A. Bibliography

  1. D.M.F. van Aalten, R. Bywater, J.B.C. Findlay, M. Hendlich, R.W.W. Hooft and G. Vriend, ``PRODRG: A Program for Generating Molecular Topologies and Unique Molecular Descriptors from Coordinates of Small Molecules'', Journal of Computer-Aided Molecular Design, Vol. 10, pp. 255-262, 1996.

  2. Sheila Ash, Malcolm A. Cline, R. Webster Homer, Tad Hurst and Gregory B. Smith, ``SYBYL Line Notation (SLN): A Versatile Language for Chemical Structure Representation'', Journal of Chemical Information and Computer Science (JCICS), Vol. 37, No. 1, pp. 71-79, 1997.

  3. Jon C. Baber and Edward E. Hodgkin, ``Automatic Assignment of Chemical Connectivity to Organic Molecules in the Cambridge Structural Database'', Journal of Chemical Information and Computer Science (JCICS), Vol. 32, No. 5, pp. 401-406, 1992.

  4. Renzo Balducci and Robert S. Pearlman, ``Efficient Exact Solution of the Ring Perception Problem'', Journal of Chemical Information and Computer Science (JCICS), Vol. 34, No. 4, pp. 822-831, 1994.

  5. Bruce L. Bush and Robert P. Sheridan, ``PATTY: A Programmable Atom Typer and Language for Automatic Classification of Atoms in Molecular Databases'', Journal of Chemical Information and Computer Science (JCICS), Vol. 33, pp. 756-762, 1993.

  6. A. Dalby, J.G. Nourse, W.D. Hounshell, Aki Gushurst, D.L. Grier, B.A. Leland and J. Laufer, ``Description of Several Chemical-Structure File Formats Used by Computer-Programs developed at Molecular Design Limited'', Journal of Chemical Information and Computer Science (JCICS), Vol. 32, No. 3, pp. 244-255, 1992.

  7. Geoffrey M. Downs, Valerie Gillet, John D. Holiday and Michael F. Lynch, ``Review of Ring Perception Algorithms for Chemical Graphs'', Journal of Chemical Information and Computer Science (JCICS), Vol. 29, No. 3, pp. 172-187, 1989.

  8. John Figueras, ``Ring Perception using Breadth-First Search'', Journal of Chemical Information and Computer Science (JCICS), Vol. 36, No. 5, pp. 986-991, 1996.

  9. J. Gasteiger and M. Marsili, ``A New Model for Calculating Atomic Charges in Molecules'', Tetrahedron Letters, pp. 3181-3184, 1978.

  10. Johann Gasteiger and Clemens Jochum, ``An Algorithm for the Perception of Synthetically Important Rings'', Journal of Chemical Information and Computer Science (JCICS), Vol. 19, No. 1, pp. 43-48, 1979.

  11. J. Gasteiger and M. Marsili, ``Iterative Partial Equalization of Orbital Electronegativity - A Rapid Access to Atomic Charges'', Tetrahedron, Vol. 36, pp. 3219-3228, 1980.

  12. M. Hendlich, F. Rippmann and G. Barnickel, ``BALI: Automatic Assignment of Bond and Atom Types for Protein Ligands in the Brookhaven Protein Databank", Journal of Chemical Information and Computer Science (JCICS), Vol. 37, No. 4, pp. 774-778, 1997.

  13. Wolf Dietrich Ihlenfeldt and Johann Gasteiger, ``Hash Codes for the Identification and Classification of Molecular Structure Elements'', Journal of Computational Chemistry, Vol. 15, No. 8, pp. 793-813, 1994.

  14. Simon K. Kearsley, ``A Quick Robust Method for Assigning A Kekulé Structure'', Computers in Chemistry, Vol. 17, No. 1, pp. 1-10, 1993.

  15. Brian Kelley, ``Graph Canonicalization'', Dr. Dobb's Journal, No. 348 (Algorithms), pp. 66-69, May 2003.

  16. Paul Labute, ``Automatic Assignment of Bond Order'', Journal of the Chemical Computing Group, On-line, May 1996.

  17. Paul Labute, ``An Efficient Algorithm for the Determination of Topological RS Chirality'', Journal of the Chemical Computing Group, On-line, November 1996.

