PMI1 to PMI2 transition guide

This page shows where to look in PMI2 for the replacement functionality for something in PMI1. Feel free to add to this page (which will migrate to the PMI docs eventually).

IMP.pmi.representation.Representation: largely replaced by IMP.pmi.topology.System and its create_state method, plus IMP.pmi.dof.DegreesOfFreedom.

Representation.create_component(): see State.create_molecule()

Representation.add_component_beads(): use Molecule.add_representation(x) where x is nonatomic.

Representation.add_component_ideal_helix(): use Molecule.add_representation(x, ideal_helix=True).

Representation.setup_component_geometry(): no longer needed?

Representation.set_rigid_body_from_hierarchies(x): use DegreesOfFreedom.create_rigid_body(x).

Representation.set_chain_of_super_rigid_bodies([a,b,c],x,y): use DegreesOfFreedom.create_super_rigid_body([a,b,c], chain_min_length=x, chain_max_length=y)

Representation.set_super_rigid_bodies(x): use DegreesOfFreedom.create_super_rigid_body(x) (unless already done for a chain of super rigid bodies, as above)