deletions | additions       diff --git a/section_Compound_Libraries_Unique_to__.tex b/section_Compound_Libraries_Unique_to__.tex  index 8523d82..ccac330 100644  --- a/section_Compound_Libraries_Unique_to__.tex  +++ b/section_Compound_Libraries_Unique_to__.tex 
...
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 2D the two-dimensional  SMILES format, or three-dimensional SDF formats. If the user uploads compounds  in which case the SMILES format, duplicate SMILES are removed, the molecules are protonated using OpenBabel, and only the largest component of a molecule is retained (salts are removed, for example). 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. compound resulting from this procedure.  This approach has been shown to generate high quality conformations \cite{Ebejer_2012}. Alternatively, if  the user may provide provides  compounds in the3D  SDF format,in which case  the provided structures are assumed to be valid conformers and are used directly. directly, except that OpenBabel is still used to protonate them.