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_drms(self):
""" Test drms measure """
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)
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_drms(self):
""" Test drms measure taking into account rigid bodies"""
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)
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")
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")
def measure_model(assembly, native_assembly, rbs, native_rbs):
"""
Get the drms, cdrms and crmsd for a model
@param assembly Hierachy for an assembly
@param native_assembly Hierarchy of the native structure
@param rbs Rigid bodies for the components of the assembly
@param native_rbs Rigid bodies for the components of the native
structure
@return cdrms, cdrms, crmsd
- drms - typical drms measure
- cdrms - drms for the centroids of the rigid bodies of the components
of the assembly
- crmsd - rmsd for the centroids
"""
drms = comparisons.get_drms_for_backbone(assembly, native_assembly)
RFs = [rb.get_reference_frame() for rb in rbs]
vs = [r.get_transformation_to().get_translation() for r in RFs]
nRFs = [rb.get_reference_frame() for rb in native_rbs]
nvs = [r.get_transformation_to().get_translation() for r in nRFs]
cdrms = atom.get_drms(vs, nvs)
crmsd, RFs = alignments.align_centroids_using_pca(RFs, nRFs)
log.debug("drms %s cdrms %s crmsd %s",drms,cdrms,crmsd)
return [drms, cdrms, crmsd]
def measure_model(assembly, native_assembly, rbs, native_rbs):
"""
Get the drms, cdrms and crmsd for a model
@param assembly Hierarchy for an assembly
@param native_assembly Hierarchy of the native structure
@param rbs Rigid bodies for the components of the assembly
@param native_rbs Rigid bodies for the components of the native
structure
@return cdrms, cdrms, crmsd
- drms - typical drms measure
- cdrms - drms for the centroids of the rigid bodies of the components
of the assembly
- crmsd - rmsd for the centroids
"""
log.debug("Measure model")
drms = comparisons.get_drms_for_backbone(assembly, native_assembly)
RFs = [rb.get_reference_frame() for rb in rbs]
vs = [r.get_transformation_to().get_translation() for r in RFs]
nRFs = [rb.get_reference_frame() for rb in native_rbs]
nvs = [r.get_transformation_to().get_translation() for r in nRFs]
cdrms = atom.get_drms(vs, nvs)
crmsd, RFs = alignments.align_centroids_using_pca(RFs, nRFs)
log.debug("drms %s cdrms %s crmsd %s", drms, cdrms, crmsd)
return [drms, cdrms, crmsd]
