The Chemical Smiler: CHEMICal Abstraction Leading to SMILEs of Reference

Linear notations such as SMILES describe molecular structure and are essential for chemical analysis and comparison. Their usability depends primarily on how much effort has been made to ensure a one-to-one correspondence between encoding and structure. Overcoming syntactical differences between notations has generally overshadowed the user's interest in a preliminary selection of chemical properties to encode. The proposed system allows for the disregarding of properties considered noncritical in the detection of molecular differences, such as tautomerism and stereochemistry, while accounting for multiple neutralized chemical forms. To this end, the system effectively extends the hierarchical structure of the nonstandard InChI notation. Several examples will demonstrate the importance of abstracting irrelevant details depending on the type of application, along with the usefulness of other functions to recover as much initial chemical information as possible, resolve any ambiguities in the register numbers used as identifiers, and facilitate secondary analyses of the SMILES produced.