MolBar: a molecular identifier for inorganic and organic molecules with full support of stereoisomerism

Abstract

Before a new molecular structure is registered to a chemical structure database, a duplicate check is essential to ensure the integrity of the database. The Simplified Molecular Input Line Entry Specification (SMILES) and the IUPAC International Chemical Identifier (InChI) stand out as widely used molecular identifiers for these checks. Notable limitations arise when dealing with molecules from inorganic chemistry or structures characterized by non-central stereochemistry. When the stereoinformation needs to be assigned to a group of atoms, widely used identifiers cannot describe axial and planar chirality due to the atom-centered description of a molecule. To address this limitation, we introduce a novel chemical identifier called the Molecular Barcode (MolBar). Motivated by the field of theoretical chemistry, a fragment-based approach is used in addition to the conventional atomistic description. In this approach, the 3D structure of fragments is normalized using a specialized force field and characterized by physically inspired matrices derived solely from atomic positions. The resulting permutation-invariant representation is constructed from the eigenvalue spectra, providing comprehensive information on both bonding and stereochemistry. The robustness of MolBar is demonstrated through duplication and permutation invariance tests on the Molecule3D dataset of 3.9 million molecules. A Python implementation is available as open source and can be installed via pip install molbar.