#4557 - Support of ambiguous monomers in small molecules mode (#5399)

- fixed ambiguous monomers in molecules mode - fixed rna builder for ambiguous monomers - fixed sequence mode for ambiguous monomers
epam · Sep 1, 2024 · 8f94e77 · 8f94e77
1 parent 919ec5c
commit 8f94e77
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Showing 15 changed files with 120 additions and 55 deletions.
diff --git a/packages/ketcher-core/src/application/editor/modes/SequenceMode.ts b/packages/ketcher-core/src/application/editor/modes/SequenceMode.ts
@@ -11,6 +11,7 @@ import {
 import { AttachmentPointName, MonomerItemType } from 'domain/types';
 import { Command } from 'domain/entities/Command';
 import {
+  AmbiguousMonomer,
   BaseMonomer,
   LinkerSequenceNode,
   Phosphate,
@@ -1438,7 +1439,7 @@ export class SequenceMode extends BaseMode {
       position,
     ) as Sugar;
 
-    let rnaBaseMonomer: RNABase | null = null;
+    let rnaBaseMonomer: RNABase | AmbiguousMonomer | null = null;
     if (rnaBase) {
       rnaBaseMonomer = editor.drawingEntitiesManager.createMonomer(
         rnaBase,

diff --git a/packages/ketcher-core/src/application/editor/operations/monomer/monomerFactory.ts b/packages/ketcher-core/src/application/editor/operations/monomer/monomerFactory.ts
@@ -7,8 +7,9 @@ import {
   PhosphateRenderer,
   UnresolvedMonomerRenderer,
   UnsplitNucleotideRenderer,
+  AmbiguousMonomerRenderer,
 } from 'application/render/renderers';
-import { MonomerItemType } from 'domain/types';
+import { MonomerOrAmbiguousType } from 'domain/types';
 import {
   Peptide,
   Chem,
@@ -17,8 +18,10 @@ import {
   RNABase,
   UnresolvedMonomer,
   UnsplitNucleotide,
+  AmbiguousMonomer,
 } from 'domain/entities';
 import { KetMonomerClass } from 'application/formatters/types/ket';
+import { isAmbiguousMonomerLibraryItem } from 'domain/helpers/monomers';
 
 type DerivedClass<T> = new (...args: unknown[]) => T;
 export const MONOMER_CONST = {
@@ -43,7 +46,7 @@ type Monomer =
   | typeof Phosphate;
 
 export const monomerFactory = (
-  monomer: MonomerItemType,
+  monomer: MonomerOrAmbiguousType,
 ): [
   Monomer: Monomer,
   MonomerRenderer: DerivedClass<BaseMonomerRenderer>,
@@ -53,7 +56,11 @@ export const monomerFactory = (
   let MonomerRenderer;
   let ketMonomerClass: KetMonomerClass;
 
-  if (monomer.props.unresolved) {
+  if (isAmbiguousMonomerLibraryItem(monomer)) {
+    Monomer = AmbiguousMonomer;
+    MonomerRenderer = AmbiguousMonomerRenderer;
+    ketMonomerClass = AmbiguousMonomer.getMonomerClass(monomer.monomers);
+  } else if (monomer.props.unresolved) {
     Monomer = UnresolvedMonomer;
     MonomerRenderer = UnresolvedMonomerRenderer;
     ketMonomerClass = KetMonomerClass.CHEM;

diff --git a/packages/ketcher-core/src/application/editor/tools/Monomer.ts b/packages/ketcher-core/src/application/editor/tools/Monomer.ts
@@ -57,7 +57,7 @@ class MonomerTool implements BaseTool {
       ),
     );
     if (isAmbiguousMonomerLibraryItem(this.monomer)) {
-      modelChanges = this.editor.drawingEntitiesManager.addVariantMonomer(
+      modelChanges = this.editor.drawingEntitiesManager.addAmbiguousMonomer(
         this.monomer,
         position,
       );

