def test_wrap_fragments(self, u, center):
ag = u.atoms[:250]
ag.wrap(compound='fragments', center=center)
if center == 'com':
ctrpos = ag.center_of_mass(pbc=False, compound='fragments')
elif center == 'cog':
ctrpos = ag.center_of_geometry(pbc=False, compound='fragments')
assert_in_box(ctrpos, u.dimensions)
def test_wrap_residues(self, u, center):
ag = u.atoms[300:400].residues
ag.wrap(compound='residues', center=center)
if center == 'com':
ctrpos = ag.center_of_mass(pbc=False, compound='residues')
elif center == 'cog':
ctrpos = ag.center_of_geometry(pbc=False, compound='residues')
assert_in_box(ctrpos, u.dimensions)
def test_wrap_pass(self, level, compound, center, is_triclinic):
# get a pristine test universe:
u = UnWrapUniverse(is_triclinic=is_triclinic)
group = u.atoms
# select topology level:
if level == 'residues':
group = group.residues
elif level == 'segments':
group = group.segments
# store original positions:
orig_pos = group.atoms.positions
# get the expected result:
ref_wrapped_pos = u.wrapped_coords(compound, center)
# first, do the wrapping out-of-place:
wrapped_pos = group.wrap(compound=compound, center=center,
inplace=False)
# check for correct result:
assert_almost_equal(wrapped_pos, ref_wrapped_pos,
decimal=self.precision)
# make sure atom positions are unchanged:
assert_array_equal(group.atoms.positions, orig_pos)
# now, do the wrapping inplace:
wrapped_pos2 = group.wrap(compound=compound, center=center,
inplace=True)
# check that result is the same as for out-of-place computation:
assert_array_equal(wrapped_pos, wrapped_pos2)
# check that wrapped positions are applied:
assert_array_equal(group.atoms.positions, wrapped_pos)
# check that nobody messed with the reference positions,
# centers of compounds must lie within the primary unit cell:
if compound == 'atoms':
assert_in_box(group.atoms.positions, group.dimensions)
elif center == 'com':
compos = group.atoms.center_of_mass(pbc=False, compound=compound)
assert_in_box(compos, group.dimensions)
else:
cogpos = group.atoms.center_of_geometry(pbc=False,
compound=compound)
assert_in_box(cogpos, group.dimensions)
def test_wrap_atoms(self, u):
ag = u.atoms[100:200]
rescom = ag.wrap(compound='atoms', center='com', inplace=False)
assert_in_box(rescom, u.dimensions)
rescog = ag.wrap(compound='atoms', center='cog', inplace=False)
assert_almost_equal(rescom, rescog, decimal=self.precision)
def test_wrap_large_box(self, u):
ag = u.atoms[:100]
box = u.dimensions
box[:3] *= 2.0
ag.wrap(box=box)
assert_in_box(ag.positions, box)
def test_wrap_small_box(self, u):
ag = u.atoms[:100]
box = u.dimensions
box[:3] *= 0.5
ag.wrap(box=box)
assert_in_box(ag.positions, box)