Structure Diagram Generation

Reviews in Computational Chemistry

Volumn 13, Issue , 1999, Pages 313-398

  Helson, Harold E ^a  

^a Cambridge Soft Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

STRUCTURE DIAGRAMS;

EID: 0033421846     PISSN: 10693599     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article

References (71)

1. +, a Generator of Connectivity Isomers and Stereoisomers for Molecular Structure Elucidation. A. Rusinko III, R. P. Sheridan, R. Nilakantan, K. Haraki, N. Bauman, and R. Venkataraghavan, J. Chem. Inf. Comput. Sci., 29, 251 (1989). Using CONCORD to Construct a Large Database of Three-Dimensional Coordinatesfrom Connection Tables. W. T. Wipke and M. Hahn, Tetrahedron Comput. Methodol., 1, 141 (1988). AIMB: Analogy and Intelligence in Model Building. System Description and Performance Characteristics. S. A. Gothe, H. E. Helson, I. Houdaverdis, I. Langerstedt, S. Sinclair, and W. L. Jorgensen, J. Org. Chem., 58, 5081 (1993). Computer-Assisted Machanism Evaluation of Organic Reactions. 22. The Generation and Use of Three-Dimensional Structures. C. W. van der Leith, R. E. Carter, D. P. Dolata, and T. Liljefors, J. Mol. Graphics, 2, 117 (1984). RINGS: A General Program to Build Ring Systems.
2. +, a Generator of Connectivity Isomers and Stereoisomers for Molecular Structure Elucidation. A. Rusinko III, R. P. Sheridan, R. Nilakantan, K. Haraki, N. Bauman, and R. Venkataraghavan, J. Chem. Inf. Comput. Sci., 29, 251 (1989). Using CONCORD to Construct a Large Database of Three-Dimensional Coordinatesfrom Connection Tables. W. T. Wipke and M. Hahn, Tetrahedron Comput. Methodol., 1, 141 (1988). AIMB: Analogy and Intelligence in Model Building. System Description and Performance Characteristics. S. A. Gothe, H. E. Helson, I. Houdaverdis, I. Langerstedt, S. Sinclair, and W. L. Jorgensen, J. Org. Chem., 58, 5081 (1993). Computer-Assisted Machanism Evaluation of Organic Reactions. 22. The Generation and Use of Three-Dimensional Structures. C. W. van der Leith, R. E. Carter, D. P. Dolata, and T. Liljefors, J. Mol. Graphics, 2, 117 (1984). RINGS: A General Program to Build Ring Systems.
3. +, a Generator of Connectivity Isomers and Stereoisomers for Molecular Structure Elucidation. A. Rusinko III, R. P. Sheridan, R. Nilakantan, K. Haraki, N. Bauman, and R. Venkataraghavan, J. Chem. Inf. Comput. Sci., 29, 251 (1989). Using CONCORD to Construct a Large Database of Three-Dimensional Coordinatesfrom Connection Tables. W. T. Wipke and M. Hahn, Tetrahedron Comput. Methodol., 1, 141 (1988). AIMB: Analogy and Intelligence in Model Building. System Description and Performance Characteristics. S. A. Gothe, H. E. Helson, I. Houdaverdis, I. Langerstedt, S. Sinclair, and W. L. Jorgensen, J. Org. Chem., 58, 5081 (1993). Computer-Assisted Machanism Evaluation of Organic Reactions. 22. The Generation and Use of Three-Dimensional Structures. C. W. van der Leith, R. E. Carter, D. P. Dolata, and T. Liljefors, J. Mol. Graphics, 2, 117 (1984). RINGS: A General Program to Build Ring Systems.
4. +, a Generator of Connectivity Isomers and Stereoisomers for Molecular Structure Elucidation. A. Rusinko III, R. P. Sheridan, R. Nilakantan, K. Haraki, N. Bauman, and R. Venkataraghavan, J. Chem. Inf. Comput. Sci., 29, 251 (1989). Using CONCORD to Construct a Large Database of Three-Dimensional Coordinatesfrom Connection Tables. W. T. Wipke and M. Hahn, Tetrahedron Comput. Methodol., 1, 141 (1988). AIMB: Analogy and Intelligence in Model Building. System Description and Performance Characteristics. S. A. Gothe, H. E. Helson, I. Houdaverdis, I. Langerstedt, S. Sinclair, and W. L. Jorgensen, J. Org. Chem., 58, 5081 (1993). Computer-Assisted Machanism Evaluation of Organic Reactions. 22. The Generation and Use of Three-Dimensional Structures. C. W. van der Leith, R. E. Carter, D. P. Dolata, and T. Liljefors, J. Mol. Graphics, 2, 117 (1984). RINGS: A General Program to Build Ring Systems.
