Parallel algorithms for graph cycle extraction using the cyclical conjunction operator

Journal of Chemical Information and Computer Sciences

Volumn 42, Issue 6, 2002, Pages 1398-1406

  Cerruela Garcia G ^a   Luque Ruiz, I ^a   Gomez Nieto M A ^a  

^a UNIVERSITY OF CÓRDOBA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

GRAPH CYCLE EXTRACTION;

COMPUTATIONAL METHODS; GRAPH THEORY; MATHEMATICAL OPERATORS; PARALLEL ALGORITHMS; SYNCHRONIZATION;

MOLECULAR DYNAMICS;

EID: 0036864886     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci020012z     Document Type: Article

References (42)

1. Parallel Computing in Computational Chemistry; Mattson, T.G., Ed.; ACS Symposium Series 592; American Chemical Society: Washington, DC, 1995.
2. Palace Carvalho, A.; Gomes, J.A.N.F.; Cordeiro, N.D.S. Parallel implementation of a Monte Carlo Molecular Simulation Program. J. Chem. Inf. Comput. Sci. 2000, 40(3), 588-592.
3. Straatsma, T.P.; Philippopoulos, M.; McCammon, J.A. NWChem: Exploiting parallelism in molecular simulations. Comput. Physics Commun. 2000, 128, 377-385.
4. Roccatano, D.; Bizzarri, R.; Chilemi, G.; Sanna, N.; Di Nola, A. Development of a parallel molecular dynamics code on SIMD computers: an algorithm for the use of the pair list criterium. J. Comput. Chem. 1998, 19, 685-691.
5. Trobec, R.; Merzel, F.; Janezic, D. The complexity of parallel symplectic molecular dynamics algorithms. J. Chem. Inf. Comput. Sci. 1997, 37(6), 1055-1062.
6. Steinbeck, C. SENECA: A Platform-Independent, Distributed, and Parallel System for Computer-Assisted Structure Elucidation in Organic Chemistry. J. Chem. Inf. Comput. Sci. 2000, 41(6), 1500-1507.
7. del Carpio, C.A. A Parallel genetic algorithm for polypeptide three-dimensional srtructure prediction. A transputer implementation. J. Chem. Inf. Comput. Sci. 1996, 36(2), 258-269.
8. Fruchtl, H.A.; Kendall, R.A.; Harrison, R.J.; Dyall, K.G. An implementation of RI-SCF on parallel computers. Intl. J. Quantum Chem. 1997, 64(1), 63-69.
9. Rasmussen, E.M.; Downs, G.M.; Willet, P. Automatic classification of chemical structure databases using a high parallel array processor. J. Computat. Chem. 1988, 9, 378-386.
10. Gillet, V.J.; Welford, S.N.; Lynch, M.F.; Willet, P.; Barnard, J.M.; Downs, G.M. Computer storage and retrieval of generic chemical structures in patents. VII. Parallel simulation of a relaxation algorihm fro chemical substructure search. J. Chem. Inf. Comput. Sci. 1986, 26, 118-126.
11. Maud, G.; Pavesi, G. A parallel algorithm fro pattern discovery in biological sequences. Future Generation Computer Systems 2002, 18, 849-854.
12. Lee, J.; Pillardy, J. et al. Efficient parallel algorithms in global optimization of potential energy functions for peptides, proteins and crystals. Comput. Physics Commun. 2000, 128, 399-411.
13. MACCS Keys. MDL Information Systems, Inc.: 14600 Catalina Street, San Leandro CA94577.
14. Rücker, G.; Rücker, C. Topogical Indices, Boiling Points and Cycloalkanes. J. Chem. Inf. Comput. Sci. 1999, 39, 788-802.
15. Ravi, M.; Hopfinger, A.J.; Hormann, R.E.; Dinan, L. 4D-QSAR Analysis of a set of ecdysteroids and a comparison to CoMFA modeling. J. Chem. Inf. Comput. Sci. 2001, 41(6), 1587-1604.
16. McGregor, M.J.; Pallai, P.V. Clustering of large databases of compounds: using MDL keys as structural descriptors. J. Chem. Inf. Comput. Sci. 1997, 37, 443-448.
17. Xue, L.; Bajorath, J. Accurate partitioning of compounds belonging to diverse activity classes. J. Chem. Inf. Comput. Sci. 2002, 42(3), 757-764.
