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\subsection{Pharmacophore Queries}  A pharmacophore \cite{Koes_2015rev,Yang_2010,Leach_2010} defines the essential features of an interaction. Importantly, a pharmacophore includes the spatial arrangement of these features.   Features supported by Pharmit include hydrogen bond acceptors and donors, negative and positive charges, aromatics, and hydrophobic features.  As shown in Figure~\ref{mainfig}, Figure~\ref{pharmfig},  a pharmacophore query specifies these features using tolerance spheres. Compounds match if they can be positioned so that their corresponding features are located within these spheres. Some features can have additional constraints, such as direction for hydrogen bonds and aromatics and size (number of atoms) for hydrophobic features. 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}.