investigation: replacing MMTK with Mosaic about mdanse HOT 2 CLOSED

Mosaic is a basic package and is essentially dedicated to interfacing with the Mosaic data model. As such it lacks a lot of functionalities beyond storing MD data in-memory and retrieving that data. The lacking methods that MDANSE currently uses are:

• Universe.setFromTrajectory()
• Universe.contiguousObjectConfiguration()
• exchanging coordinates between real and box
• Collection.normalizingTransformation()
• MMTK.Transformations
• MMTK.Trajectory.RigidBodyTrajectory
• MMTK.Collections.Collection (the object as a collection of atom/molecule object could perhaps be substituted by mosaic.Fragment, but this lacks the required methods like centerOfMass)
• MMTK.NucleicAcids and MMTK.Proteins (have to be specified using the general mosaic.Fragment)

Mosaic handles writing trajectories into file very differently than MMTK, so all Trajectory Jobs will have to be rewritten.

from mdanse.

This will not be used, instead the replacement for MMTK will be bespoke, as detailed in #64.

from mdanse.