The second disadvantage of SMILES is lack of adequate representation of fragment-specific information, a useful search feature when a chemical structure descriptor is embedded in an HTML document. First of all, canonical numbering requires use of a proprietary SMILES2 algorithm. The SMILES code is the de facto standard for computer-readable linear notation, although it has some disadvantages. Other types of linear molecular descriptors include computer-readable formats, such as Wiswesser Line Notation (WLN), SYBYL ®, SMILES (Daylight Chemical Information Systems), and InChI codes. The list of rules restricting the names of compounds that are supported by this program is published on the home page of the software vendor. NameExpert TM, a product of ChemInnovation, converts IUPAC names to chemical structures, but the program cannot handle the names of certain specific classes of molecules, such as names of element-organic compounds. As with naming, drawing of polycyclic and abnormal valence element molecules is the most difficult task, even for the latest versions of the software. The reverse task-chemical structure graph generation from the chemical name-has it set of problems too. Ambiguity in IUPAC naming complicates searching and chemical identity comparison. In addition, chemical names generated by various computer programs are often not unique. In many cases the existing name-generating programs cannot process some classes of compounds, such as cage structures or molecules with abnormal valence elements. Chemical names are relatively long and have sophisticated formats, thus impeding computer structure recognition.

IUPAC and CAS names are the most understandable notation for a chemist, but their use in databases or as Internet descriptors is a complicated task. CAS and IUPAC nomenclature are examples of the chemical name approach.

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