def test_drms(self):
""" Test drms measure """
m = IMP.Model()
sel = atom.CAlphaPDBSelector()
prot1 = atom.read_pdb(self.open_input_file("mini.pdb"), m, sel)
prot2 = atom.read_pdb(self.open_input_file("mini.pdb"), m, sel)
xyzs1 = core.XYZs(atom.get_leaves(prot1))
xyzs2 = core.XYZs(atom.get_leaves(prot2))
drms = atom.get_drms(xyzs1, xyzs2)
# Molecule with itself
self.assertAlmostEqual(drms, 0)
R = IMP.algebra.get_random_rotation_3d()
v = IMP.algebra.get_random_vector_in(
IMP.algebra.get_unit_bounding_box_3d())
T = IMP.algebra.Transformation3D(R, v)
for x in xyzs2:
core.transform(x, T)
drms = atom.get_drms(xyzs1, xyzs2)
# Same thing after transformation
self.assertAlmostEqual(drms, 0)
#
for x in xyzs2:
R = IMP.algebra.get_random_rotation_3d()
T = IMP.algebra.Transformation3D(R, v)
core.transform(x, T)
drms = atom.get_drms(xyzs1, xyzs2)
self.assertTrue(drms > 0)
def test__rigid_bodies_drmsd_Q(self):
""" Test drmsd_Q measure"""
m = IMP.Model()
sel = atom.CAlphaPDBSelector()
prot1 = atom.read_pdb(self.open_input_file("mini.pdb"), m, sel)
prot2 = atom.read_pdb(self.open_input_file("mini.pdb"), m, sel)
xyzs1 = core.XYZs(atom.get_leaves(prot1))
xyzs2 = core.XYZs(atom.get_leaves(prot2))
R = IMP.algebra.get_random_rotation_3d()
v = IMP.algebra.get_random_vector_in(
IMP.algebra.get_unit_bounding_box_3d())
T = IMP.algebra.Transformation3D(R, v)
for x in xyzs2:
core.transform(x, T)
thresholds = [10, 20, 30, 40, 60]
for threshold in thresholds:
#
for x in xyzs2:
R = IMP.algebra.get_random_rotation_3d()
T = IMP.algebra.Transformation3D(R, v)
core.transform(x, T)
# test that the function is correctly implemented
drmsd = 0.
npairs = 0.
for i in range(0, len(xyzs1) - 1):
for j in range(i + 1, len(xyzs2)):
dist0 = IMP.core.get_distance(xyzs1[i], xyzs1[j])
dist1 = IMP.core.get_distance(xyzs2[i], xyzs2[j])
if dist0 <= threshold or dist1 <= threshold:
drmsd += (dist0 - dist1)**2
npairs += 1.
drmsd = math.sqrt(drmsd / npairs)
drmsd_target = atom.get_drmsd_Q(xyzs1, xyzs2, threshold)
self.assertAlmostEqual(drmsd, drmsd_target)
drmsd_Q = atom.get_drmsd_Q(xyzs1, xyzs2, 1000000.0)
drmsd = atom.get_drmsd(xyzs1, xyzs2)
self.assertAlmostEqual(drmsd, drmsd_Q)
def test__rigid_bodies_drmsd(self):
""" Test drmsd measure"""
m = IMP.Model()
sel = atom.CAlphaPDBSelector()
prot1 = atom.read_pdb(self.open_input_file("mini.pdb"), m, sel)
prot2 = atom.read_pdb(self.open_input_file("mini.pdb"), m, sel)
xyzs1 = core.XYZs(atom.get_leaves(prot1))
xyzs2 = core.XYZs(atom.get_leaves(prot2))
drmsd = atom.get_drmsd(xyzs1, xyzs2)
# Molecule with itself
self.assertAlmostEqual(drmsd, 0)
R = IMP.algebra.get_random_rotation_3d()
v = IMP.algebra.get_random_vector_in(
IMP.algebra.get_unit_bounding_box_3d())
T = IMP.algebra.Transformation3D(R, v)
for x in xyzs2:
core.transform(x, T)
drmsd = atom.get_drmsd(xyzs1, xyzs2)
# Same thing after transformation
self.assertAlmostEqual(drmsd, 0)
#
for x in xyzs2:
R = IMP.algebra.get_random_rotation_3d()
T = IMP.algebra.Transformation3D(R, v)
core.transform(x, T)
# test that the function is correctly implemented
drmsd = 0.
npairs = 0.
for i in range(0, len(xyzs1) - 1):
for j in range(i + 1, len(xyzs2)):
dist0 = IMP.core.get_distance(xyzs1[i], xyzs1[j])
dist1 = IMP.core.get_distance(xyzs2[i], xyzs2[j])
drmsd += (dist0 - dist1)**2
npairs += 1.
drmsd1 = math.sqrt(drmsd / npairs)
drmsd2 = atom.get_drmsd(xyzs1, xyzs2)
self.assertAlmostEqual(drmsd1, drmsd2)
def test__rigid_bodies_drms(self):
""" Test drms measure taking into account rigid bodies"""
m = IMP.kernel.Model()
sel = atom.CAlphaPDBSelector()
prot1 = atom.read_pdb(self.open_input_file("mini.pdb"), m, sel)
prot2 = atom.read_pdb(self.open_input_file("mini.pdb"), m, sel)
hchains1 = atom.get_by_type(prot1, atom.CHAIN_TYPE)
hchains2 = atom.get_by_type(prot2, atom.CHAIN_TYPE)
xyzs1 = core.XYZs(atom.get_leaves(prot1))
xyzs2 = core.XYZs(atom.get_leaves(prot2))
x = 0
ranges = []
for h in hchains1:
ls1 = (atom.get_leaves(h))
y = x + len(ls1)
ranges.append((x, y))
x = y
drms = atom.get_drms(xyzs1, xyzs2)
rb_drms = atom.get_rigid_bodies_drms(xyzs1, xyzs2, ranges)
self.assertAlmostEqual(rb_drms, 0)
self.assertAlmostEqual(
drms,
rb_drms,
delta=1e-3,
msg="rb_drms != drms")
# Same thing after transformation of each of the chains
for h in hchains2:
R = alg.get_random_rotation_3d()
v = alg.get_random_vector_in(alg.get_unit_bounding_box_3d())
T = alg.Transformation3D(R, v)
ls = atom.get_leaves(h)
for l in ls:
core.transform(l.get_as_xyz(), T)
drms = atom.get_drms(xyzs1, xyzs2)
rb_drms = atom.get_rigid_bodies_drms(xyzs1, xyzs2, ranges)
self.assertAlmostEqual(drms, rb_drms, delta=0.3, msg="rb_drms != drms")