18. Lipkus, A.H. Mining a Large database fro Peptidomimetic Ring Structures Using Topological Index. J. Chem. Inf. Comput. Sci. 1999, 39(3), 582-586.
19. Lipkus, A.H. Exploring chemical rings in a simple topological-descriptor space. J. Chem. Inf. Comput. Sci. 2001, 41(2), 430-438.
20. Flower, D.R. On the properties of hit string-based measures of chemical similarity. J. Chem. Inf. Comput. Sci. 1998, 38, 379-386.
21. Godden, J.; Xae, L.; Bajorath, J. Combinatorial preferences affect molecular similarity/diversity calculations using binary fingerprints and Tanimoto coefficients. J. Chem. Inf. Comput. Sci. 2000, 40, 163-166.
22. Bollobás, B.; Fenner, T.I.; Frieze, A.M. An Algorithm for Finding Hamilton Paths and Cycles in Random Graphs. Combinatoria 1987, 7(4), 327-341.
23. Frieze, A.M. Parallel Algorithms for Finding Hamilton Cycles in Random Graphs. Inform. Process. Lett. 1987, 25, 111-117.
24. MacKenzie, P.D.; Stout, Q.F. Optimal Parallel Construction of Hamiltonian Cycles and Spanning Trees in Random Graphs. ACM-SPAA Velen Germany 1993, 224-229.
25. Thomason, A. A Simple Linear Expected Time Algorithm for the Hamilton Cycle Problem. Discrete Math. 1989, 75, 373-379.
26. Edmonds, J. Optimum Branching. J. Res. Nat. Bur. Stand. 1967, 71, 233-240.
27. Nepomniaschaya, A.S. An Associative Parallel Algorithm for Finding a Critical Cycle in Directed Graphs. 7th International Conference on Parallel and Distributed Systems (ICPADS'00), 2000.
28. Boukerche, A.; Tropper, C. A Distributed Graph Algorithm for the Detection of Local Cycles and Knots. IEEE Trans. Parallel Distributed Systems 1998, 9(8), 748-757.
29. Steinbeck, C. SENECA: A Platform-Independent, Distributed, and Parallel System for Computer-Assisted Structure Elucidation in Organic Chemistry. J. Chem. Inf. Comput. Sci., Published on Web, 2000.
30. Chua, L.O.; Chen, L.K. On Optimally Sparce Cycle and Coboundary Basis for a Linear Graph. IEEE Trans. Circuit Theory 1973, 20, 495-503.
31. Downs, G.M.; Gillet, V.J.; Holliday, J.D.; Lynch, M.F. Theoretical Aspects of Ring Perception and Development of the Extended Set of Smallest Rings Concept. American Chemical Society 1988, 29(3), 187-206.
32. Knuth, D.E. The Art of Computer Programing, 1; Addinson-Wesley: 1968; pp 363-370.
33. Cerruela García, G.; Luque Ruiz, I.; Gómez-Nieto, M.A. Cyclical Conjunction: an Efficient Operator for the Extraction of Cycles from a Graph. J. Chem. Inf. Comput. Sci. 2002, 42, 1415-1424.
34. Cerruela García, G.; Luque Ruiz, I.; Gómez-Nieto, M.A. Un algoritmo en zigzag para la obtención de un conjunto de ciclos característicos de un grafo; Internal Report UCO-ISCBD-JCVG93-00; University of Córdoba: 2000.
35. Fox, G.C.; et al. Solving Problems on Comcurrent Proccesors; Prentice-Hall: Englewood Cliffs, NJ, 1988.
36. Pancake, C.M. Is Parallelism for You. IEEE Comput. Sci. Eng. 1996, 18-37.
37. Amdahl, G. Validity of the Single-Processor Approach to Achiving Large-Scale Computing Capabilities. Proc. AFIPS Conf. 1967.
38. Gustafson, J.L. Reevaluating Amdahl's Law. Comm. ACM 1988, 31, 5.
39. Silicon Graphics. The Iris Power C. User's Guide (007-0702-030), 1999.
40. Silicon Graphics. MIPSpro Power C Manual Kit (M4-PWRC-7.1), 1999.
41. OpenMP C and C++ Aplication Program Interface. OpenMP Architecture Review Board, March 2002.
42. Chandra, R.; Menon, R.; Dagum, L.; Kohr, D.; Maydan, D.; McDonald, J. Parallel Programming in OpenMP; Morgan Kaufmann: 2000.