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Abstract  Molecular shape is a useful tool for identifying small-molecules for therapeutics. Shape similarity can be found through both alignment methods, a computationally demanding approach, or through feature vector methods, computationally less demanding. Maximization of both volume overlap and various feature points makes alignment methods computationally intensive. The computational burden of alignment can be reduced by pre-aligning shapes, as is done with the Volumetric-Aligned Molecular Shapes (VAMS) method. Here we introduce and evaluate Fragment Oriented Molecular Shapes (FOMS), where shapes are aligned based on molecular fragments. FOMS performs equivalently or better than both VAMS and an optimizing alignment method. More significantly, FOMS enables the use of \textit{shape constraints}, a novel method for precisely  specifying molecular shape queries that provides the ability to perform partial shape matching and supports  search algorithms that function on an interactive time scale.