MOLGEN-CID - A canonizer for molecules and graphs accessible through the internet

Journal of Chemical Information and Computer Sciences

Volumn 44, Issue 2, 2004, Pages 542-548

  Braun, Joachim ^a   Gugisch, Ralf ^a   Kerber, Adalbert ^a   Laue, Reinhard ^a   Meringer, Markus ^a   Rücker, Christoph ^a  

^a UNIVERSITY OF BAYREUTH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; ATOMS; CHEMICAL COMPOUNDS; COMPUTER SOFTWARE; GRAPH THEORY; INTERNET;

MOLECULE GENERATOR SOFTWARE; SOFTWARE PACKAGE MOLGEN;

MOLECULAR STRUCTURE;

EID: 1842740167     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci030404l     Document Type: Article

References (42)

1. If this process, due to a lack of proper canonization, goes astray, then a compound will be registered under more than one registry number. Such happens both in the CAS Registry ("alternate registry number", "deleted registry number") and notoriously in the Beilstein system. The reverse may also happen: Two similar compounds may erroneously be identified in a database. Such cases are more difficult to detect.
2. (a) Wieland, T.; Kerber, A.; Laue, R. Principles of the Generation of Constitutional and Configurational Isomers. J. Chem. Inf. Comput. Sci. 1996, 36, 413-419.
3. (b) Benecke, C.; Grüner, T.; Kerber, A.; Laue, R.; Wieland, T. MOLecular Structure GENeration with MOLGEN, new Features and Future Developments. Fresenius' J. Anal. Chem. 1997, 359, 23-32.
4. Molchanova, M. S.; Zefirov, N. S. Irredundant Generation of Isomeric Molecular Structures with Some Known Fragments. J. Chem. Inf. Comput. Sci. 1998, 38, 8-22.
5. Jochum, C.; Gasteiger, J. Canonical numbering and Constitutional Symmetry. J. Chem. Inf. Comput. Sci. 1977, 17, 113-117.
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8. (a) Kvasnicka, V.; Pospichal, J. Canonical Indexing and Constructive Enumeration of Molecular Graphs. J. Chem. Inf. Comput. Sci. 1990, 30, 99-105.
9. (b) Kvasnicka, V.; Pospichal, J. An Improved Method of Constructive Enumeration of Graphs. J. Math. Chem. 1992, 9, 181-196.
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15. Weininger, D.; Weininger, A.; Weininger, J. L. SMILES. 2. Algorithm for Generation of Unique SMILES Notation. J. Chem. Inf. Comput. Sci. 1989, 29, 97-101.
16. (a) Rücker, G.; Rücker, C. On Using the Adjacency Matrix Power Method for Perception of Symmetry and for Isomorphism Testing of Highly Intricate Graphs. J. Chem. Inf. Comput. Sci. 1991, 31, 123-126.
17. (b) Rücker, G.; Rücker, C. On Finding Nonisomorphic Connected Subgraphs and Distinct Molecular Substructures. J. Chem. Inf. Comput. Sci. 2001, 41, 314-320.
18. Balaban, A. T.; Liu, X.; Klein, D. J.; Babić, D.; Schmalz, T. G.; Seitz, W. A.; Randić, M. Graph Invariants for Fullerenes. J. Chem. Inf. Comput. Sci. 1995, 35, 396-404.
19. Ratkiewicz, A.; Truong, T. N. Application of Chemical Graph Theory for Automated Mechanism Generation. J. Chem. Inf. Comput. Sci. 2003, 43, 36-44.
20. Rücker, C.; Rücker, G.; Meringer, M. Exploring the Limits of Graph Invariant- and Spectrum-Based Discrimination of (Sub)structures. J. Chem. Inf. Comput. Sci. 2002, 42, 640-650.
21. (a) Freemantle, M. Unique Labels for Compounds. Chem. Eng. News 2002, December 2, 33-35.
22. (b) stephen.heller@nist.gov; stephen.stein@nist.gov.
23. www.mathe2.uni-bayreuth.de/molgen4. Various preliminary versions of the canonizer have been available at our Web site for more than 2 years.
24. www.acdlabs.com/download/chemsk.html.
25. McKay, B. D. Computing Automorphisms and Canonical Labeling of Graphs. In Proc. Intern. Conf. on Combinatorial Theory; Lecture Notes in Mathematics No. 686; Springer: Berlin, 1977; pp 223-232.
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27. Classification of iterative refinement (steps 1 and 2) can be made even more powerful by slight variations in the procedure. Thus use of further vertex-in-graph invariants is an obvious option. In step 2 instead of the immediate neighborship, relations of longer distance or even of all distances could be used for better discrimination. This would require initially constructing and then evaluating the graph's distance matrix. Further, the restriction of unique atoms only to be used for refinement could be alleviated. This alternative, however, was shown often not to be of an advantage (ref 22). We decided not to exploit iterative classification to its limits since backtracking is needed anyway for cases of symmetry.
28. Knuth, D. E. Estimating the Efficiency of Backtrack Programs. Math. Comput. 1975, 29, 121-136.
29. The refinement resulting from artificially marking a vertex usually reduces the number of alternatives on the next backtrack level, thus preventing exponential growth of the backtrack tree.
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31. (b) Jerrum, M. A Compact Representation for Permutation Groups. J. Algorithms 1986, 7, 60-78.
32. Grund, R. Symmetrieklassen von Abbildungen und die Konstruktion von diskreten Strukturen. Bayreuther Mathematische Schriften 1990, 31, 19-54.
33. There are applications even in organic chemistry where undirected graphs containing vertices of degree >4 have to be canonized, see e.g. so-called macroatoms of high degree in the former DENDRAL project and in MOLGEN 3.5.
34. Rücker, C.; Meringer, M. How Many Organic Compounds are Graph-Theoretically Nonplanar? MATCH - Commun. Math. Comput. Chem. 2002, 45, 153-172.
35. Read, R. C.; Corneil, D. G. The Graph Isomorphism Disease. J. Graph Theory 1977, 1, 339-363.
36. Weisfeiler, B. On Construction and Identification of Graphs; Lecture Notes in Mathematics No. 558; Springer: Berlin, 1976.
37. Mathon, R. Sample Graphs for Isomorphism Testing. Proc. 9th S.-E. Conf. Combinatorics, Graph Theory and Computing 1978, 499-517 (Congressus Numerantium 21).
38. Walter, C. D. Adjacency Matrices. SIAM J. Alg. Disc. Methods 1986, 7, 18-29.
39. 11,15]pentadecane. The uniqueness of these so-called von-Baeyer names is ensured by requirements such as "The main ring shall contain as many carbon atoms as possible", "The main bridge shall be as large as possible", "The main ring shall be divided as symmetrically as possible by the main bridge", "The superscripts locating the other bridges shall be as small as possible ⋯" (rule A-32, International Union of Pure and Applied Chemistry, Nomenclature of Organic Chemistry, Sections A,B,C,D,E,F,H, Pergamon Press: Oxford, 1979)
40. See also Moss, G. P. Extension and Revision of the Von Baeyer System for Naming Polycyclic Compounds (Including Bicycle Compounds). Pure Appl. Chem. 1999, 71, 513-529.
41. The above name was composed by the program POLCYC modified for vertex degrees higher than four, see Rücker, G.; Rücker, C. Nomenclature of Organic Polycycles out of the Computer - How to Escape the Jungle of the Secondary Bridges. Chimia 1990, 44, 116-120.
42. Shrikhande, S. S. On a Characterization of the Triangular Association Scheme. Ann. Math. Statist. 1959, 30, 39-47.