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\subsection*{Shape Representation}  A molecular shape in FOMS is a discretized solvent-excluded volume that is calculated from the heavy atoms of a molecular conformation using a water probe with radius 1.4{\AA}. The volume is discretized into 0.5{\AA} voxels (three dimensional pixels) and stored as an oct-tree, an efficient data structure for representing volumetric data.\cite{Zhang2009} Most oct-tree operations take time proportional to the surface area of a shape ($\approx n^2$) instead of the volume ($\approx n^3$).We represent a molecular shapes as a solvent-excluded volume that is calculated from the heavy atoms of a molecule conformation using a water probe of radius 1.4{\AA}. This volume is discretized onto a 0.5{\AA} resolution grid where each grid point represents a voxel (three dimensional pixel). Voxelized volumes are stored as oct-trees, an efficient data structure for storing and comparing shapes An example of a voxelized representation of a molecule is shown in Figure~\ref{voxelshape}. In cases where we grow or shrink a molecular shape, these operations are performed on the grid by removing the appropriate number of surface voxels.  The grid coordinates of a molecular shape are all computed relative to the identified anchor fragment. If a molecule contains multiple instances of an anchor fragment or if there are inherent symmetries in the fragment, then a distinct voxelized shape is generated for every valid alignment of the fragment(s).  We grow/shrink molecular shapes by adding/removing the appropriate number of surface voxels.  %((Place Computational Methods here. Not needed for review articles))  \subsection*{\sffamily \large \subsection*{  Shape Constraints} Since we assume all shapes are registered to a common coordinate system defined by the anchor fragment, it is possible to exactly specify regions of space that a molecule should and should not occupy. We refer to these constraints as included and excluded shapes. The \textit{included shape} is a set of voxels that must be part of the target shape. An included shape can be used to require that the desired shape makes key contacts with the receptor or has sufficient bulk to fill a binding pocket.  An \textit{excluded shape} is a set voxels that must not be present in the desired shape. An excluded shape can be used to require that the desired shape does not clash with the receptor or exceed some maximum volume. Included shape and excluded shape constraints permit a user to `sculpt' a precise specification of the desired shape. An expert user may be able to create highly specific custom shape constraints. However, for purposes of our evaluation we consider only shape constraints derived directly and automatically from existing receptor-ligand complexes. These shape constraints would serve as starting points for modifications by an expert user, for example, to better incorporate tolerances to receptor flexibility in specific areas.