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Pharmit will identify all pharmacophore features present in a provided ligand structure. If a receptor structure is provided, it will identify which of these features are relevant to the protein-ligand interaction using distance cutoffs between corresponding features on the receptor and ligand (e.g., a hydrogen donor on the ligand and acceptor on the receptor). Only the interacting features will be enabled. Alternatively, a pharmacophore query can be initialized using pharmacophore files in MOE \cite{moe}, LigBuilder \cite{Wang_2000}, LigandScout \cite{Wolber_2005}, PharmaGist \cite{Schneidman_Duhovny_2008} or Pharmer \cite{Koes_2011} query formats. The features of the query can be interactively edited within the Pharmit interface as changes to the query editor are immediately reflected in the molecular viewer and clicking on a feature in the viewer selects it for editing, as shown in Figure~\ref{pharmfig}.  Pharmacophore search is implemented using the Pharmer algorithm \cite{Koes_2011}, similar to, ZINCPharmer \cite{Koes_2012}. Pharmer was independently validated and its performance was compared with other methods in \cite{Sanders_2012}.  \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 color ROCS, but it does not optimize the position with respect to the pharmacophores.