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Chemical Graohs. 4. Enumeration and drocarbons. I. The Formal Graph-Theoretical Description. MATCH 1976, 2, 63-90. Entriger, R. C.; Jackson, D. E.; Snyder, D. A. Distance in Graphs, Czech. Marh. J. 1976, 26, 283-296. Skorobogatov, V. A.; Khvorostov, P. V. Analiz Metricheskikh svoistv grafov. Vychisl. Sist. 1981, 91, 1-20. Balaban, A. T.; Mekenyan, 0.; Bonchev, D. Unique Description of Chemical Structures Based on Hierarchical Ordered Extended Connectivities (HOC Procedures). I. Algorithms for Finding Graph Orbits and Canonical Numbering of Atoms. J. Compur. Chem. 1985, 6, 538-551. Skorobogatov, V. A.; Dobrynin, A. A. Metric Analysis of Graphs. MATCH 1988, 23, 105-151. Polanskv. 0. E.: Bonchev. D. The Wiener Number of Grauhs. I. Generai Theory 'and Changes Due to Graph Operations. niATCH 1987, 21, 133-186. . , Proposed Nomenclaturk'of Benzenoid Caticondensed Polycyclic Aromatic Hydrocarbons. Tetrahedron 1968,24,2505-25 16. Polansky, 0. E.; Rouvray, D. H. Graph-Theoretical Treatment of Aromatic Hy-(30) Bonchev, D.; Mekenyan, 0.; Karabunarliev, S.The chemical notation language SMILES is designed for the conversion of an arbitrarily chosen description of a chemical structure to one unique notation. This is accomplished in a two-stage algorithm, CANGEN. The first stage involves CANonicalization of structure, whereby the molecule is treated as a graph with nodes (atoms) and edges (bonds). Each atom is canonically ordered and labeled. In the second stage, starting with the lowest labeled atom, a molecular graph is GENerated, which is the unique SMILES structure.

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An algorithm, Stigmata, is described, which extracts structural commonalities from chemical datasets. It is discussed using several illustrative examples and a pharmaceutically interesting set of dopamine D2 agonists. The commonalities are determined using two-dimensional topological chemical descriptions and are incorporated into the key feature of the algorithm, the modal fingerprint. Flexibility is built into the algorithm by means of a user-defined threshold value, which affects the information content of the modal fingerprint. The use of the modal fingerprint as a diversity assessment tool, as a database similarity query, and as a basis for color mapping the determined commonalities back onto the chemical structures is demonstrated.