deletions | additions       diff --git a/section_Compound_Libraries_Unique_to__.tex b/section_Compound_Libraries_Unique_to__.tex  index 2a6f75c..5512e7d 100644  --- a/section_Compound_Libraries_Unique_to__.tex  +++ b/section_Compound_Libraries_Unique_to__.tex 
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Users may submit their own libraries for screening. In the spirit of the open access and open-source nature of Pharmit, users are encouraged to make their submitted libraries publicly accessible, in which case they are available to all users for screening as a user contributed library. However, registered users have the ability to create a private library, as well as remove or update previously submitted libraries.   In order to create a library, compounds may be provided either in the two-dimensional SMILES or three-dimensional SDF formats. If the user uploads compounds in the SMILES format, duplicated canonical SMILES are removed, the molecules are protonated using OpenBabel, OpenBabel \cite{O_Boyle_2011} using default settings,  and only the largest component of a molecule is retained (e.g., salts are removed). Then RDKit (\url{rdkit.org}) and the UFF force field \cite{Rappe_1992} are used to generate up to 10 3D conformers for each compound resulting from this procedure. This approach has been shown to generate high quality conformations \cite{Ebejer_2012}. Alternatively, if the user provides compounds in the SDF format, the provided structures are assumed to be valid conformers and are used directly, except that OpenBabel is still used to protonate them. with protonation states determined by OpenBabel.