refactor: simplify molecule initialization

Author: hamed-musallam

src/data/molecules/Molecule.ts

@@ -31,37 +31,24 @@ export const DRAGGABLE_STRUCTURE_INITIAL_BOUNDING_REACT: MoleculeBoundingRect =
 
 export type MoleculesView = Record<string, MoleculeView>;
 
-type MoleculeInput = { molecule: Molecule } | { molfile: string };
-type StateMoleculeOptions = Omit<Partial<StateMolecule>, 'molfile'>;
-type InitializeMoleculeOptions = MoleculeInput & StateMoleculeOptions;
+type InitializeMoleculeOptions = { text: string } & Omit<
+  Partial<StateMolecule>,
+  'molfile'
+>;
 
-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: InitializeMoleculeOptions,
 ): StateMoleculeExtended {
-  const { id = crypto.randomUUID(), label = 'p#' } = options;
+  const { id = crypto.randomUUID(), label = 'p#', text } = options;
 
-  const { molecule, molfile } = resolveMolecule(options);
+  const molecule = Molecule.fromText(text);
+
+  if (!molecule) {
+    throw new Error(
+      'Failed to parse SMILES or molfile. Please paste a valid format',
+    );
+  }
+  const molfile = molecule.toMolfileV3();
   const mfInfo = molecule.getMolecularFormula();
 
   return {

src/data/molecules/MoleculeManager.ts

@@ -14,22 +14,23 @@ export function fromJSON(
 
   const molecules: StateMoleculeExtended[] = [];
   for (const mol of mols) {
-    const molecule = Molecule.fromMolfile(mol.molfile);
-
-    const atomCount = molecule.getAllAtoms();
-
-    if (atomCount === 0) {
-      continue;
-    }
-
+    const {
+      molfile,
+      label = `P${getLabelNumber(reservedNumbers)}`,
+      id,
+      ...others
+    } = mol;
     const moleculeOverride = {
-      ...mol,
-      molfile: molecule.toMolfileV3(),
-      label: mol.label || `P${getLabelNumber(reservedNumbers)}`,
-      id: mol.id,
+      ...others,
+      text: molfile,
+      label,
+      id,
     };
-
-    molecules.push(initMolecule(moleculeOverride));
+    try {
+      molecules.push(initMolecule(moleculeOverride));
+    } catch {
+      continue;
+    }
   }
 
   return molecules;
@@ -49,10 +50,9 @@ export function addMolfile(
 
   // try to parse molfile
   // this will throw if the molecule can not be parsed !
-  const molecule = Molecule.fromMolfile(molfile);
   molecules.push(
     initMolecule({
-      molfile: molecule.toMolfileV3(),
+      text: molfile,
       label: label ?? `P${getLabelNumber(reservedNumbers)}`,
       id,
     }),
@@ -66,9 +66,8 @@ export function setMolfile(
   const { molfile, id, label } = currentMolecule;
   // try to parse molfile
   // this will throw if the molecule can not be parsed !
-  const molecule = Molecule.fromMolfile(molfile);
   const _mol = initMolecule({
-    molfile: molecule.toMolfileV3(),
+    text: molfile,
     id,
     label,
   });
@@ -148,26 +147,12 @@ function parseSDF(text: string) {
   }
 }
 
-function parseMolText(text: string) {
-  let molecule: Molecule | null;
-  try {
-    molecule = Molecule.fromText(text);
-  } catch (error) {
-    throw new Error(parseErrorMessage, { cause: error });
-  }
-
-  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);
+  return isSDF ? parseSDF(text) : [initMolecule({ text })];
 }