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 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 read_component(model, fn_pdb, name=False):
""" Read a PDB molecule, add atoms, and set a name
"""
if name:
log.debug("reading component %s from %s", name, fn_pdb)
else:
log.debug("reading component from %s", fn_pdb)
hierarchy = atom.read_pdb(fn_pdb, model,
atom.NonWaterNonHydrogenPDBSelector())
if name:
hierarchy.set_name(name)
atom.add_radii(hierarchy)
return hierarchy
def test_filter_transformations(self):
"""
Check if the filtered conformation are the conformations that I
computed before
"""
try:
import subprocess
import IMP.em2d.buildxlinks as bx
except ImportError as e:
self.skipTest(str(e))
dock = self.import_python_application('emagefit_dock')
sel = atom.NonWaterNonHydrogenPDBSelector()
ligand = IMP.kernel.Model()
fn_ligand = self.get_input_file_name("3sfdB-3sfdA_initial_docking.pdb")
h_ligand = atom.read_pdb(fn_ligand, ligand, sel)
rb_ligand = atom.create_rigid_body(h_ligand)
receptor = IMP.kernel.Model()
fn_receptor = self.get_input_file_name("3sfdB.pdb")
h_receptor = atom.read_pdb(fn_receptor, receptor, sel)
# read_hex_transformations
fn = self.get_input_file_name("hex_solutions_3sfdB-3sfdA.txt")
residue_receptor = 23
residue_ligand = 456
distance = 30
xl = bx.Xlink("3sfdB", "B", residue_receptor, "3sfdA", "A",
residue_ligand, distance)
xlinks_list = [xl]
fn_filtered = "filtered_transforms.txt"
dock.filter_docking_results(h_receptor, h_ligand, xlinks_list, fn,
fn_filtered)
fn_stored = self.get_input_file_name(
"hex_solutions_3sfdB-3sfdA_filtered.txt")
filtered = dock.read_hex_transforms(fn_filtered)
stored = dock.read_hex_transforms(fn_stored)
# check that the filtered transforms match the stored ones
self.assertEqual(len(filtered), len(stored))
for Tf, Ts in zip(filtered, stored):
tf = Tf.get_translation()
ts = Ts.get_translation()
qf = Tf.get_rotation().get_quaternion()
qs = Ts.get_rotation().get_quaternion()
for k in range(3):
self.assertAlmostEqual(tf[k], ts[k])
for k in range(4):
self.assertAlmostEqual(qf[k], qs[k])
os.remove(fn_filtered)