def test_perturbed(self):
"""Test reading and writing particles"""
m= IMP.Model()
p0= IMP.Particle(m)
p1= IMP.Particle(m)
ik= IMP.IntKey("hi int")
fk= IMP.FloatKey("hi float")
p0.add_attribute(ik, 1)
p1.add_attribute(fk, 2.0)
p1.add_attribute(ik, 3)
name= self.get_tmp_file_name("particles.rmf")
rmf= RMF.create_rmf_file(name)
IMP.set_log_level(IMP.VERBOSE)
IMP.rmf.add_particles(rmf, [p0, p1])
IMP.rmf.save_frame(rmf, 0)
IMP.set_log_level(IMP.MEMORY)
onames= RMF.get_open_hdf5_handle_names()
print "before", onames
del rmf
IMP.set_log_level(IMP.VERBOSE)
onames= RMF.get_open_hdf5_handle_names()
print "closed", onames
self.assertEqual(len(onames), 0)
rmf= RMF.open_rmf_file_read_only(name)
bps= IMP.rmf.create_particles(rmf, m)
#IMP.rmf.load_frame(0)
self.assertEqual(len(bps), 2)
self.assertTrue(bps[0].has_attribute(ik))
self.assertEqual(bps[0].get_value(ik), 1);
self.assertTrue(bps[1].has_attribute(ik))
self.assertEqual(bps[1].get_value(ik), 3);
self.assertTrue(bps[1].has_attribute(fk))
self.assertEqual(bps[1].get_value(fk), 2.0);
def test_part1(self):
"""Test round trip 1"""
m= IMP.Model()
print "reading pdb"
h= IMP.atom.read_pdb(self.get_input_file_name("simple.pdb"), m,
IMP.atom.NonAlternativePDBSelector())
IMP.set_log_level(IMP.SILENT)
IMP.atom.add_bonds(h)
print "done"
IMP.set_log_level(IMP.VERBOSE)
print "writing hierarchy"
name=self.get_tmp_file_name("test_rt_parts.rmf")
f= RMF.create_rmf_file(name)
print f, type(f)
IMP.rmf.add_hierarchy(f, h)
del f
self.assertEqual( RMF.get_open_hdf5_handle_names(), [])
f= RMF.open_rmf_file_read_only(name)
print "reading"
print f, type(f)
h2=IMP.rmf.create_hierarchies(f, m)
self.assertEqual(len(h2), 1)
del f
m= IMP.Model()
print "reopening"
f= RMF.open_rmf_file_read_only(name)
print "reading"
h2=IMP.rmf.create_hierarchies(f, m)
def _test_round_trip(self, h0, name):
f= RMF.create_rmf_file(name)
IMP.rmf.add_hierarchy(f, h0)
IMP.rmf.save_frame(f, 0)
del f
self.assertEqual( RMF.get_open_hdf5_handle_names(), [])
f= RMF.open_rmf_file(name)
h1= IMP.rmf.create_hierarchies(f, h0.get_model())
IMP.rmf.load_frame(f, 0)
self._assert_same(h0, h1[0])
def test_perturbed(self):
"""Test closing an RMF file"""
f= RMF.create_rmf_file(self.get_tmp_file_name("test_file.rmf"))
r= f.get_root_node()
print r.get_type()
sc= f.add_category("sequence")
ik= f.add_int_key(sc, "ik0", True)
r.set_value(ik, 1, 0)
del r
del f
del ik
del sc
names= RMF.get_open_hdf5_handle_names()
print names
self.assertEqual(len(names), 0)
def test_navigation(self):
"""Test that navigation of read hierarchies works"""
m= IMP.Model()
print "reading pdb"
h= IMP.atom.read_pdb(self.get_input_file_name("simple.pdb"), m,
IMP.atom.NonAlternativePDBSelector())
IMP.set_log_level(IMP.SILENT)
IMP.atom.add_bonds(h)
name=self.get_tmp_file_name("test_large_nav.rmf")
f= RMF.create_rmf_file(name)
IMP.rmf.add_hierarchy(f, h)
del f
