PaCh (Packed Chemicals): Computationally Effective Binary Format for Chemical Structure Encoding.

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Abstract

In this work, we propose a versatile molecule and reaction encoding binary data format that aims to bridge the gap between the advantages of SMILES, like local stereo- and implicit hydrogen encoding, and block-structured MDL MOL with a 2D layout and explicit bond encoding, while addressing their respective limitations. Our new format introduces a balance between size efficiency, processing speed, and comprehensive representation, making it well-suited for various applications in cheminformatics, including deep learning, data storage, and searching. By offering an explicit approach to store atom connectivity (including implicit hydrogens), electronic state, stereochemistry, and other crucial molecular attributes, our proposal seeks to enhance data storage efficiency and promote interoperability among different software tools.