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fix: prevent adding molecule when molfile is corrupted #3666

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Merged
hamed-musallam merged 1 commit into from
Aug 29, 2025
Merged

fix: prevent adding molecule when molfile is corrupted #3666

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8 changes: 8 additions & 0 deletions src/data/molecules/MoleculeManager.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ import { Molecule } from 'openchemlib';
import type { StateMolecule, StateMoleculeExtended } from './Molecule.js';
import { initMolecule } from './Molecule.js';

//TODO: Move molecule initialization to nmrium-core and log an error if the molecule cannot be parsed.
export function fromJSON(
mols: StateMolecule[],
reservedMolecules: StateMolecule[] = [],
Expand All @@ -13,6 +14,13 @@ 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;
}

molecules.push(
initMolecule({
molfile: molecule.toMolfileV3(),
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