diff --git a/packages/ketcher-core/src/application/render/renderers/AmbiguousMonomerRenderer.ts b/packages/ketcher-core/src/application/render/renderers/AmbiguousMonomerRenderer.ts
@@ -109,8 +109,8 @@ export class AmbiguousMonomerRenderer extends BaseMonomerRenderer {
   public show(theme) {
     super.show(theme);
     this.appendNumberOfMonomers();
+    this.appendEnumeration();
     if (this.CHAIN_BEGINNING) {
-      this.appendEnumeration();
       this.appendChainBeginning();
     }
   }

diff --git a/packages/ketcher-core/src/application/render/renderers/RenderersManager.ts b/packages/ketcher-core/src/application/render/renderers/RenderersManager.ts
@@ -187,7 +187,7 @@ export class RenderersManager {
       const nextMonomer = getNextMonomerInChain(monomerRenderer.monomer);
 
       if (
-        !(nextMonomer instanceof Peptide) ||
+        !isPeptideOrAmbiguousPeptide(nextMonomer) ||
         nextMonomer === peptideRenderer.monomer
       ) {
         return;
@@ -311,10 +311,7 @@ export class RenderersManager {
       ]);
 
     this.monomers.forEach((monomerRenderer) => {
-      if (
-        monomerRenderer instanceof PeptideRenderer ||
-        monomerRenderer instanceof AmbiguousMonomerRenderer
-      ) {
+      if (isPeptideOrAmbiguousPeptide(monomerRenderer.monomer)) {
         this.recalculatePeptideEnumeration(
           monomerRenderer as PeptideRenderer,
           firstMonomersInCyclicChains,

diff --git a/packages/ketcher-core/src/application/render/renderers/sequence/RNASequenceItemRenderer.ts b/packages/ketcher-core/src/application/render/renderers/sequence/RNASequenceItemRenderer.ts
@@ -1,15 +1,43 @@
 import { BaseSequenceItemRenderer } from 'application/render/renderers/sequence/BaseSequenceItemRenderer';
-import { Nucleoside, Nucleotide } from 'domain/entities';
+import {
+  AmbiguousMonomer,
+  Nucleoside,
+  Nucleotide,
+  Vec2,
+} from 'domain/entities';
+import { BaseSubChain } from 'domain/entities/monomer-chains/BaseSubChain';
 
 export abstract class RNASequenceItemRenderer extends BaseSequenceItemRenderer {
-  get symbolToDisplay(): string {
-    return (
-      this.node.monomer.attachmentPointsToBonds.R3?.getAnotherMonomer(
-        this.node.monomer,
-      )?.monomerItem?.props.MonomerNaturalAnalogCode || '@'
+  constructor(
+    public node: Nucleoside | Nucleotide,
+    _firstNodeInChainPosition: Vec2,
+    _monomerIndexInChain: number,
+    _isLastMonomerInChain: boolean,
+    _subChain: BaseSubChain,
+    _isEditingSymbol: boolean,
+    public monomerSize: { width: number; height: number },
+    public scaledMonomerPosition: Vec2,
+  ) {
+    super(
+      node,
+      _firstNodeInChainPosition,
+      _monomerIndexInChain,
+      _isLastMonomerInChain,
+      _subChain,
+      _isEditingSymbol,
+      monomerSize,
+      scaledMonomerPosition,
     );
   }
 
