Add utility functions for secondary structure / torsions

[jlmaccal]

@splenz @ccccclw You both have some routines for extracting torsion restraints and/or secondary structures from pdb files using mdtraj. I think you also both have code for extracting internal elastic network type restraints. It might be worth thinking about how to incorporate these as utility functions in MELD, so that we have a single, reliable version that can be re-used.

@ccccclw your version is in test_emap script. Those look quite good, but we would want to make sure that they work reliably with multiple chains.

[ccccclw]

You mean including a function for setting up local secondary structure restraints on defined range of a system? e.g. secondary structure restraints on every 5 residues on residue 1 to 100. For the "internal elastic network type restraints", it means defining a cutoff around an atom and setting up the distance and/or dihedral restraints with the cutoff?

[jlmaccal]

I'm just looking at your emap test script. You have code in their for extracting restraints from pdb files, which is a common thing to do. It would helpful to capture some of that in utility functions.

[ccccclw]

Oh, got it.