1. A computer implemented drug discovery method utilizing a specifically programmed computer for aligning in three dimensions molecular fragments derived from molecules in a molecular database to a specified three dimensional template comprising the following steps: a) fragmenting a candidate template molecule; b) specifying the template fragment or fragments to which alignment is desired; c) fragmenting a molecular database molecule; d) specifying the database molecule fragment candidate that is to be aligned to a template fragment; e) generating 3D structures for the candidate fragment; f) orienting both the template and candidate fragments by superimposing each fragment attachment bond onto a fixed vector root position; g) identifying for both template and candidate fragments all atoms and atom/property types excluding all hydrogen atoms; h) matching identical atoms in the template and candidate fragments by sequential traversals of the fragments that start at the fragment root and end wherever no more identical matches exist along any branch; i) aligning the candidate fragment to the template fragment by assigning the coordinates of template atoms to the matching identical candidate atoms identified in step h; j) positioning any atoms in the candidate fragment that do not have matching atoms in the template fragment so as to maintain their relative positions to those atoms in the candidate fragment that had matching atoms in the template fragment; k) topomericaly aligning atoms in any branch that includes uncoordinated-copied atoms where the root of any branch will be a bond between a coordinate-copied and a coordinate-uncopied bond; l) outputting the candidate alignment if only one template fragment was generated in step b); m) repeating steps b) through h) for each additional template fragment that was generated in step b); n) selecting the alignment for the candidate fragment that has the largest number of atom-to-atom matches with a template fragment in step h); and o) outputting the candidate alignment.