+  get symbolToDisplay(): string {
+    return this.node.rnaBase instanceof AmbiguousMonomer
+      ? this.node.monomer.label
+      : this.node.monomer.attachmentPointsToBonds.R3?.getAnotherMonomer(
+          this.node.monomer,
+        )?.monomerItem?.props.MonomerNaturalAnalogCode || '@';
+  }
+
   protected drawCommonModification(node: Nucleoside | Nucleotide) {
     if (node.rnaBase.isModification) {
       this.backgroundElement?.attr(

diff --git a/packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts b/packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts
@@ -51,6 +51,7 @@ import {
   getNextMonomerInChain,
   getPhosphateFromSugar,
   isAmbiguousMonomerLibraryItem,
+  isRnaBaseOrAmbiguousRnaBase,
   isValidNucleoside,
   isValidNucleotide,
 } from 'domain/helpers/monomers';
@@ -85,7 +86,7 @@ type RnaPresetAdditionParams = {
 type NucleotideOrNucleoside = {
   sugar: Sugar;
   phosphate?: Phosphate;
-  rnaBase: RNABase;
+  rnaBase: RNABase | AmbiguousMonomer;
   baseMonomer: Sugar | Phosphate;
 };
 
@@ -938,27 +939,38 @@ export class DrawingEntitiesManager {
     let previousMonomer: BaseMonomer | undefined;
     const sugarMonomer = node.monomers.find(
       (monomer) => monomer instanceof Sugar,
-    ) as Sugar;
+    ) as Sugar | AmbiguousMonomer;
     const phosphateMonomer = node.monomers.find(
       (monomer) => monomer instanceof Phosphate,
-    ) as Phosphate;
-    const rnaBaseMonomer = node.monomers.find(
-      (monomer) => monomer instanceof RNABase,
-    ) as RNABase;
+    ) as Phosphate | AmbiguousMonomer;
+    const rnaBaseMonomer = node.monomers.find((monomer) =>
+      isRnaBaseOrAmbiguousRnaBase(monomer),
+    ) as RNABase | AmbiguousMonomer;
     const monomers = [rnaBaseMonomer, sugarMonomer, phosphateMonomer].filter(
       (monomer) => monomer !== undefined,
     ) as BaseMonomer[];
 
     monomers.forEach((monomer) => {
-      const monomerAddOperation = new MonomerAddOperation(
-        this.addMonomerChangeModel.bind(
-          this,
-          monomer.monomerItem,
-          monomer.position,
-          monomer,
-        ),
-        this.deleteMonomerChangeModel.bind(this),
-      );
+      const monomerAddOperation =
+        monomer instanceof AmbiguousMonomer
+          ? new MonomerAddOperation(
+              this.addAmbiguousMonomerChangeModel.bind(
+                this,
+                monomer.variantMonomerItem,
+                monomer.position,
+                monomer,
+              ),
+              this.deleteMonomerChangeModel.bind(this),
+            )
+          : new MonomerAddOperation(
+              this.addMonomerChangeModel.bind(
+                this,
+                monomer.monomerItem,
+                monomer.position,
+                monomer,
+              ),
+              this.deleteMonomerChangeModel.bind(this),
+            );
 
       command.addOperation(monomerAddOperation);
       if (previousMonomer) {
@@ -1513,7 +1525,7 @@ export class DrawingEntitiesManager {
     this.monomers.forEach((monomer) => {
       const monomerAddCommand =
         monomer instanceof AmbiguousMonomer
-          ? targetDrawingEntitiesManager.addVariantMonomer(
+          ? targetDrawingEntitiesManager.addAmbiguousMonomer(
               {
                 ...monomer.variantMonomerItem,
               },
@@ -1848,7 +1860,7 @@ export class DrawingEntitiesManager {
     return command;
   }
 
-  private addVariantMonomerChangeModel(
+  private addAmbiguousMonomerChangeModel(
     variantMonomerItem: AmbiguousMonomerType,
     position: Vec2,
     _monomer?: BaseMonomer,
@@ -1866,13 +1878,13 @@ export class DrawingEntitiesManager {
     return monomer;
   }
 
