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 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 get_residues_distance(hierarchy1, chain_id1, residue1,
hierarchy2, chain_id2, residue2):
"""
Distance between two residues. See the help for get_residue_particle()
@param hierarchy1
@param chain_id1
@param residue1
@param hierarchy2
@param chain_id2
@param residue2
"""
coords1 = get_residue_coordinates(hierarchy1, chain_id1, residue1)
coords2 = get_residue_coordinates(hierarchy2, chain_id2, residue2)
d = alg.get_distance(coords1, coords2)
return d
def get_residues_distance(hierarchy1, chain_id1, residue1, hierarchy2,
chain_id2, residue2):
"""
Distance between two residues. See the help for get_residue_particle()
@param hierarchy1
@param chain_id1
@param residue1
@param hierarchy2
@param chain_id2
@param residue2
"""
coords1 = get_residue_coordinates(hierarchy1, chain_id1, residue1)
coords2 = get_residue_coordinates(hierarchy2, chain_id2, residue2)
d = alg.get_distance(coords1, coords2)
return d
def get_xlinks_are_good(coords_rec, coords_lig, distances):
"""
Compare distances between points in coords_rec and coords_lig
@param coords_rec A set of Vector3D objects containing coordinates from
the receptor
@param coords_lig Coordinates from the ligand
@param distances The set of maximum distances for each pair of
(coord_rec, coord_lig)
@return True if all the distances between the pairs of coordinates are
below the thresholds contained in the argument "distances""
"""
for vi,vj,d in zip(coords_rec, coords_lig, distances):
if alg.get_distance(vi, vj) > d:
return False
return True
# rotate and translate the chains
for rbd in rigid_bodies:
# rotation
rotation= alg.get_random_rotation_3d()
transformation1=alg.get_rotation_about_point(rbd.get_coordinates(),rotation)
# translation
transformation2=alg.Transformation3D(alg.get_random_vector_in(bb))
# Apply
final_transformation = alg.compose(transformation1,transformation2)
core.transform(rbd,final_transformation)
print "Writing transformed assembly"
atom.write_pdb (prot,"1z5s-transformed.pdb")
# set distance restraints measusring some distances between rigid bodies
# for the solution.
d01 = alg.get_distance(native_chain_centers[0],native_chain_centers[1])
r01 = core.DistanceRestraint(core.Harmonic(d01,1),chains[0],chains[1])
r01.set_name("distance 0-1")
d12 = alg.get_distance(native_chain_centers[1],native_chain_centers[2])
r12 = core.DistanceRestraint(core.Harmonic(d12,1),chains[1],chains[2])
r12.set_name("distance 1-2")
d23 = alg.get_distance(native_chain_centers[2],native_chain_centers[3])
r23 = core.DistanceRestraint(core.Harmonic(d23,1),chains[2],chains[3])
r23.set_name("distance 2-3")
d30 = alg.get_distance(native_chain_centers[3],native_chain_centers[0])
r30 = core.DistanceRestraint(core.Harmonic(d30,1),chains[3],chains[0])
r30.set_name("distance 3-0")
print "Distances in the solution: d01 =", \
d01,"d12 =",d12,"d23 =",d23,"d30 =",d30
# set distance restraints
