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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, duplicate SMILES are removed, the molecules are protonated using OpenBabel, and only the largest component of a molecule is retained (salts (e.g., salts  are removed, for example). 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.