self.assertEqual( RMF.get_open_hdf5_handle_names(), [])
f= RMF.open_rmf_file(name)
h1= IMP.rmf.create_hierarchies(f, m)
res= IMP.atom.get_by_type(h1[0], IMP.atom.RESIDUE_TYPE)
nres= IMP.atom.get_next_residue(IMP.atom.Residue(res[0]))
def test_navigation(self):
"""Test loading and saving of rigid bodies implicitly"""
m= IMP.Model()
r= IMP.atom.Hierarchy.setup_particle(IMP.Particle(m))
r.set_name("rt")
rbd= IMP.core.RigidBody.setup_particle(IMP.Particle(m, "rb"), IMP.algebra.ReferenceFrame3D())
for i in range(0,3):
p = IMP.Particle(m)
v= IMP.algebra.Vector3D(0,0,0)
v[i]=1
d=IMP.core.XYZR.setup_particle(p)
d.set_coordinates(v)
d.set_radius(.5)
IMP.atom.Mass.setup_particle(p, .1)
r.add_child(IMP.atom.Hierarchy.setup_particle(p))
rbd.add_member(p)
fn= self.get_tmp_file_name("rigid_implicit.rmf")
f= RMF.create_rmf_file(fn)
IMP.rmf.add_hierarchies(f, [r])
IMP.rmf.save_frame(f, 0)
frames=[rbd.get_reference_frame()]
for i in range(0,10):
bb= IMP.algebra.get_unit_bounding_box_3d()
tr= IMP.algebra.Transformation3D(IMP.algebra.get_random_rotation_3d(),
IMP.algebra.get_random_vector_in(bb))
rf=IMP.algebra.ReferenceFrame3D(tr)
rbd.set_reference_frame(rf)
frames.append(rf)
m.update()
IMP.rmf.save_frame(f, i+1)
del f
self.assertEqual( RMF.get_open_hdf5_handle_names(), [])
f= RMF.open_rmf_file(fn)
r2=IMP.rmf.create_hierarchies(f, m)[0]
self.assert_(IMP.core.RigidMember.particle_is_instance(r2.get_child(0)))
print frames
for i in range(0,11):
IMP.rmf.load_frame(f, i)
print rbd.get_reference_frame()
for j, c in enumerate(r2.get_children()):
oc= IMP.core.XYZ(c).get_coordinates()
m.update()
nc= IMP.core.XYZ(c).get_coordinates()
self.assertAlmostEqual((oc-nc).get_magnitude(), 0,
delta=.1)
def test_rt(self):
"""Test round trip"""
m= IMP.Model()
print "reading pdb"
name=self.get_tmp_file_name("test_round_trip.rmf")
h= IMP.atom.read_pdb(self.get_input_file_name("simple.pdb"), m,
IMP.atom.NonAlternativePDBSelector())
IMP.set_log_level(IMP.SILENT)
IMP.atom.add_bonds(h)
print "done"
IMP.set_log_level(IMP.VERBOSE)
print "writing hierarchy"
f= RMF.create_rmf_file(name)
IMP.rmf.add_hierarchy(f, h)
IMP.rmf.save_frame(f, 0)
print "reopening"
del f
self.assertEqual( RMF.get_open_hdf5_handle_names(), [])
print "after closing"
#print RMF.get_open_hdf5_handle_names()
f= RMF.open_rmf_file_read_only(name)
print "reading"
print f, type(f)
h2=IMP.rmf.create_hierarchies(f, m)
IMP.rmf.load_frame(f,0)
IMP.atom.show_molecular_hierarchy(h2[0])
print "checking"
self.assertEqual(len(h2), 1)
self.assertEqual(len(IMP.atom.get_leaves(h)),
len(IMP.atom.get_leaves(h2[0])))
self.assertAlmostEqual(IMP.atom.get_mass(h),
IMP.atom.get_mass(h2[0]), delta=1e-4)
if hasattr(IMP.atom, 'get_surface_area'):
self.assertAlmostEqual(IMP.atom.get_surface_area(h),
IMP.atom.get_surface_area(h2[0]), delta=1e-4)
self.assertAlmostEqual(IMP.atom.get_volume(h),
IMP.atom.get_volume(h2[0]), delta=1e-4)