5. +, a Generator of Connectivity Isomers and Stereoisomers for Molecular Structure Elucidation. A. Rusinko III, R. P. Sheridan, R. Nilakantan, K. Haraki, N. Bauman, and R. Venkataraghavan, J. Chem. Inf. Comput. Sci., 29, 251 (1989). Using CONCORD to Construct a Large Database of Three-Dimensional Coordinatesfrom Connection Tables. W. T. Wipke and M. Hahn, Tetrahedron Comput. Methodol., 1, 141 (1988). AIMB: Analogy and Intelligence in Model Building. System Description and Performance Characteristics. S. A. Gothe, H. E. Helson, I. Houdaverdis, I. Langerstedt, S. Sinclair, and W. L. Jorgensen, J. Org. Chem., 58, 5081 (1993). Computer-Assisted Machanism Evaluation of Organic Reactions. 22. The Generation and Use of Three-Dimensional Structures. C. W. van der Leith, R. E. Carter, D. P. Dolata, and T. Liljefors, J. Mol. Graphics, 2, 117 (1984). RINGS: A General Program to Build Ring Systems.
6. +, a Generator of Connectivity Isomers and Stereoisomers for Molecular Structure Elucidation. A. Rusinko III, R. P. Sheridan, R. Nilakantan, K. Haraki, N. Bauman, and R. Venkataraghavan, J. Chem. Inf. Comput. Sci., 29, 251 (1989). Using CONCORD to Construct a Large Database of Three-Dimensional Coordinatesfrom Connection Tables. W. T. Wipke and M. Hahn, Tetrahedron Comput. Methodol., 1, 141 (1988). AIMB: Analogy and Intelligence in Model Building. System Description and Performance Characteristics. S. A. Gothe, H. E. Helson, I. Houdaverdis, I. Langerstedt, S. Sinclair, and W. L. Jorgensen, J. Org. Chem., 58, 5081 (1993). Computer-Assisted Machanism Evaluation of Organic Reactions. 22. The Generation and Use of Three-Dimensional Structures. C. W. van der Leith, R. E. Carter, D. P. Dolata, and T. Liljefors, J. Mol. Graphics, 2, 117 (1984). RINGS: A General Program to Build Ring Systems.
7. The invention of structure diagram "readily understandable to the modern reader" is attributed to Couper (1858). A. Crum Brown's diagrams (1864)are more familiar, however. See, for example, A. Ihde, The Development of Modern Chemistry, Dover, New York, 1984, pp. 305-309.
8. D. Weininger, J. Chem. Inf. Comput. Sci., 28, 31 (1988). SMILES, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules. J. Chem. Inf. Comput. Sci., 29, 97 (1989). SMILES. 2. Algorithm for Generation Unique SMILES notation.
9. D. Weininger, J. Chem. Inf. Comput. Sci., 28, 31 (1988). SMILES, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules. J. Chem. Inf. Comput. Sci., 29, 97 (1989). SMILES. 2. Algorithm for Generation Unique SMILES notation.
10. B. L. Zimmerman, Ph.D. Thesis, University of Pennsylvania, 1971. Computerized-Generated Structural Formulas with Standard Ring Orientations.
11. Ring perception is beyond the purview of this chapter. For procedures, see: R. Balducci and R. Pearlman, J. Chem. Inf. Comput. Sci., 34, 822 (1994). Efficient Exact Solution of the Ring Perception Problem. J. Figueras, J. Chem. Inf. Comput. Sci., 36, 986 (1996). Ring Perception Using Breadth-First Search. G. M. Downs, V. J. Gillet, J. D. Holliday, and M. F. Lynch, J. Chem. Inf. Comput. Sci., 29, 172 (1989). Review of Ring Perception Algorithms for Chemical Graphs.
