Molecular Libraries that are available from PubChem or elsewhere, usually contain 2D structures generated from molecular formulas or SMILES strings. To prepare these files for docking, PyRx is using OpenBabel to parse Structured Data Format (SDF). TableEditor from enthought.traits allows users to sort/filter molecules. The results are displayed in TVTK scene as sticks and balls. PyRx also provides options to run energy minimization for selected or all molecules. Energy minimization is done using OpenBabel and we have a GUI that can be used to change energy minimization parameters.

Finally, PyRx has menus for converting selected or all molecules to AutoDock Ligand format (PDBQT). Users have options for removing fragments smaller that specific number (OpenBable.StripSalts) and an option to choose partial charges (OpenBabel or PyBabel from MGLTools).