Daylight substructure specification

The basis of ALADDIN is the Daylight Chemical Information Systems software, particularly GENIE, a substructure specification language. When GENIE finds a query substructure in an input SMILES structure, it can return to the user those atoms in the structure that correspond to those hit. Since in a MENTHOR database the coordinates of the atoms are stored in the order in which they occur in the SMILES for that molecule, the coordinates of the atoms of interest are thereby identified. Thus, our geometric objects are established from this set of atoms, and geometric tests are performed on them. Steric tests are performed on molecules that meet the geometric criteria. 

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