void OEDetermineConnectivity(OEMolBase &mol)
Perceives the covalent bonds of a molecule from 3D coordinates. This routine creates a bond between any pair of atoms that are closer than the sum of their covalent radii plus a slop factor of 0.45 Angstroms. The covalent radii of each atom are as defined by the Cambridge Crystallographic Database (http://www.ccdc.cam.ac.uk), and are those returned by the OEChem TK function OEGetCovalentRadius. Bonds are not created by atoms separated by less than 0.4 Å. All bonds are created with bond order 1. The OEChem TK function OEPerceiveBondOrders may be used to assign bond orders from the 3D geometry and connectivity.