The aim of the RDKit interoperability project is to give MDAnalysis the ability to use RDKit’s
Chem.Mol structure as an input to an MDAnalysis’
Universe, but also to convert a
AtomGroup to an RDKit molecule.
RDKit is one of the most complete and one of the most commonly used chemoinformatics package, yet it lacks file readers for formats typically encountered in MD simulations. Adding to MDAnalysis the ability to switch back and forth between a Universe and an RDKit molecule to perform typical chemoinformatics calculations would add a lot of value to both packages.