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 get_drms_for_backbone(assembly, native_assembly):
"""
Measure the DRMS ob the backbone between two assemblies.
@param assembly The DRMS is computed for this assembly
@param native_assembly The assembly that acts as a reference
Notes:
1) The components of the assembly can be proteins or nucleic acids
2) If a protein, the c-alphas are used for calculating the drms
3) If a nucleic acid, the backbone of C4' atoms is used
4) The chains are treated as rigid bodies to speed the calculation.
WARNING: if the function fails with a segmentation fault, one of the
possible problems is that IMP reads some HETATM as calphas. Check that
the chain does not have heteroatoms.
"""
begin_range = 0
ranges = []
backbone = []
h_chains = atom.get_by_type(assembly, atom.CHAIN_TYPE)
for h in h_chains:
atoms = representation.get_backbone(h)
backbone.extend(atoms)
end_range = begin_range + len(atoms)
ranges.append((begin_range, end_range ))
begin_range = end_range
# log.debug("Ranges %s number of CA %s", ranges, len(calphas1))
xyzs = [core.XYZ(l) for l in backbone]
native_chains = atom.get_by_type(native_assembly, atom.CHAIN_TYPE)
native_backbone = []
for h in native_chains:
native_backbone.extend( representation.get_backbone(h))
native_xyzs = [core.XYZ(l) for l in native_backbone]
if(len(xyzs) != len(native_xyzs)):
raise ValueError(
"Cannot compute DRMS for sets of atoms of different size")
drms = atom.get_rigid_bodies_drms(xyzs, native_xyzs, ranges)
if(drms < 0 or math.isnan(drms) or drms > 100):
log.debug("len(xyzs) = %s. len(native_xyzs) = %s",len(xyzs), len(native_xyzs))
log.debug("drms = %s",drms)
atom.write_pdb(native_assembly, "drms_filtering_calphas.pdb")
raise ValueError("There is a problem with the drms")
return drms
def get_drms_for_backbone(assembly, native_assembly):
"""
Measure the DRMS ob the backbone between two assemblies.
@param assembly The DRMS is computed for this assembly
@param native_assembly The assembly that acts as a reference
Notes:
1) The components of the assembly can be proteins or nucleic acids
2) If a protein, the c-alphas are used for calculating the drms
3) If a nucleic acid, the backbone of C4' atoms is used
4) The chains are treated as rigid bodies to speed the calculation.
WARNING: if the function fails with a segmentation fault, one of the
possible problems is that IMP reads some HETATM as calphas. Check that
the chain does not have heteroatoms.
"""
log.debug("Measuring DRMS of the backbone")
begin_range = 0
ranges = []
backbone = []
h_chains = atom.get_by_type(assembly, atom.CHAIN_TYPE)
for h in h_chains:
atoms = representation.get_backbone(h)
""""
for a in atoms:
print "atom ===> ",
at = atom.Atom(a)
hr = at.get_parent()
res = atom.Residue(hr)
ch = atom.Chain(h)
ch.show()
print " - ",
res.show()
print " - ",
at.show()
print ""
"""
backbone.extend(atoms)
end_range = begin_range + len(atoms)
ranges.append((begin_range, end_range))
begin_range = end_range
log.debug("Ranges %s number of atoms %s", ranges, len(backbone))
xyzs = [core.XYZ(l) for l in backbone]
native_chains = atom.get_by_type(native_assembly, atom.CHAIN_TYPE)
names = [atom.Chain(ch).get_id() for ch in native_chains]
native_backbone = []
for h in native_chains:
native_backbone.extend(representation.get_backbone(h))
native_xyzs = [core.XYZ(l) for l in native_backbone]
if len(xyzs) != len(native_xyzs):
raise ValueError(
"Cannot compute DRMS for sets of atoms of different size")
log.debug("Getting rigid bodies rmsd")
drms = atom.get_rigid_bodies_drms(xyzs, native_xyzs, ranges)
if drms < 0 or math.isnan(drms): # or drms > 100:
log.debug(
"len(xyzs) = %s. len(native_xyzs) = %s",
len(xyzs),
len(native_xyzs))
log.debug("drms = %s", drms)
atom.write_pdb(assembly, "drms_model_calphas.pdb")
atom.write_pdb(native_assembly, "drms_native_calphas.pdb")
raise ValueError("There is a problem with the drms. I wrote the pdbs "
"for you: drms_model_calphas.pdb drms_native_calphas.pdb")
return drms
def get_drms_for_backbone(assembly, native_assembly):
"""
Measure the DRMS ob the backbone between two assemblies.
@param assembly The DRMS is computed for this assembly
@param native_assembly The assembly that acts as a reference
Notes:
1) The components of the assembly can be proteins or nucleic acids
2) If a protein, the c-alphas are used for calculating the drms
3) If a nucleic acid, the backbone of C4' atoms is used
4) The chains are treated as rigid bodies to speed the calculation.
WARNING: if the function fails with a segmentation fault, one of the
possible problems is that IMP reads some HETATM as calphas. Check that
the chain does not have heteroatoms.
"""
log.debug("Measuring DRMS of the backbone")
begin_range = 0
ranges = []
backbone = []
h_chains = atom.get_by_type(assembly, atom.CHAIN_TYPE)
for h in h_chains:
atoms = representation.get_backbone(h)
""""
for a in atoms:
print "atom ===> ",
at = atom.Atom(a)
hr = at.get_parent()
res = atom.Residue(hr)
ch = atom.Chain(h)
ch.show()
print " - ",
res.show()
print " - ",
at.show()
print ""
"""
backbone.extend(atoms)
end_range = begin_range + len(atoms)
ranges.append((begin_range, end_range))
begin_range = end_range
log.debug("Ranges %s number of atoms %s", ranges, len(backbone))
xyzs = [core.XYZ(l) for l in backbone]
native_chains = atom.get_by_type(native_assembly, atom.CHAIN_TYPE)
names = [atom.Chain(ch).get_id() for ch in native_chains]
native_backbone = []
for h in native_chains:
native_backbone.extend(representation.get_backbone(h))
native_xyzs = [core.XYZ(l) for l in native_backbone]
if len(xyzs) != len(native_xyzs):
raise ValueError(
"Cannot compute DRMS for sets of atoms of different size")
log.debug("Getting rigid bodies rmsd")
drms = atom.get_rigid_bodies_drms(xyzs, native_xyzs, ranges)
if drms < 0 or math.isnan(drms): # or drms > 100:
log.debug(
"len(xyzs) = %s. len(native_xyzs) = %s",
len(xyzs),
len(native_xyzs))
log.debug("drms = %s", drms)
atom.write_pdb(assembly, "drms_model_calphas.pdb")
atom.write_pdb(native_assembly, "drms_native_calphas.pdb")
raise ValueError("There is a problem with the drms. I wrote the pdbs "
"for you: drms_model_calphas.pdb drms_native_calphas.pdb")
return drms