The projections in MoleculeKit. These are a set of classes which take Molecule objects and calculate some projections (or features if you wish) for each conformation inside the Molecule. They range from typical RMSD calculations to more complex calculations such as SASA, secondary structure, Plumed2 projections and more.

These can be used to analyse your simulations as well as build Markov models in conjunction with the HTMD package.