-  public addVariantMonomer(
+  public addAmbiguousMonomer(
     variantMonomerItem: AmbiguousMonomerType,
     position: Vec2,
   ) {
     const command = new Command();
     const operation = new MonomerAddOperation(
-      this.addVariantMonomerChangeModel.bind(
+      this.addAmbiguousMonomerChangeModel.bind(
         this,
         variantMonomerItem,
         position,

diff --git a/packages/ketcher-core/src/domain/entities/Nucleoside.ts b/packages/ketcher-core/src/domain/entities/Nucleoside.ts
@@ -17,9 +17,13 @@ import {
   getSugarBySequenceType,
 } from 'domain/helpers/rna';
 import { BaseMonomer } from 'domain/entities/BaseMonomer';
+import { AmbiguousMonomer } from 'domain/entities/AmbiguousMonomer';
 
 export class Nucleoside {
-  constructor(public sugar: Sugar, public rnaBase: RNABase) {}
+  constructor(
+    public sugar: Sugar,
+    public rnaBase: RNABase | AmbiguousMonomer,
+  ) {}
 
   static fromSugar(sugar: Sugar, needValidation = true) {
     if (needValidation) {

diff --git a/packages/ketcher-core/src/domain/entities/Nucleotide.ts b/packages/ketcher-core/src/domain/entities/Nucleotide.ts
@@ -17,11 +17,12 @@ import {
 } from 'domain/helpers/rna';
 import { RNA_DNA_NON_MODIFIED_PART } from 'domain/constants/monomers';
 import { BaseMonomer } from 'domain/entities/BaseMonomer';
+import { AmbiguousMonomer } from 'domain/entities/AmbiguousMonomer';
 
 export class Nucleotide {
   constructor(
     public sugar: Sugar,
-    public rnaBase: RNABase,
+    public rnaBase: RNABase | AmbiguousMonomer,
     public phosphate: Phosphate,
   ) {}
 

diff --git a/packages/ketcher-core/src/domain/serializers/ket/fromKet/monomerToDrawingEntity.ts b/packages/ketcher-core/src/domain/serializers/ket/fromKet/monomerToDrawingEntity.ts
@@ -88,7 +88,7 @@ export function variantMonomerToDrawingEntity(
 
   const monomers = createMonomersForVariantMonomer(template, parsedFileContent);
 
-  return drawingEntitiesManager.addVariantMonomer(
+  return drawingEntitiesManager.addAmbiguousMonomer(
     {
       monomers,
       id: template.id,

diff --git a/packages/ketcher-core/src/domain/serializers/ket/ketSerializer.ts b/packages/ketcher-core/src/domain/serializers/ket/ketSerializer.ts
@@ -644,7 +644,7 @@ export class KetSerializer implements Serializer<Struct> {
     }
 
     fileContent[templateNameWithPrefix] = {
-      type: 'variantMonomerTemplate',
+      type: 'ambiguousMonomerTemplate',
       id: templateId,
       alias: variantMonomer.label,
       idtAliases: variantMonomer.variantMonomerItem.idtAliases,

diff --git a/...her-macromolecules/src/components/monomerLibrary/RnaBuilder/RnaAccordion/RnaAccordion.tsx b/...her-macromolecules/src/components/monomerLibrary/RnaBuilder/RnaAccordion/RnaAccordion.tsx
@@ -58,7 +58,11 @@ import {
 } from 'state/rna-builder';
 import { useDispatch } from 'react-redux';
 import { IRnaPreset } from '../types';
-import { KetMonomerClass, MonomerItemType } from 'ketcher-core';
+import {
+  isAmbiguousMonomerLibraryItem,
+  KetMonomerClass,
+  MonomerItemType,
+} from 'ketcher-core';
 import {
   selectEditor,
   selectIsSequenceEditInRNABuilderMode,
@@ -173,7 +177,9 @@ export const RnaAccordion = ({ libraryName, duplicatePreset, editPreset }) => {
       return;
     }
 
