On the perception of molecules from 3D atomic coordinates

A method is presented for perceiving chemical types of atoms in molecules given 3D atomic coordinates and element identities. The method assigns hybridizations, bond orders, and formal charges for structures whether hydrogen atoms are present. The Maximum Weighted Matching algorithm for nonbipartite graphs is used to assign bond orders with weights derived from statistics of a large collection of organic molecules. Results form tests on a collection of functional groups, heterocycles, entries from the Protein Data Bank, and Cambridge Structural Database as well as a comparison to other methods, are presented and discussed.