  18. Andrew R. Leach, Daniel P. Dolata and Keith Prout, ``Automated Conformational Analysis and Structure Generation: Algorithms for Molecular Perception'', Journal of Chemical Information and Computer Science (JCICS), Vol. 30, No. 3, pp. 316-324, 1990.

  19. Douglas Lloyd, ``What Is Aromaticity?'', Journal of Chemical Information and Computer Science (JCICS), Vol. 36, No. 3, pp. 442-447, 1996.

  20. James J. McGregor, ``Backtrack Search Algorithms and the Maximal Common Subgraph Problem'', Software - Practice and Experience, Vol. 12, pp. 23-34, 1982.

  21. Elaine C. Meng and Richard A. Lewis, ``Determination of Molecular Topology and Atomic Hybridization States from Heavy Atom Coordinates'', Journal of Computational Chemistry, Vol. 12, No. 7, pp. 891-898, 1991.

  22. H.L. Morgan, ``The Generation of a Unique Machine Description for Chemical Structures Developed at Chemical Abstracts Service'', Journal of Chemical Documentation, Vol. 5, pp. 107-113, 1965.

  23. T.J. O'Donnell, Shashidar N. Rao, Konrad Koehler, Yvonne C. Martin and Beverley Eccles, ``A General Approach for Atom-Type Assignment and the Inter-conversion of Molecular Structure Files'', Journal of Computational Chemistry, Vol. 12, No. 2, pp. 209-214, 1991.

  24. A. Pedretti, L. Villa and G. Vistoli, ``Atom-type Description Language: A Universal Language to Recognize Atom Types Implemented in the VEGA program'', Theoretical Chemistry Accounts, Vol. 109, pp. 229-232, 2003.

  25. Ed Regis, ``The Info Mesa: Science, Business and New Age Alchemy on the Santa Fe Plateau'', Norton Publishers, 2003.

  26. Barbara L. Roos-Kozel and William L. Jorgensen, ``Computer-Assisted Mechanistic Evaluation of Organic Reactions 2: Perception of Rings, Aromaticity and Tautomers'', Journal of Chemical Information and Computer Science (JCICS), Vol. 21, No. 2, pp. 101-111, 1981.

  27. Craig A. Shelley and Morton E. Munk, ``Computer Perception of Topological Symmetry'', Journal of Chemical Information and Computer Science (JCICS), Vol. 17, No. 2, pp. 110-113, 1977.

  28. Craig A. Shelley and Morton E. Munk, ``An Approach to the Assignment of Canonical Connection Tables and Topological Symmetry Perception'', Journal of Chemical Information and Computer Science (JCICS), Vol. 19, No. 4, pp. 247-250, 1979.

  29. A. Ting, R. McGuire, A.P. Johnson and S. Green, ``Expert System Assisted Pharmacophore Identification'', Journal of Chemical Information and Computer Science (JCICS), Vol. 40, No. 2, pp. 347-353, 2000.

  30. J.R. Ullman, ``An Algorithm for Subgraph Isomorphism'', Journal of the Association of Computing Machinery (JACM), Vol. 23, pp. 31-42, 1976.

  31. W.P. Walters and S.H. Yalkowsky, ``ESCHER - A Computer Program for the Determination of External Rotational Symmetry Numbers from Molecular Topology'', Journal of Chemical Information and Computer Science (JCICS), Vol. 36, No. 5, pp. 1015-1017, 1996.

  32. David Weininger, ``SMILES: A Chemical Language and Information System: 1. Introduction to Methodology and Encoding Rules'', Journal of Chemical Information and Computer Science (JCICS), Vol. 29, No. 2, pp. 97-101, 1989.

  33. David Weininger, Arthur Weininger and Joseph L. Weininger, ``SMILES 2: Algorithm for Generation of Unique SMILES Notation'', Journal of Chemical Information and Computer Science (JCICS), Vol. 29, No. 2, pp. 97-101, 1989.