-    const monomerClass = monomer.props.MonomerClass.toLowerCase();
+    const monomerClass = isAmbiguousMonomerLibraryItem(monomer)
+      ? monomer.monomers[0].monomerItem.props.MonomerClass?.toLowerCase()
+      : monomer.props.MonomerClass.toLowerCase();
     const currentPreset = {
       ...newPreset,
       [monomerClass]: monomer,

diff --git a/packages/ketcher-macromolecules/src/helpers/getPreset.ts b/packages/ketcher-macromolecules/src/helpers/getPreset.ts
@@ -6,6 +6,8 @@ import {
   setMonomerTemplatePrefix,
   KetMonomerClass,
   IRnaLabeledPreset,
+  isAmbiguousMonomerLibraryItem,
+  setAmbiguousMonomerTemplatePrefix,
 } from 'ketcher-core';
 import { getMonomerUniqueKey } from 'state/library';
 
@@ -20,7 +22,9 @@ export const getPresets = (
 ): IRnaPreset[] => {
   const monomerLibraryItemByMonomerIDMap = new Map<string, MonomerItemType>(
     monomers.map((monomer) => {
-      const monomerID = setMonomerTemplatePrefix(getMonomerUniqueKey(monomer));
+      const monomerID = isAmbiguousMonomerLibraryItem(monomer)
+        ? setAmbiguousMonomerTemplatePrefix(monomer.id)
+        : setMonomerTemplatePrefix(getMonomerUniqueKey(monomer));
       return [monomerID, monomer];
     }),
   );
@@ -37,6 +41,7 @@ export const getPresets = (
             rnaPartsMonomerTemplateRef.$ref,
           ) as MonomerItemType;
           const [, , monomerClass] = monomerFactory(monomer);
+
           return [monomerClass, monomer];
         }),
       );
@@ -53,16 +58,12 @@ export const getPresets = (
       ) as MonomerItemType;
 
       const result: IRnaPreset = {
-        base: rnaBase
-          ? { ...rnaBase, label: rnaBase.props.MonomerName }
-          : undefined,
+        base: rnaBase ? { ...rnaBase, label: rnaBase.label } : undefined,
         name: rnaPresetsTemplate.name,
         phosphate: phosphate
-          ? { ...phosphate, label: phosphate.props.MonomerName }
-          : undefined,
-        sugar: ribose
-          ? { ...ribose, label: ribose.props.MonomerName }
+          ? { ...phosphate, label: phosphate.label }
           : undefined,
+        sugar: ribose ? { ...ribose, label: ribose.label } : undefined,
         favorite: rnaPresetsTemplate.favorite,
         default: isDefault || rnaPresetsTemplate.default,
       };

diff --git a/packages/ketcher-macromolecules/src/state/rna-builder/rnaBuilderSlice.helper.ts b/packages/ketcher-macromolecules/src/state/rna-builder/rnaBuilderSlice.helper.ts
@@ -2,6 +2,7 @@ import omit from 'lodash/omit';
 import {
   IRnaLabeledPreset,
   IRnaPreset,
+  setAmbiguousMonomerTemplatePrefix,
   setMonomerTemplatePrefix,
 } from 'ketcher-core';
 
@@ -15,9 +16,15 @@ export const transformRnaPresetToRnaLabeledPreset = (rnaPreset: IRnaPreset) => {
 
   rnaLabeledPreset.templates = [];
   for (const monomerName of fieldsToLabel) {
-    if (!rnaPreset[monomerName]?.props?.id) continue;
+    const monomerLibraryItem = rnaPreset[monomerName];
+    const templateId = monomerLibraryItem?.props?.id || monomerLibraryItem?.id;
+
+    if (!templateId) continue;
+
     rnaLabeledPreset.templates.push({
-      $ref: setMonomerTemplatePrefix(rnaPreset[monomerName].props.id),
+      $ref: monomerLibraryItem.isAmbiguous
+        ? setAmbiguousMonomerTemplatePrefix(templateId)
+        : setMonomerTemplatePrefix(templateId),
     });
   }