def test_docking_one_crosslink(self):
"""
Test the initial docking that is done based on minimizing the
distances of the cross-linking restraints
"""
mydock = bx.InitialDockingFromXlinks()
xl = self.xlinks.get_xlinks_for_pair(("3sfdB", "3sfdA"))
mydock.set_xlinks(xl)
self.assertEqual(len(mydock.xlinks_list), 1)
mydock.clear_xlinks()
self.assertEqual(len(mydock.xlinks_list), 0)
model = IMP.kernel.Model()
fn_receptor = self.get_input_file_name("3sfdB.pdb")
h_receptor = atom.read_pdb(fn_receptor, model,
atom.NonWaterNonHydrogenPDBSelector())
fn_ligand = self.get_input_file_name("3sfdA.pdb")
h_ligand = atom.read_pdb(fn_ligand, model,
atom.NonWaterNonHydrogenPDBSelector())
mydock.set_xlinks(xl)
mydock.set_hierarchies(h_receptor, h_ligand)
p = IMP.kernel.Particle(model)
core.RigidBody.setup_particle(p, atom.get_leaves(h_receptor))
rb_receptor = core.RigidBody(p)
p = IMP.kernel.Particle(model)
core.RigidBody.setup_particle(p, atom.get_leaves(h_ligand))
rb_ligand = core.RigidBody(p)
mydock.set_rigid_bodies(rb_receptor, rb_ligand)
mydock.move_ligand()
c1 = mydock.get_residue_coordinates(h_ligand, "A", 456)
c2 = mydock.get_residue_coordinates(h_receptor, "B", 23)
dist = alg.get_distance(c1, c2)
self.assertLessEqual(dist, self.max_distance)
def test_docking_multiple_crosslinks(self):
"""
Test the initial docking that is done based on minimizing the
distances of the cross-linking restraints
"""
mydock = bx.InitialDockingFromXlinks()
xl = self.xlinks.get_xlinks_for_pair(("3sfdC", "3sfdD"))
mydock.set_xlinks(xl)
model = IMP.kernel.Model()
fn_receptor = self.get_input_file_name("3sfdC.pdb")
h_receptor = atom.read_pdb(fn_receptor, model,
atom.NonWaterNonHydrogenPDBSelector())
fn_ligand = self.get_input_file_name("3sfdD.pdb")
h_ligand = atom.read_pdb(fn_ligand, model,
atom.NonWaterNonHydrogenPDBSelector())
mydock.set_hierarchies(h_receptor, h_ligand)
p = IMP.kernel.Particle(model)
core.RigidBody.setup_particle(p, atom.get_leaves(h_receptor))
rb_receptor = core.RigidBody(p)
p = IMP.kernel.Particle(model)
core.RigidBody.setup_particle(p, atom.get_leaves(h_ligand))
rb_ligand = core.RigidBody(p)
mydock.set_rigid_bodies(rb_receptor, rb_ligand)
mydock.move_ligand()
for res1, res2 in zip([9, 78], [37, 128]):
c1 = mydock.get_residue_coordinates(h_receptor, "C", res1)
c2 = mydock.get_residue_coordinates(h_ligand, "D", res2)
dist = alg.get_distance(c1, c2)
self.assertLessEqual(dist, self.max_distance + 4.0)
def create_rigid_bodies(assembly):
""" set the children of a molecule type hierarchy as rigid bodies
In this case, all the children are the components of the complex.
I use the function create_rigid_body(), that creates a lot of
sub-rigid bodies.
I have changed the function and now build the rigid body directly from
the leaves of each of the components. With this I guarantee that the
number of rigid members is going to be the same if the components have
the same number of atoms.
"""
molecule = assembly.get_as_molecule()
if (not molecule.get_is_valid(True)):
raise TypeError("create_rigid_bodies(): The argument is not a valid "
"hierarchy")
rbs = []
for c in molecule.get_children():
p = IMP.kernel.Particle(c.get_model())
core.RigidBody.setup_particle(p, atom.get_leaves(c))
rb = core.RigidBody(p)
# rb = atom.create_rigid_body(c)
rb.set_name(get_rb_name(c.get_name()))
rbs.append(rb)
return rbs