deletions | additions       diff --git a/section_Search_Pharmit_provides_two__.tex b/section_Search_Pharmit_provides_two__.tex  index 82a5acc..0295c90 100644  --- a/section_Search_Pharmit_provides_two__.tex  +++ b/section_Search_Pharmit_provides_two__.tex 
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If a pharmacophore query is present, it is used to filter the shape-aligned results. In this case, the pharmacophore features of the hit compound must fall within the tolerance spheres of the pharamacophore query with the compound in the shape-aligned pose. That is, a compound that would match a pharmacophore query if the query were the primary query may still be filtered out.    \subsection{Filters}  Additional hit reduction and screening options are provided in the "Filters" menu. The three options for hit reduction include restricting the maximum hits returned for every configuration, for every molecule, and overall. The maximum hits per configuration constraint is applied greedily, returning the first n results found without prioritizing any other aspects of those results. The other two constraints are applied after the results are sorted, giving priority \subsection{Additional Filters}  Pharmit allows users  to those of higher rank (lower RMSD for pharmacophore searches and higher similarity scores for shape searches). There are seven options given for hit screening. These include constraints specify additional, non-structural filters  onmolecular weight,  the results. The  number of rotatable bonds, LogP (a measure of lipophilicity), polar surface area (indicative of ability to permeate cell membranes), compounds returned can be reduced by restricting  the number of aromatic groups, poses returned for every conformation,  the number of hydrogen bond acceptors, conformations returned for every compound,  and the total  number of hydrogen bond donors. Properties are computing using OpenBabel. compounds.  \subsection{Hit Reduction} Compounds may be filtered by specifying desired ranges for molecular properties that are commonly used to identify drug-like molecule.  These include molecular weight, the number of rotatable bonds, LogP (a measure of lipophilicity), polar surface area (indicative of ability to permeate cell membranes), the number of aromatic groups, the number of hydrogen bond acceptors, and the number of hydrogen bond donors. Properties are precomputed using OpenBabel \cite{openbabel}.  \subsection{Result Browser}  When a database search is initiated, a right sidebar opens to display the search results. This sidebar may be hidden by pressing the right-facing arrow at the top left of the sidebar, or it may be closed by pressing the "x" in the upper right corner. Results may be sorted in increasing or decreasing order based on RMSD, mass, or number of rotatable bonds; the sorting method is determined by pressing on the name of desired sorting method, and pressing the name again to toggle between increasing and decreasing order. Lavender arrowheads to the right of the sorting method names indicate whether sorting is being performed in increasing (up) or decreasing (down) order.