Dump system PDB or XML by default

[IAlibay]

Something I've realise, we don't have a good way to post process coordinates at the moment since we don't have a "topology" equivalent we dump out by default to then pass out to MDA or MDTraj.

[richardjgowers]

I'm tempted to say this is just ChemicalSystem, but then that doesn't actually necessarily correspond to what was simulated (solvation and/or Protocol having free will).

PDB is awful for this, but also I'm not actually sure if there is a nice Topology format easily read by common tools....

I don't think it would be that hard to write the attributes to json, then have a moljson_to_mdtraj/analysis/whatever function. The subtlety being we're not introducing a format that others are meant to read, but instead an opaque blob from which we offer outward routes.

[richardjgowers]

pdbs are created now