Allow control over automatic bond assignment

[andrewtarzia]

Hey all, This is working great so far. Except that my models are coarse-grained, so the bonds that come out from automatic assignment are not correct.

I have the topology information, so I can provide bonds (ideal solution), or I was think I could generate cylinder shapes for each bond. An alternative is that I could scale, or modify, the radii constrain for determining bonding information.

Any suggestions on which approach is best?