def test_gaussian_rb(self):
mdl = IMP.Model()
s, m1, m2, m3 = self.init_topology_densities(mdl)
densities = [r.get_hierarchy() for r in m3.get_non_atomic_residues()]
gem_xtal = IMP.pmi.restraints.em.GaussianEMRestraint(
densities,
self.get_input_file_name('prot_gmm.txt'),
target_is_rigid_body=True)
gem_xtal.get_restraint_set().set_was_used(True)
em_rb = gem_xtal.get_rigid_body()
em_rb.set_coordinates_are_optimized(False)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
movers, rb = dof.create_rigid_body(em_rb)
# Check assigning of names to existing rigid bodies
self.assertEqual(movers[0].get_name(), 'created rigid body')
movers, rb = dof.create_rigid_body(em_rb, name='foo')
self.assertEqual(movers[0].get_name(), 'foo')
self.assertTrue(em_rb in dof.get_rigid_bodies())
self.assertEqual(len(dof.get_rigid_bodies()), 2)
self.assertTrue(em_rb.get_coordinates_are_optimized())
self.assertEqual(len(dof.get_movers()), 2)
def test_gaussian_rb(self):
mdl = IMP.Model()
m1, m2, m3 = self.init_topology_densities(mdl)
densities = [r.get_hierarchy() for r in m3.get_non_atomic_residues()]
gem_xtal = IMP.pmi.restraints.em.GaussianEMRestraint(densities,
self.get_input_file_name('prot_gmm.txt'),
target_is_rigid_body=True)
em_rb = gem_xtal.get_rigid_body()
em_rb.set_coordinates_are_optimized(False)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
dof.create_rigid_body(em_rb)
self.assertTrue(em_rb in dof.get_rigid_bodies())
self.assertEqual(len(dof.get_rigid_bodies()), 1)
self.assertTrue(em_rb.get_coordinates_are_optimized())
self.assertEqual(len(dof.get_movers()), 1)
def test_gaussian_rb(self):
mdl = IMP.Model()
m1, m2, m3 = self.init_topology_densities(mdl)
densities = [r.get_hierarchy() for r in m3.get_non_atomic_residues()]
gem_xtal = IMP.pmi.restraints.em.GaussianEMRestraint(
densities,
self.get_input_file_name('prot_gmm.txt'),
target_is_rigid_body=True)
em_rb = gem_xtal.get_rigid_body()
em_rb.set_coordinates_are_optimized(False)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
dof.create_rigid_body(em_rb)
self.assertTrue(em_rb in dof.get_rigid_bodies())
self.assertEqual(len(dof.get_rigid_bodies()), 1)
self.assertTrue(em_rb.get_coordinates_are_optimized())
self.assertEqual(len(dof.get_movers()), 1)
def test_gaussian_rb(self):
mdl = IMP.Model()
s, m1, m2, m3 = self.init_topology_densities(mdl)
densities = [r.get_hierarchy() for r in m3.get_non_atomic_residues()]
gem_xtal = IMP.pmi.restraints.em.GaussianEMRestraint(densities,
self.get_input_file_name('prot_gmm.txt'),
target_is_rigid_body=True)
gem_xtal.get_restraint_set().set_was_used(True)
em_rb = gem_xtal.get_rigid_body()
em_rb.set_coordinates_are_optimized(False)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
movers, rb = dof.create_rigid_body(em_rb)
# Check assigning of names to existing rigid bodies
self.assertEqual(movers[0].get_name(), 'created rigid body')
movers, rb = dof.create_rigid_body(em_rb, name='foo')
self.assertEqual(movers[0].get_name(), 'foo')
self.assertTrue(em_rb in dof.get_rigid_bodies())
self.assertEqual(len(dof.get_rigid_bodies()), 2)
self.assertTrue(em_rb.get_coordinates_are_optimized())
self.assertEqual(len(dof.get_movers()), 2)
def test_shuffle(self):
"""Test moving rbs, fbs"""
mdl = IMP.Model()
s = IMP.pmi.topology.System(mdl)
seqs = IMP.pmi.topology.Sequences(self.get_input_file_name('chainA.fasta'))
st1 = s.create_state()
mol = st1.create_molecule("GCP2_YEAST",sequence=seqs["GCP2_YEAST"][:100],chain_id='A')
atomic_res = mol.add_structure(self.get_input_file_name('chainA.pdb'),
chain_id='A',
res_range=(1,100))
mol.add_representation(mol.get_atomic_residues(),resolutions=[10])
mol.add_representation(mol.get_non_atomic_residues(), resolutions=[10])
hier = s.build()
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
dof.create_rigid_body(mol, nonrigid_parts=mol.get_non_atomic_residues())
rbs = dof.get_rigid_bodies()
IMP.pmi.tools.shuffle_configuration(hier)
def test_shuffle(self):
"""Test moving rbs, fbs"""
mdl = IMP.Model()
s = IMP.pmi.topology.System(mdl)
seqs = IMP.pmi.topology.Sequences(
self.get_input_file_name('chainA.fasta'))
st1 = s.create_state()
mol = st1.create_molecule("GCP2_YEAST",
sequence=seqs["GCP2_YEAST"][:100],
chain_id='A')
atomic_res = mol.add_structure(self.get_input_file_name('chainA.pdb'),
chain_id='A',
res_range=(1, 100))
mol.add_representation(mol.get_atomic_residues(), resolutions=[10])
mol.add_representation(mol.get_non_atomic_residues(), resolutions=[10])
hier = s.build()
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
dof.create_rigid_body(mol,
nonrigid_parts=mol.get_non_atomic_residues())
rbs = dof.get_rigid_bodies()
IMP.pmi.tools.shuffle_configuration(hier)
output_objects.append(crA)
sample_objects.append(crA)
crs.append(crA)
atomic = mol.get_atomic_residues()
dof.create_rigid_body(atomic,
max_trans=0,
max_rot=0,
resolution='all')
dof.create_flexible_beads(mol.get_non_atomic_residues(),
max_trans=1.0,
resolution=1)
active_tri_mol.append(mol)
# ______Composite Restraint for Fibril___________________________________________________________________
shuffle_exclude_rbs = dof.get_rigid_bodies()[:-1]
# Constrain the fibril trimer unit copies with z-trans. symmetry ### This is very important
for i in range(0, len(chains)):
for t in range(0, len(fibril_transforms)):
threefold_trans = fibril_transforms[t]
dof.constrain_symmetry(protofil_mols[i][0], protofil_mols[i][t + 1], threefold_trans)
mdl.update()
print("||||| All sym constraints added |||||")
# Write a single-frame RMF to view the system
out = IMP.pmi.output.Output()
out.init_rmf("symmetry_test1.rmf3", hierarchies=[root_hier])
out.write_rmf("symmetry_test1.rmf3")