1. A computer implemented method for identifying the candidate molecule or molecules in a large array of molecules that are similar in three dimensional shape to query molecules, comprising the following steps: a) defining a set of topologically distinct steric features that taken together cover the substructures found in each molecule; b) identifying the positions of the steric features in each conformer of a query molecule; c) selecting a class of multiplet for use; d) using the selected multiplet class, for each query molecule, identifying the multiplet or multiplets that occur within at least one conformer of the molecule; e) dividing the set of conformations for each query molecule into at least two subpopulations by randomly assigning each conformer to one subpopulation; f) creating bitmaps indicating which multiplets occur in each conformer subpopulation of each molecule; g) logically ORing the bitmaps of each conformer for each molecule; h) generating a steric multiplet hypothesis by identifying discriminating multiplets from the bitmaps based upon how many conformers each multiplet occurs in and the size of the multiplet; i) identifying the positions of the steric features in each conformer of the molecules in the large array; j) using the previously selected multiplet class, for each molecule in the array identifying the multiplet or multiplets that occur within at least one conformer of the molecule; k) creating bitmaps indicating which multiplets occur in each conformer of each molecule; l) logically ORing the bitmaps of each conformer for each molecule; and m) comparing the bitmap for each array molecule to the steric multiplet hypothesis bitmap to determine those array molecules most similar in three dimensional shape to the query molecule.