refactor: simplify molecule parsing

Simplify molecule parsing with Molecule.fromText(text) which introduced in OpenChemLib (v9.19+)

close #3972

Author: hamed-musallam

src/data/molecules/Molecule.ts

@@ -5,8 +5,8 @@ import getAtomsFromMF from '../utilities/getAtomsFromMF.js';
 
 export interface StateMoleculeExtended
   extends
-    Required<Pick<StateMolecule, 'id' | 'molfile' | 'label'>>,
-    Omit<StateMolecule, 'id' | 'molfile' | 'label'> {
+  Required<Pick<StateMolecule, 'id' | 'molfile' | 'label'>>,
+  Omit<StateMolecule, 'id' | 'molfile' | 'label'> {
   mf: string;
   em: number;
   mw: number;
@@ -22,24 +22,47 @@ export interface MoleculeBoundingRect {
 }
 
 export const DRAGGABLE_STRUCTURE_INITIAL_BOUNDING_REACT: MoleculeBoundingRect =
-  {
-    x: 10,
-    y: 10,
-    width: 130,
-    height: 120,
-  };
+{
+  x: 10,
+  y: 10,
+  width: 130,
+  height: 120,
+};
 
 export type MoleculesView = Record<string, MoleculeView>;
 
+type MoleculeInput = { molecule: Molecule } | { molfile: string };
+type StateMoleculeOptions = Omit<Partial<StateMolecule>, 'molfile'>;
+type InitializeMoleculeOptions = MoleculeInput & StateMoleculeOptions;
+
+function resolveMolecule(options: MoleculeInput) {
+  if ('molecule' in options) {
+    const { molecule } = options;
+    return {
+      molecule,
+      molfile: molecule.toMolfileV3(),
+    };
+  }
+  const { molfile } = options;
+  return {
+    molecule: Molecule.fromMolfile(molfile),
+    molfile,
+  };
+}
+
+export function initMolecule(
+  options: { molecule: Molecule } & StateMoleculeOptions,
+): StateMoleculeExtended;
+export function initMolecule(
+  options: { molfile: string } & StateMoleculeOptions,
+): StateMoleculeExtended;
 export function initMolecule(
-  options: Partial<StateMolecule> = {},
+  options: InitializeMoleculeOptions,
 ): StateMoleculeExtended {
-  const id = options.id || crypto.randomUUID();
-  const label = options.label || 'p#';
-  const molfile = options.molfile || '';
+  const { id = crypto.randomUUID(), label = 'p#' } = options;
 
-  const mol = Molecule.fromMolfile(molfile);
-  const mfInfo = mol.getMolecularFormula();
+  const { molecule, molfile } = resolveMolecule(options);
+  const mfInfo = molecule.getMolecularFormula();
 
   return {
     id,
@@ -49,7 +72,7 @@ export function initMolecule(
     mf: mfInfo.formula,
     em: mfInfo.absoluteWeight,
     mw: mfInfo.relativeWeight,
-    svg: mol.toSVG(50, 50),
+    svg: molecule.toSVG(50, 50),
     atoms: getAtomsFromMF(mfInfo.formula),
   };
 }

src/data/molecules/MoleculeManager.ts

@@ -1,5 +1,5 @@
 import type { StateMolecule } from '@zakodium/nmrium-core';
-import { readSDF, readSMILES } from '@zakodium/nmrium-core-plugins';
+import { readSDF } from '@zakodium/nmrium-core-plugins';
 import { Molecule } from 'openchemlib';
 
 import type { StateMoleculeExtended } from './Molecule.js';
@@ -137,20 +137,37 @@ function validateMolecules(molecules: StateMolecule[]) {
  * @param text - text containing one or several molecules in SMILES, molfile or SDF format
  * @returns
  */
-export function getMolecules(text?: string) {
-  if (!text?.trim()) {
-    throw new Error(parseErrorMessage);
+
+function parseSDF(text: string) {
+  try {
+    const molecules = readSDF(text);
+    validateMolecules(molecules);
+    return molecules;
+  } catch (error) {
+    throw new Error(parseErrorMessage, { cause: error });
   }
+}
 
-  // parse SDF
-  let molecules = [];
-  const parse = /v[23]000/i.test(text) ? readSDF : readSMILES;
+function parseMolText(text: string) {
+  let molecule: Molecule | null;
   try {
-    molecules = parse(text);
+    molecule = Molecule.fromText(text);
   } catch (error) {
     throw new Error(parseErrorMessage, { cause: error });
   }
 
-  validateMolecules(molecules);
-  return molecules;
+  if (!molecule) {
+    throw new Error(parseErrorMessage);
+  }
+
+  return [initMolecule({ molecule })];
+}
+export function getMolecules(text?: string) {
+  if (!text?.trim()) {
+    throw new Error(parseErrorMessage);
+  }
+
+  const isSDF = /v[23]000/i.test(text);
+
+  return isSDF ? parseSDF(text) : parseMolText(text);
 }