This example shows how to use the MSConnectivityRestraint to ensure that all the particles that are part of complexes end up in a connected conformation following the optimization. It allows multiple copies of particles and takes an experimental tree as an input.
39 pa = r.add_type([ds[0], ds[1]])
40 pb = r.add_type([ds[2], ds[3]])
41 pc = r.add_type([ds[4]])
42 pd = r.add_type([ds[5]])
48 i1 = r.add_composite([pa, pa, pb, pb, pc])
49 i2 = r.add_composite([pa, pb, pb, pc], i1)
50 i3 = r.add_composite([pa, pa, pb, pb], i1)
51 i4 = r.add_composite([pa, pb], i1)
52 i5 = r.add_composite([pa, pb, pb], i2)
53 i6 = r.add_composite([pb, pc], i2)
54 i7 = r.add_composite([pa, pa, pb], i3)
55 i8 = r.add_composite([pa, pb], i5)