International Journal of Chemoinformatics and Chemical Engineering, 2(2), 1-14, July-December 2012 1 Copyright © 2012, IGI Global. Copying or distributing in print or electronic forms without written permission of IGI Global is prohibited. Keywords: Automating Classiication, Bond-Electron Matrix, Chemical Reaction Classiication, Reaction Matrix, Ugi’s Scheme INTRODUCTION One of the major tasks of chemoinformatics is to predict the outcome of a chemical reaction. For this purpose the first step is to classify exist- ing chemical reactions, on the basis of which unknown reactions can be predicted. In the mid 1970s, Ugi and his co-workers developed a tech- nique to represent chemical reactions by means of Reaction matrices (R-matrices) (Dugundji & Ugi, 1973; Ivanciuc, 2010). Later researchers had studied (Bart & Garagnani, 1977) several reaction schemes and finally, Ugi’s work, which classifies chemical reactions into 30 different classes, came to be known as Ugi’s scheme (Bart & Garagnani, 1977; Gasteiger & Engel, 2003). In this paper we have proposed an ef- ficient algorithm to automate classification of chemical reactions based on Ugi’s scheme. In the following section we first describe the background to elaborate the representation of molecules and chemical reactions using graph theoretic techniques - Bond-Electron matrix (BE-matrix) and Reaction matrix (R-matrix) An Eficient Algorithm for Automating Classiication of Chemical Reactions into Classes in Ugi’s Reaction Scheme Sanjay Ram, Bengal Engineering and Science University, Shibpur, India Somnath Pal, Bengal Engineering and Science University, Shibpur, India ABSTRACT There are two approaches for classiication of chemical reactions: Model-Driven and Data-Driven. In this paper, the authors develop an eficient algorithm based on a model-driven approach developed by Ugi and co-workers for classiication of chemical reactions. The authors’algorithm takes reaction matrix of a chemical reaction as input and generates its appropriate class as output. Reaction matrices being symmetric, matrix implementation of Ugi’s scheme using upper/lower tri-angular matrix is of O(n 2 ) in terms of space complexity. Time complexity of similar matrix implementation is O(n 4 ), both in worst case as well as in average case. The proposed algorithm uses two ixed size look-up tables in a novel way and requires constant space complexity. Time complexity both in worst and average cases of the algorithm is linear. DOI: 10.4018/ijcce.2012070101