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Others include SLN (SYBYL Line Notation), ROSDAL (from the Beilstein Institute), WLN (Wiswesser Line Notation ), MCDL (Modular Chemical Descriptor Language ), the InChIKey (a hashed representation of the InChI) and more. Apart from IUPAC nomenclature, the two most widely used line notations and the focus of the current work are the SMILES (Simplified Molecular Input Line Entry System) string developed by Weininger and Daylight Chemical Information Systems, and IUPACвЂ™s InChI (International Chemistry Identifier) representation. While line notations typically do not allow the incorporation of additional information beyond the connection table and its associated chemistry (with the notable exception of SYBYL Line Notation ), even where the underlying data is stored in a 2D or 3D file format as in several web databases (for example, PubChem ), linear representations of the data are usually provided for convenience.

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Their popularity derives from one or more of the following: they encode the chemical structure in a compact form they may be human-readable and/or human-writable they are easily entered into software (for example, by copying and pasting into a text entry box on a website or a dialog box in a GUI, or entered into a spreadsheet cell) they may be canonical (that is, provide a unique representation for a particular molecule), in which case they may easily be used to check identity, search databases or even search the web. They are widely used for storing, representing, communicating and checking the identity of chemical structures. Line notations are linear representations of chemical structures that encode the connection table and (usually) the stereochemistry of a molecule as a line of text. While challenges remain вЂ“ such as the development of a standard aromatic model for SMILES вЂ“ the ability to create the same SMILES using different toolkits will mean that for the first time it will be possible to easily compare the chemical models used by different toolkits. The InChI canonicalisation algorithm can successfully be used as the basis for a common standard for canonical SMILES. Using Universal SMILES, 99.79% of the ChEMBL database was canonicalised successfully and 99.77% of the PubChem subset. When tested on the 1.1 m compounds in the ChEMBL database, and a 1 m compound subset of the PubChem Substance database, no canonicalisation failures were found with Inchified SMILES. This is the first description of a method to generate canonical SMILES that takes stereochemistry into account.

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I describe how to use the InChI canonicalisation to derive a canonical SMILES string in a straightforward way, either incorporating the InChI normalisations (Inchified SMILES) or not (Universal SMILES). The InChI aims to provide a unique, or canonical, identifier for chemical structures, while SMILES strings are widely used for storage and interchange of chemical structures, but no standard exists to generate a canonical SMILES string.

There are two line notations of chemical structures that have established themselves in the field: the SMILES string and the InChI string.

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