Add a SingleChain system class.

[chrisjonesBSU]

I often need a single chain in a vacuum, and using Pack for this isn't a great option, since the density you have to choose isn't intuitive. Also, for single chain simulations it is helpful for visualization purposes that the chain starts the in the center of the volume, which will almost never happen when using Pack.

[chrisjonesBSU]

Here is an example of a custom one I was using in a project

    class SingleChainSystem(System):
        def __init__(self, molecules, base_units=dict()):
            super(SingleChainSystem, self).__init__(
                    molecules=molecules,
                    base_units=base_units
            )

        def _build_system(self):
            chain = self.all_molecules[0]
            head = chain.children[0]
            tail = chain.children[-1]
            chain_length = np.linalg.norm(tail.pos - head.pos)
            box = mb.Box(lengths=np.array([chain_length] * 3) * 1.05)
            comp = mb.Compound()
            comp.add(chain)
            comp.box = box
            chain.translate_to((box.Lx / 2, box.Ly / 2, box.Lz / 2))
            return comp

[chrisjonesBSU]

We might need to think about automating finding the chain length rather than hard coding first and last indices, but also without requiring that the user manually finds them. We could just take the largest pair distance between particles and call that the "chain length"

SciPy has this method which is pretty fast

https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.pdist.html

[StephMcCallum]

• doc strings
• add to library/systems.py
• make it work for AA atom models and atom indices (different ways to get length of polymer or mbuild compound, spicy.pdist)
• unit tests