IMP.pmi.dof Namespace Reference

Create movers and setup constraints for PMI objects. More...

Detailed Description

Create movers and setup constraints for PMI objects.

• Start by creating the DegreesOfFreedom class with dof = IMP::pmi::dof::DegreesOfFreedom(model)
• The various "create X" functions make movers for system components as well as setup necessary constraints. For each of these functions, you can generally pass PMI objects like Molecule or slices thereof.
  • DegreesOfFreedom.create_rigid_body() lets you rigidify a molecule (but allows you to also pass "nonrigid" components which move with the body and also independently).
  • DegreesOfFreedom.create_super_rigid_body() sets up a special "Super Rigid Body" which moves rigidly but is not always constrained to be rigid (so you can later move the parts separately). Good for speeding up sampling.
  • DegreesOfFreedom.create_flexible_beads() sets up particles to move individually.
  • DegreesOfFreedom.setup_md() sets up particles to move with molecular dynamics. Note that this is not (yet) compatible with rigid bodies, and only some restraints.
  • DegreesOfFreedom.constrain_symmetry() makes a symmetry constraint so that clones automatically move with their references. If instead you want a softer restraint, check out the SymmetryRestraint.
• When you are done you can access all movers with DegreesOfFreedom.get_movers(). If you have set up rigid, super rigid, or flexible beads, pass the movers to the monte_carlo_sample_objects argument of ReplicaExchange0.
• If you are running MD, you have to separately pass the particles (also returned from DegreesOfFreedom.setup_md()) to the molecular_dynamics_sample_objects argument of ReplicaExchange0. Check out an MD example here.

Classes
class	DegreesOfFreedom
	A class to simplify create of constraints and movers for an IMP Hierarchy. More...