text: The first Machine Learning model used on large datasets is the Substructure Analysis that was created in 1973. Each fragment substructure make a continuous contribution an activity of specific type. Substructure is a method that overcomes the difficulty of massive dimensionality when it comes to analyzing structures in drug design. An efficient substructure analysis is used for structures that have similarities to a multi-level building or tower. Geometry is used for numbering boundary joints for a given structure in the onset and towards the climax. When the method of special static condensation and substitutions routines are developed this method is proved to be more productive than the previous substructure analysis models.