12. Ring perception is beyond the purview of this chapter. For procedures, see: R. Balducci and R. Pearlman, J. Chem. Inf. Comput. Sci., 34, 822 (1994). Efficient Exact Solution of the Ring Perception Problem. J. Figueras, J. Chem. Inf. Comput. Sci., 36, 986 (1996). Ring Perception Using Breadth-First Search. G. M. Downs, V. J. Gillet, J. D. Holliday, and M. F. Lynch, J. Chem. Inf. Comput. Sci., 29, 172 (1989). Review of Ring Perception Algorithms for Chemical Graphs.
13. Ring perception is beyond the purview of this chapter. For procedures, see: R. Balducci and R. Pearlman, J. Chem. Inf. Comput. Sci., 34, 822 (1994). Efficient Exact Solution of the Ring Perception Problem. J. Figueras, J. Chem. Inf. Comput. Sci., 36, 986 (1996). Ring Perception Using Breadth-First Search. G. M. Downs, V. J. Gillet, J. D. Holliday, and M. F. Lynch, J. Chem. Inf. Comput. Sci., 29, 172 (1989). Review of Ring Perception Algorithms for Chemical Graphs.
14. M. Frèrejacque, Bull. Soc. Chim. Fr. (Memoires), 5, 1008 (1939). Condensation d'une Molécule Organique.
15. H. E. Helson, Ph.D. Thesis, Purdue University, 1993. Simulation of Carbene Chemistry and Other Problems in Computer-Assisted Organic Synthesis. [For an overview of CAMEO, see: W. L. Jorgensen, E. Laird, A. Gushurst, J. Fleischer, S. Gothe, H. Helson, G. Paderes, and S. Sinclair, Pure Appl. Chem., 62, 1921 (1990). CAMEO: A Program for the Logical Prediction of the Products of Organic Reactions.]
16. H. E. Helson, Ph.D. Thesis, Purdue University, 1993. Simulation of Carbene Chemistry and Other Problems in Computer-Assisted Organic Synthesis. [For an overview of CAMEO, see: W. L. Jorgensen, E. Laird, A. Gushurst, J. Fleischer, S. Gothe, H. Helson, G. Paderes, and S. Sinclair, Pure Appl. Chem., 62, 1921 (1990). CAMEO: A Program for the Logical Prediction of the Products of Organic Reactions.]
17. ChemDraw program, Copyright 1985-1999, CambridgeSoft, Inc., 100 Cambridge Park Drive, Cambridge, MA 02140. E-mail: info@camsoft.com.
18. For historical reasons, the DEPICT program uses integral coordinates. David Weininger, Daylight Chemical Information Systems, personal communication.
19. The median bond length is preferable to the average bond length in most drawing contexts. Implicit in this discussion of bond lengths is that the diagram will be drawn with equal lengths rather than distinguishing between short and long bonds.
20. D. Weininger, J. Chem. Inf. Comput. Sci., 30, 237 (1990). SMILES. 3. Depict. Graphical Depiction of Chemical Structures. (For several years, the DEPICT program has been available for free; live usage on the Internet is at http://www.daylight.com.)
21. R. E. Carhart, J. Chem. Inf. Comput. Sci., 16, 82 (1976). A Model-Based Approach to the Teletype Printing of Chemical Structures.
22. CambridgeSoft, Inc., unpublished results.
23. C. A. Shelley, J. Chem. Inf. Comput. Sci., 23, 61 (1983). Heuristic Approach for Displaying Chemical Structures.
24. For a recent review of genetic algorithms, see: R. Judson, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1997, Vol. 10, pp. 1-73. Genetic Algorithms and Their Use in Chemistry.
25. Douglas R. Henry, MDL Information Systems, Inc., personal communication, 1997.
26. A concept first used in Ref. 7, where it was called an irregular polygon. An alternative analytical procedure for computing the polygon's coordinates can be found there.
27. A. Bertrand, R. Barone, M. Arbelot, and M. Chanon, J. Chem. Res. (S), 158 (1994). Desmol - A Subroutine for the Generation of Molecular Structures with Stereochemical Information from Connectivity Data.
28. Values in a list are the same if they all lie within 10% of the mean, or perhaps if their standard deviation is less than 5% of the mean.
29. It is appropriate to use the local distance. If the PFU arose from frozen atoms and bonds, or from tough rings, this distance is by definition correct. If it arose from SDG-designed rings, a standard bond length was applied, and once again the local bond length is appropriate.
30. P. G. Dittmar, J. Mockus, and K. M. Couvreur, J. Chem. Inf. Comput. Sci., 17, 186 (1977). An Algorithmic Computer Graphics Program for Generating Chemical Structure Diagrams.
