Joining multiple topologies together

[uppittu11]

Is there a way to join several topologies to make one big topology? An example use case would be if you have one molecule typed with a particular force field and another molecule typed with another and then you want to combine them to build up a fully typed system. Here is how I imagine it would look in action:

typed_full = gmso.join_topologies([typed_protein]+[typed_water]*10000)

This could warrant another GH issue, but it might also be nice to have an update coordinates method in topology, similar to what we have in mbuild. Then we can do something like this:

full_compound = mb.fill_box([protein_compound, water_compound], n_compounds=[1, 10000], density=1100)
typed_full = gmso.join_topologies([typed_protein]+[typed_water]*10000)
typed_full.update_coordinates(full_compound)

where the protein and water were typed with different force fields.

[rsdefever]

I think this would be very useful. It would also make it easier to manually verify the parameterization (i.e., its much easier to glance through the parameters assigned to a single molecule than to 10k). It could also be helpful for assigning charges, where you might take a single molecule, run it through RESP, and then use those charges for every molecule of the same species.

We'll need to be careful with how we handle updates to the box information.

[daico007]

Older discussion here: #32