
                 monomer.hydrogenBonds.some((hydrogenBond) => {
                   const anotherMonomer =
                     hydrogenBond.getAnotherMonomer(monomer);
 
                   return (
-                    anotherMonomer instanceof RNABase &&
+                    isRnaBaseOrAmbiguousRnaBase(anotherMonomer) &&
                     Boolean(getSugarFromRnaBase(anotherMonomer))
                   );
                 })
@@ -2782,6 +2794,14 @@ export class DrawingEntitiesManager {
     return command;
   }
 
+  private getAntisenseBaseLabel(rnaBase: RNABase | AmbiguousMonomer) {
+    return this.antisenseChainBasesMap[
+      rnaBase instanceof AmbiguousMonomer
+        ? rnaBase.monomerItem.label
+        : rnaBase.monomerItem.props.MonomerNaturalAnalogCode
+    ];
+  }
+
   public createAntisenseChain() {
     const editor = CoreEditor.provideEditorInstance();
     const command = new Command();
@@ -2795,6 +2815,7 @@ export class DrawingEntitiesManager {
           subChain.nodes.some(
             (node) =>
               (node instanceof Nucleotide || node instanceof Nucleoside) &&
+              Boolean(this.getAntisenseBaseLabel(node.rnaBase)) &&
               node.monomer.selected,
           ),
         );
@@ -2814,14 +2835,18 @@ export class DrawingEntitiesManager {
         }
 
         if (node instanceof Nucleotide || node instanceof Nucleoside) {
+          const antisenseBaseLabel = this.getAntisenseBaseLabel(node.rnaBase);
+
+          if (!antisenseBaseLabel) {
+            return;
+          }
+
           const { modelChanges: addNucleotideCommand, node: addedNode } = (
             node instanceof Nucleotide && node.phosphate.selected
               ? Nucleotide
               : Nucleoside
           ).createOnCanvas(
-            this.antisenseChainBasesMap[
-              node.rnaBase.monomerItem.props.MonomerNaturalAnalogCode
-            ],
+            antisenseBaseLabel,
             node.monomer.position.add(new Vec2(0, 3)),
             RNA_DNA_NON_MODIFIED_PART.SUGAR_RNA,
           );

packages/ketcher-core/src/domain/entities/Nucleoside.ts

@@ -18,6 +18,7 @@ import { AmbiguousMonomer } from 'domain/entities/AmbiguousMonomer';
 import { RNA_MONOMER_DISTANCE } from 'application/editor/tools/RnaPreset';
 import { SugarRenderer } from 'application/render';
 import { RNA_DNA_NON_MODIFIED_PART } from 'domain/constants/monomers';
+import { KetMonomerClass } from 'application/formatters';
 
 export class Nucleoside {
   constructor(
@@ -46,8 +47,16 @@ export class Nucleoside {
     isAntisense = false,
   ) {
     const editor = CoreEditor.provideEditorInstance();
-    const rnaBaseLibraryItem = getRnaPartLibraryItem(editor, rnaBaseName);
-    const sugarLibraryItem = getRnaPartLibraryItem(editor, sugarName);
+    const rnaBaseLibraryItem = getRnaPartLibraryItem(
+      editor,
+      rnaBaseName,
+      KetMonomerClass.Base,
+    );
+    const sugarLibraryItem = getRnaPartLibraryItem(
+      editor,
+      sugarName,
+      KetMonomerClass.Sugar,
+    );
 
     assert(sugarLibraryItem);
     assert(rnaBaseLibraryItem);

packages/ketcher-core/src/domain/entities/Nucleotide.ts

@@ -18,6 +18,7 @@ import { AmbiguousMonomer } from 'domain/entities/AmbiguousMonomer';
 import { RNA_MONOMER_DISTANCE } from 'application/editor/tools/RnaPreset';
 import { SugarRenderer } from 'application/render';
 import { SNAKE_LAYOUT_CELL_WIDTH } from 'domain/entities/DrawingEntitiesManager';
+import { KetMonomerClass } from 'application/formatters';
 
 export class Nucleotide {
   constructor(
@@ -53,12 +54,20 @@ export class Nucleotide {
     sugarName: RNA_DNA_NON_MODIFIED_PART = RNA_DNA_NON_MODIFIED_PART.SUGAR_RNA,
   ) {
     const editor = CoreEditor.provideEditorInstance();
-    const rnaBaseLibraryItem = getRnaPartLibraryItem(editor, rnaBaseName);
+    const rnaBaseLibraryItem = getRnaPartLibraryItem(
+      editor,
+      rnaBaseName,
+      KetMonomerClass.Base,
+    );
     const phosphateLibraryItem = getRnaPartLibraryItem(
       editor,
       RNA_DNA_NON_MODIFIED_PART.PHOSPHATE,
     );
-    const sugarLibraryItem = getRnaPartLibraryItem(editor, sugarName);
+    const sugarLibraryItem = getRnaPartLibraryItem(
+      editor,
+      sugarName,
+      KetMonomerClass.Sugar,
+    );
 
     assert(sugarLibraryItem);
     assert(rnaBaseLibraryItem);

packages/ketcher-core/src/domain/helpers/rna.ts

@@ -1,13 +1,23 @@
 import { CoreEditor } from 'application/editor/internal';
-import { SequenceType } from 'domain/entities';
+import { AmbiguousMonomer, SequenceType } from 'domain/entities';
 import { RNA_DNA_NON_MODIFIED_PART } from 'domain/constants/monomers';
 import { MONOMER_CONST } from 'application/editor';
+import { isAmbiguousMonomerLibraryItem } from 'domain/helpers/monomers';
+import { KetMonomerClass } from 'application/formatters';
 
-export function getRnaPartLibraryItem(editor: CoreEditor, rnaBaseName: string) {
-  return editor.monomersLibrary.find(
-    (libraryItem) =>
-      libraryItem.props.MonomerType === MONOMER_CONST.RNA &&
-      libraryItem.props.MonomerName === rnaBaseName,
+export function getRnaPartLibraryItem(
+  editor: CoreEditor,
+  rnaBaseName: string,
+  monomerClass?: KetMonomerClass,
+) {
+  return editor.monomersLibrary.find((libraryItem) =>
+    isAmbiguousMonomerLibraryItem(libraryItem)
+      ? (!monomerClass ||
+          AmbiguousMonomer.getMonomerClass(libraryItem.monomers) ===
+            monomerClass) &&
+        libraryItem.label === rnaBaseName
+      : (!monomerClass || libraryItem.props.MonomerClass === monomerClass) &&
+        libraryItem.props.MonomerName === rnaBaseName,
   );
 }