31. W. T. Wipke, in Computer Representation and Manipulation of Chemical Information, W. T. Wipke, S. Heller, R. J. Feldmann, and E. Hyde, Eds., Krieger, New York, 1981, pp. 147-174.
32. Additional stereochemistry may of course have been added after the original publication. Such is the case with the Weininger, the CAS, and the Shelley approaches. Craig A. Shelley, personal communication.
33. David Weininger, Daylight Chemical Information Systems, personal communication.
34. Craig A. Shelley, personal communication.
35. H. E. Helson and W. L. Jorgensen, J. Chem. Inf. Comput. Sci., 34, 962 (1994). Computer Assisted Mechanistic Evaluation of Organic Reactions. 25. Structure Diagram Positioning.
36. A. M. Patterson, L. T. Capell, and D. F. Walker, The Ring Index, 2nd ed., American Chemical Society, Washington, DC, 1960.
37. For a discussion of hashing, see any good book on computer science algorithms; for example T. Cormen, C. Leiserson, and R. Rivest, Introduction to Algorithms, McGraw-Hill, New York, 1996. Chapter 12. A little additional information about hashing for RTDs appears in Ref. 7.
38. See for example M. Razinger, K. Balasubramanian, and M. E. Munk, J. Chem. Inf. Comput. Sci., 33, 197 (1993). Graph Automorphism Perception Algorithms in Computer-Enhanced Structure Elucidation. C. Jochum and J. Gasteiger, J. Chem Inf. Comput. Sci., 17, 113 (1977). Canonical Numbering and Constitutional Symmetry. See also Ret. 7
39. See for example M. Razinger, K. Balasubramanian, and M. E. Munk, J. Chem. Inf. Comput. Sci., 33, 197 (1993). Graph Automorphism Perception Algorithms in Computer-Enhanced Structure Elucidation. C. Jochum and J. Gasteiger, J. Chem Inf. Comput. Sci., 17, 113 (1977). Canonical Numbering and Constitutional Symmetry. See also Ret. 7
40. For symmetry perception algorithms, see Ref. 29, and: J. Figueras, J. Chem. Inf. Comput. Sci., 32, 153 (1992). Automorphism and Equivalence Classes K. Balasubramanian, J. Chem. Inf. Comput. Sci., 35, 761 (1995). Computer Perception of Molecular Symmetry. C. A. Shelley and M. E. Munk, J. Chem. Inf. Comput. Sci., 19, 247 (1979). An Approach to the Assignment of Canonical Tables and Topological Symmetry Perception.
41. For symmetry perception algorithms, see Ref. 29, and: J. Figueras, J. Chem. Inf. Comput. Sci., 32, 153 (1992). Automorphism and Equivalence Classes K. Balasubramanian, J. Chem. Inf. Comput. Sci., 35, 761 (1995). Computer Perception of Molecular Symmetry. C. A. Shelley and M. E. Munk, J. Chem. Inf. Comput. Sci., 19, 247 (1979). An Approach to the Assignment of Canonical Tables and Topological Symmetry Perception.
42. For symmetry perception algorithms, see Ref. 29, and: J. Figueras, J. Chem. Inf. Comput. Sci., 32, 153 (1992). Automorphism and Equivalence Classes K. Balasubramanian, J. Chem. Inf. Comput. Sci., 35, 761 (1995). Computer Perception of Molecular Symmetry. C. A. Shelley and M. E. Munk, J. Chem. Inf. Comput. Sci., 19, 247 (1979). An Approach to the Assignment of Canonical Tables and Topological Symmetry Perception.
43. MDL Information Systems, Inc., a division of Reed Elsevier, San Leandro, CA 94577.
44. (a) E. Hyde and L. Thomson, J. Chem. Doc., 8, 138 (1968). Structure Display.
45. (b) L. H. Thomson, E. Hyde, and F. W. Matthews, J. Chem. Doc., 7, 204 (1967). Organic Search and Display Using a Connectivity Matrix Derived from Wiswesser Notation.
46. B. D. Cox, Ph. D. Thesis, Arizona State University, 1973. Computer Program STR3.
47. M. Zippel, J. Mowitz, I. Koehler, and H. J. Opferkuch, Anal. Chim. Acta, 140, 123 (1982). Spektren - A Computer System for the Identification and Structure Elucidation of Organic Compounds.
