TransformationSymmetry not applied correctly

[benmwebb]

Jan reports on imp-users that the following script (using example_protein.pdb from modules/core/examples) results in wonky coordinates for one rigid body related by TransformationSymmetry:

import IMP
import IMP.core
import IMP.atom
import IMP.container
import IMP.rmf
import RMF
import sys

IMP.setup_from_argv(sys.argv, "rigid bodies")

m = IMP.Model()
rbs = []
hs = []
for i in range(4):
    mp1 = IMP.atom.read_pdb(IMP.core.get_example_path('example_protein.pdb'), m)
    chains = IMP.atom.get_by_type(mp1, IMP.atom.CHAIN_TYPE)
    hs.append(IMP.atom.Hierarchy(chains[0]))
    rbs.append(IMP.atom.create_rigid_body(chains[0]))

for i, rb in enumerate(rbs[1:]):
    # the other 3 particles are all symmetric copies of the first
    IMP.core.Reference.setup_particle(rb, rbs[0])
    # the symmetry operation is rotation around the z axis
    tr = IMP.algebra.Transformation3D(
        IMP.algebra.get_rotation_about_axis(IMP.algebra.get_basis_vector_3d(2),
                                            2 * 3.14 / len(rbs) * (i + 1)),
        IMP.algebra.Vector3D(0, 0, 0))
    sm = IMP.core.TransformationSymmetry(tr)
    c = IMP.core.SingletonConstraint(sm, None, m, rb)
    m.add_score_state(c)

#crazy code block:
for rb in rbs:
    rb.update_members()
m.update()
for rb in rbs:
    rb.set_reference_frame(rb.get_reference_frame()) #this updates the members immediately too
m.update()
#end of the crazy code block

modelrmf = RMF.create_rmf_file('model.rmf')
IMP.rmf.add_hierarchies(modelrmf, hs)
IMP.rmf.save_frame(modelrmf)

[benmwebb]

The problem here is that TransformationSymmetry operates on the reference frame of the rigid body, and there is no guarantee that these are the same. The solution here is to use create_compatible_rigid_body() for all but the first rigid body. The resulting script looks like:

import IMP
import IMP.core
import IMP.atom
import IMP.container
import IMP.rmf
import RMF
import sys

IMP.setup_from_argv(sys.argv, "rigid bodies")

m = IMP.Model()
rbs = []
hs = []
for i in range(4):
    mp1 = IMP.atom.read_pdb(IMP.core.get_example_path('example_protein.pdb'), m)
    chains = IMP.atom.get_by_type(mp1, IMP.atom.CHAIN_TYPE)
    c = IMP.atom.Hierarchy(chains[0])
    if hs:
        rbs.append(IMP.atom.create_compatible_rigid_body(c, hs[0]))
    else:
        rbs.append(IMP.atom.create_rigid_body(c))
    hs.append(c)

for i, rb in enumerate(rbs[1:]):
    # the other 3 particles are all symmetric copies of the first
    IMP.core.Reference.setup_particle(rb, rbs[0])
    # the symmetry operation is rotation around the z axis
    tr = IMP.algebra.Transformation3D(
        IMP.algebra.get_rotation_about_axis(IMP.algebra.get_basis_vector_3d(2),
                                            2 * 3.14 / len(rbs) * (i + 1)),
        IMP.algebra.Vector3D(0, 0, 0))
    sm = IMP.core.TransformationSymmetry(tr)
    c = IMP.core.SingletonConstraint(sm, None, m, rb)
    m.add_score_state(c)

m.update()
modelrmf = RMF.create_rmf_file('model.rmf')
IMP.rmf.add_hierarchies(modelrmf, hs)
IMP.rmf.save_frame(modelrmf)