def test_relative_position_mover(self, ):
""" Test the RelativePositionMover """
log.info("test RelativePositionMover")
fn_rec1 = self.get_input_file_name("1suvA_xlinked.pdb")
fn_rec2 = self.get_input_file_name("1suvC_xlinked.pdb")
fn_lig = self.get_input_file_name("1suvE_xlinked.pdb")
fn_tr1 = \
self.get_input_file_name("transforms-1suvA-1suvE_reduced.txt")
fn_tr2 = \
self.get_input_file_name("transforms-1suvC-1suvE_filtered.txt")
m = IMP.kernel.Model()
sel = atom.ATOMPDBSelector()
h_rec1 = atom.read_pdb(fn_rec1, m, sel)
rb_rec1 = atom.create_rigid_body(h_rec1)
rec1_coords = [core.XYZ(l).get_coordinates()
for l in atom.get_leaves(h_rec1)]
h_rec2 = atom.read_pdb(fn_rec2, m, sel)
rb_rec2 = atom.create_rigid_body(h_rec2)
rec2_coords = [core.XYZ(l).get_coordinates()
for l in atom.get_leaves(h_rec2)]
h_ligand = atom.read_pdb(fn_lig, m, sel)
rb_lig = atom.create_rigid_body(h_ligand)
Ts = get_relative_transforms(fn_tr1)
Tis1 = []
for i, T in enumerate(Ts):
V = get_internal_transform3(T, rb_rec1, rb_lig)
Tis1.append(V)
docked_refs1 = get_docked_reference_frames(Ts, rb_lig)
Ts = get_relative_transforms(fn_tr2)
Tis2 = []
for i, T in enumerate(Ts):
V = get_internal_transform3(T, rb_rec2, rb_lig)
Tis2.append(V)
docked_refs2 = get_docked_reference_frames(Ts, rb_lig)
mv = em2d.RelativePositionMover(rb_lig, 10, 20)
mv.add_internal_transformations(rb_rec1, Tis1)
mv.add_internal_transformations(rb_rec2, Tis2)
for i in range(2):
# prob_random = 0
ref_before = rb_lig.get_reference_frame()
ps = mv.propose() # _move(prob_random)
ref_after = rb_lig.get_reference_frame()
found = False
current_coords = [core.XYZ(l).get_coordinates()
for l in atom.get_leaves(h_ligand)]
# check all possible reference frames where the ligand could be
for r in itertools.chain(docked_refs1, docked_refs2):
rb_lig.set_reference_frame(r)
docked_coords = [core.XYZ(l).get_coordinates()
for l in atom.get_leaves(h_ligand)]
rmsd = alg.get_rmsd(current_coords, docked_coords)
if rmsd < 0.1:
found = True
self.assertTrue(found, msg="the proposed move is not "
"in the relative solutions")
mv.accept()
def set_pdbs(self, fn_receptor, fn_ligand):
"""
Set the name of the PDB files of the receptor and the ligand
@param fn_receptor
@param fn_ligand
"""
sel = atom.ATOMPDBSelector()
self.m_receptor = IMP.kernel.Model()
self.h_receptor = atom.read_pdb(fn_receptor, self.m_receptor, sel)
self.m_ligand = IMP.kernel.Model()
self.h_ligand = atom.read_pdb(fn_ligand, self.m_ligand, sel)
def test_ccs_value(self):
"""Test the calculation of the collision cross section of a complex"""
IMP.set_log_level(IMP.TERSE)
m = IMP.Model()
fn = self.get_input_file_name("1z5s.pdb")
prot = atom.read_pdb(fn, m, atom.ATOMPDBSelector())
atom.add_radii(prot)
projections = 20
resolution = 7.0
pixel_size = 1.5
img_size = 80
ccs = em2d.CollisionCrossSection(projections, resolution, pixel_size,
img_size)
ccs.set_model_particles(IMP.atom.get_leaves(prot))
ccs_calculated = ccs.get_ccs()
ccs_value = 3838 # A**2
# good within 2%
self.assertAlmostEqual(ccs_calculated,
ccs_value,
delta=ccs_value * 0.02)
## \example em2d/collision_cross_section.py
# Example of how to compute the collision cross section of a molecule.
#
import IMP
import IMP.em2d as em2d
import IMP.atom as atom
"""
Example of how to compute the collision cross section of a molecule
"""
IMP.base.set_log_level(IMP.base.TERSE)
m = IMP.kernel.Model()
fn = em2d.get_example_path("1z5s.pdb")
prot = atom.read_pdb(fn, m, atom.ATOMPDBSelector())
atom.add_radii(prot)
projections = 20
resolution = 1.0
pixel_size = 1.5
img_size = 80
ccs = em2d.CollisionCrossSection(projections, resolution, pixel_size, img_size)
ccs.set_model_particles(IMP.atom.get_leaves(prot))
print "CCS", ccs.get_ccs(), "A**2"