Chemical graphs, chemical reaction graphs, and chemical graph transformation

Electronic Notes in Theoretical Computer Science

Volumn 127, Issue 1, 2005, Pages 157-166

  Rosselló, Francesc ^a   Valiente, Gabriel ^b  

^a UNIVERSITAT DE LES ILLES BALEARS   (Spain)

^b UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

Author keywords

Chemical graph; Chemical reaction; Edge relabeling; Explicit chemical reaction; Graph transformation; PerlMol

Indexed keywords

CHEMICAL GRAPHS; COMPUTER SOFTWARE- PERLMOL; EDGE RELABELING; EXPLICIT CHEMICAL REACTION; GRAPH TRANSFORMATION;

ATOMS; CHEMICAL BONDS; COMPUTER GRAPHICS; GRAPH THEORY; OBJECT ORIENTED PROGRAMMING; PATTERN MATCHING; SUBSTRATES;

CHEMICAL REACTIONS;

EID: 14944368662     PISSN: 15710661     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.entcs.2004.12.033     Document Type: Conference Paper

References (17)

1. G. Benkö, C. Flamm, and P.F. Stadler A graph-based toy model of chemistry Journal of Chemical Information and Computer Sciences 43 2003 1085 1093
2. A. Corradini, U. Montanari, F. Rossi, H. Ehrig, R. Heckel, and M. Löwe Algebraic approaches to graph transformation. Part I: Basic concepts and double pushout approach G. Rozenberg Handbook of Graph Grammars and Computing by Graph Transformation, Volume 1: Foundations 1997 World Scientific 163 246
3. A. Dalby, J.G. Nourse, W.D. Hounshell, A.K.I. 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 Sciences 32 1992 244 255
4. F. Fringuelli, and A. Taticchi The Diels-Alder Reaction: Selected Practical Methods 2002 John Wiley & Sons Chichester, England
5. S. Fujita Computer-Oriented Representation of Organic Reactions 2001 Yoshioka Shoten Kyoto
6. A. Hassner, and C. Stumer Organic Syntheses based on Name Reactions 2nd edition Tetrahedron Organic Chemistry Series 22 2002 Pergamon Press Oxford, England
7. C.A. James, D. Weininger, and J. Delany Daylight theory manual available at http://www.daylight.com/dayhtml/doc/theory/ 2004
8. T. Laue, and A. Plagens Named Organic Reactions 1998 John Wiley & Sons Chichester, England
9. J.J. Li Name Reactions: A Collection of Detailed Reaction Mechanisms 2nd edition 2003 Springer-Verlag Berlin
10. B.P. Mundy, and M.G. Ellerd Name Reactions and Reagents in Organic Synthesis 1988 John Wiley & Sons Chichester, England
11. F. Rosselló, and G. Valiente Analysis of metabolic pathways by graph transformation Proc. 2nd Int. Conf. Graph Transformation Lecture Notes in Computer Science 3256 2004 70 82
12. I. Tubert-Brohman Perl and chemistry The Perl Journal 8 2004 3 5
13. I. Tubert-Brohman PerlMol - Perl modules for molecular chemistry available at http://www.perlmol.org/ 2004
14. D. Weininger SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules Journal of Chemical Information and Computer Sciences 28 1988 31 36
15. D. Weininger SMILES. 3. DEPICT. Graphical depiction of chemical structures Journal of Chemical Information and Computer Sciences 30 1990 237 243
16. D. Weininger, A. Weininger, and J.L. Weininger SMILES. 2. Algorithm for generation of unique SMILES notation Journal of Chemical Information and Computer Sciences 29 1989 97 101
17. J.D. Westbrook, and P.M.D. Fitzgerald The PDB format, mmCIF formats and other data formats P.E. Bourne H. Weissig Structural Bioinformatics Methods of Biochemical Analysis 44 2003 John Wiley & Sons Hoboken, New Jersey 161 179