PURY (Andrejasic et al., 2008) is a database of geometric restrains for refinement of molecules based on the Cambridge Structural Database (CSD). One of its limitation is that atom classes were assigned using extensive prior chemical knowledge arising from connectivity and planarity, which resulted in over two thousand classes and hundreds of thousands of geometric restraints. Half were statistically under represented and many classes were redundant. The new generation of parameters will be in the public domain since it is based on the Crystallography Open Database (COD) rather than the proprietary CSD. We think that they will be as accurate as the set derived from the CSD since the COD includes over 220,000 entries by March, 2013, and steadily grows. Python programs were written to access the crystallographic entries and filter out problematic files and molecular structures.Using filtered data an iterative process for atom class definition was developed based only on the topology of the molecules and the distribution of atom distances among classes. This scheme starts identifying the atom class with its plain atom name and then increasing the atom class complexity by gradually including information from the neighbors only for those classes whose distribution of distances are multi-modal or have a high standard deviation. This process leads to a set of atom classes of uneven complexity, with atoms on hybridized structures reaching the highest level of complexity.
COBISS.SI-ID: 27630887