Subclasses of Connection should have a function measure() that measures that bond/angle/dihedral. This will be good for sanity-checking your simulation.
Things to consider:
How we want to implement (define C functions like mdtraj vs just use scipy)
Considering minimum image convention (which means the Connection instance will need to know something about the topology.box
I think this would be a nice feature but (imo) is tangential to the core objectives and may require a good bit of work to implement in more than a primitive manner.
Subclasses of
Connection
should have a functionmeasure()
that measures that bond/angle/dihedral. This will be good for sanity-checking your simulation.Things to consider:
Connection
instance will need to know something about thetopology.box