Evaluate use of other packages reading molecular simulation result files

[ptmerz]

Connected to #51 #52 #53 #54 - is having our own parsers the best way to move forward? Could MDTraj / MDAnalysis / pytraj / other packages make our lives easier? Note that physical_validation has some very specific requirements of what information is needed, which were not fulfilled by any other package last we checked.

Related to do: Make list of information physical_validation needs to read from simulation results files.

[mattwthompson]

I think relying on packages like you listed is the preferred approach in general, but this may not be feasible if we'd need to make a lot of changes to them to get them to include the necessary information. Agreed that the first step is documenting specifically what is needed here

[SimonBoothroyd]

Note that physical_validation has some very specific requirements of what information is needed

It would be great to list the exact requirements!

[ptmerz]

Actually, my documentation was better than I remembered 😄

All requirements here: https://physical-validation.readthedocs.io/en/latest/parsers.html

[SimonBoothroyd]

Awesome - thanks!

[ptmerz]

Also, as stated during group meeting today, feeding physical_validation energies, trajectories, or details about the simulated ensemble through python data structures is relatively easy. The most tedious part handled by the parser is topological information for the equipartition tests (all other tests use at most the total number of degrees of freedom from the topological information). Having an external package that is able to return atomic masses and information on bonds might save us a lot of hassle.