48. Douglas R. Henry, personal communication. 1982 was the year LAYOUT was initiated.
49. U. Shmueli, J. Mol. Graphics, 2, 111 (1984). Simple and Efficient Approach to Preparation of Molecular Drawings.
50. D. I. Cooke-Fox, G. H. Kirby, M. R. Lord, and J. D. Rayner, J. Chem. Inf. Comput. Sci., 30, 122 (1990). Computer Translation of IUPAC Systematic Organic Chemical Nomenclature. 4. Concise Connection Tables to Structure Diagrams.
51. K. Bley, J. Brandt, A. Dengler, R. Frank, and I. Ugi, J. Chem. Res. (S), 261 (1991); J. Chem. Res. (M), 2601 (1991). Constitutional Formulae Generated from Connectivity Information: The Program MDRAW.
52. K. Bley, J. Brandt, A. Dengler, R. Frank, and I. Ugi, J. Chem. Res. (S), 261 (1991); J. Chem. Res. (M), 2601 (1991). Constitutional Formulae Generated from Connectivity Information: The Program MDRAW.
53. H. E. Helson, CambridgeSoft, Inc., unpublished work, 1996.
54. M. S. Molchanova, V. V. Scherbukhin, and N. S. Zerfirov, J. Chem. Inf. Comput. Sci., 36, 888 (1996). Computer Generation of Molecular Structures by the SMOG Program.
55. Zimmerman (Ref. 4) cites an internal document dated November 1967, but it is not now available.
56. David Weinmger described (personal communication) an 18-line implementation in APL, a hardwired program on the equivalent of an 8 Kb chip, and his own first effort, 240 lines of BASIC.
57. CIDS stands for Chemical Information and Data System, a collaboration between the University of Pennsylvania and the Walter Reed Army Institute.
58. Some additional thought has been given to how to rotate 3-D structures tor an optimal 2-D view, see Ref. 36.
59. Chemical Abstracts Service, Columbus, OH 43210.
60. J. D. Rayner, S. Milward, and G. H. Kirby, J. Mol. Graphics, 1, 107 (1983). A Character Set for Molecular Structure Display.
61. Daylight Chemical Information Systems, Santa Fe, NM 87501, and Mission Viejo, CA 92691.
62. An interesting observation by David Weininger (personal communication) is that feeding a canonical SMILES to DEPICT yields what is termed a "canonical structure diagram."
63. I. Bauer, E. Fontain, and I. Ugi, Informal Commun. Math. Chem. (MATCH), 27, 31 (1992). IGOR and RAIN: The First Mathematically Based General Purpose Computer Programs for the Solution of Constitutional Problems in Chemistry and Their Use as Generators of Constitutional Formulas.
64. Eric Fontain, personal communication. The ARGOS program was withdrawn due to lack of demand.
65. Eric Fontain, unpublished results, Technical University Munich, Institute for Organic Chemistry and Biochemistry. MOLCOORD, Ab Initio Coordinate Generation for Mol Files. The program is written in FORTRAN, runs under DOS, and requires merely 51 kilobytes.
66. A. Dalby, J. Nourse, W. D. Hounshell, A. Gushurst, D. Grier, B. Leland, and J. Laufer, J. Chem. Inf. Comput. Sci., 32, 244 (1992). Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited.
67. This measure was established by Michael Hughey, who initiated the SDG module in CAMEO.
68. ChemSketch 3.0 and ISIS/Draw 2.1.3, for example, have the bad habit of converting certain cis bonds to trans! Of course, no program is perfect. . . .
69. D. M. Bayada, R. W. Simpson, A. P. Johnson, C. Laurenco, J. Chem. Inf. Comput. Sci., 32, 680 (1992). An Algorithm for the Multiple Common Subgraph Problem.
70. For example, the MOLGEN reference in Ref. 1 uses Shelley's algorithm, and SMOG uses a synthesis of Shelley's and Carhart's methods.
71. DEPICT like all Daylight software, is free for bona fide educational use, and inexpensive otherwise. The source code for MDRAW is published (Ref. 38). MOLCOORD (Ref 51) and Desmol (Ref. 18) may be other good bets. The commercial concerns would no doubt be willing to contract large-scale translations. Most recently, Christoph Steinbeck has extended and recast the MDRAW program as a JAVA applet available for public use (http:// seneca.ice.mgp.de/~stein/).