Secondary structure monitoring in simulations

[jamesmkrieger]

This should be fairly easy to implement through monitoring dihedral angles and could be annoying to do as a user so we should make functions for checking it. I guess we'd want to return 0 or 1 for each residue and secondary structure type and format the data for easy accessing and plotting.

We'd probably have a show function for this too. Maybe we could generate a plot like this https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-285/figures/5

[jamesmkrieger]

We could also use dssp, which we have a wrapper for. I'll have to look into what that does.

[jamesmkrieger]

Our wrapper for dssp acts on individual PDB files and not on frames. However, mdtraj has an implementation that can handle a trajectory. We may therefore want a converter between ProDy Ensemble/PDBEnsemble/Trajectory and MDTraj Trajectory.