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\subsection{Shape Queries}  Similarity of molecular shape is a common method of structure-based virtual screening \cite{Nicholls_2010}. Pharmit uses the Volumetric Aligned Molecular Shapes (VAMS) \cite{vams} method of shape search, which uses inclusive and exclusive shape constraints to identify matching molecular shapes. In Pharmit, inclusive constraints are specified using the shape of the provided ligand or by manually specified inclusion spheres. Inclusive constraints specify a minimum bound on the desired molecular shape; matching compounds will overlap these constraints. Exclusive constraints are specified using the shape of the provided receptor or by manually specified exclusion spheres. Exclusive constraints are used to limit the desired molecular shape; matching compounds are prohibited from overlapping these constraints. Both constraints are represented using voxelized volumes, as shown in Figure~\ref{shapefig}, and can be adjusted by growing or shrinking the constraint volume. A shape-first search with pharmacophore restraints is similar to distinct from the commonly used ROCS with  color ROCS, but shape method \cite{Hawkins_2007} as  it does not optimize the position with respect to the pharmacophores.