The aim is a description of discrete mathematics used in a project devoted to the implementation of a software package for the simulation of combinatorial chemistry.

In this introduction we summarize both the Lunn-Senior’s mathematical model from [3], and the content of the present paper. 1.1. Let AR be a set of atoms and radicals we are interesting in. The structural (connectivity) formula of a given chemical molecule is usually drawn as an AR-labelled

Some of the mathematical methods will be described which are implemented in the software package MOLCOMB 1 that allows to simulate combinatorial chemistry by generating combinatorial libraries and to do screening according to geometric substructures. 1 Combinatorial Chemistry To begin with, we consider the examples described in the prominent papers [1] and [2] on combinatorial chemistry. The authors introduce particular combinatorial libraries obtained by starting from the central molecules Cl Cl Cl Cl O O O O O Cl Cl Cl Cl O O O O Cl Cl O Cl O O i.e. they start from cubane, xanthene, benzene triacid chlorine as central molecules to which they attach amino acids according to the reaction scheme that describes the reaction between the active sites 1 MOLCOMB is the outcome of a research project supported by the federal ministery for technology, under contract 03 KE7BA 1-4 C 3 2 1 Cl O of the central molecule and the active parts of the aminoacids in question: C O 1 2 3 4 5 C...