def _check_point(self, meth, periodic):
sel = Parser.parse('point 5.0 5.0 5.0 3.0', self.u.atoms)
sel = self.choosemeth(sel, meth, periodic)
result = sel.apply(self.u.atoms)
box = self.u.dimensions if periodic else None
d = distance_array(np.array([[5.0, 5.0, 5.0]], dtype=np.float32),
self.u.atoms.positions,
box=box)
ref = set(np.where(d < 3.0)[1])
assert_(ref == set(result.indices))
def test_spherical_zone(self, u, meth, periodic):
sel = Parser.parse('sphzone 5.0 resid 1', u.atoms)
sel = self.choosemeth(sel, meth, periodic)
result = sel.apply(u.atoms)
r1 = u.select_atoms('resid 1')
box = u.dimensions if periodic else None
cog = r1.center_of_geometry(pbc=periodic).reshape(1, 3)
d = distance_array(u.atoms.positions, cog, box=box)
ref = set(np.where(d < 5.0)[0])
assert ref == set(result.indices)
def _check_point(self, meth, periodic):
sel = Parser.parse('point 5.0 5.0 5.0 3.0', self.u.atoms)
sel = self.choosemeth(sel, meth, periodic)
result = sel.apply(self.u.atoms)
box = self.u.dimensions if periodic else None
d = distance_array(np.array([[5.0, 5.0, 5.0]], dtype=np.float32),
self.u.atoms.positions,
box=box)
ref = set(np.where(d < 3.0)[1])
assert_(ref == set(result.indices))
def _check_spherical_layer(self, meth, periodic):
sel = Parser.parse('sphlayer 2.4 6.0 resid 1', self.u.atoms)
sel = self.choosemeth(sel, meth, periodic)
result = sel.apply(self.u.atoms)
r1 = self.u.select_atoms('resid 1')
cog = r1.center_of_geometry().reshape(1, 3)
box = self.u.dimensions if periodic else None
d = distance_array(self.u.atoms.positions, cog, box=box)
ref = set(np.where((d > 2.4) & (d < 6.0))[0])
assert_(ref == set(result.indices))
def _check_spherical_zone(self, meth, periodic):
sel = Parser.parse('sphzone 5.0 resid 1', self.u.atoms)
sel = self.choosemeth(sel, meth, periodic)
result = sel.apply(self.u.atoms)
r1 = self.u.select_atoms('resid 1')
cog = r1.center_of_geometry().reshape(1, 3)
box = self.u.dimensions if periodic else None
d = distance_array(self.u.atoms.positions, cog, box=box)
ref = set(np.where(d < 5.0)[0])
assert_(ref == set(result.indices))
def _check_around(self, meth, periodic):
sel = Parser.parse('around 5.0 resid 1', self.u.atoms)
sel = self.choosemeth(sel, meth, periodic)
result = sel.apply(self.u.atoms)
r1 = self.u.select_atoms('resid 1')
cog = r1.center_of_geometry().reshape(1, 3)
box = self.u.dimensions if periodic else None
d = distance_array(self.u.atoms.positions, r1.positions, box=box)
ref = set(np.where(d < 5.0)[0])
# Around doesn't include atoms from the reference group
ref.difference_update(set(r1.indices))
assert_(ref == set(result.indices))
def test_point(self, u, periodic):
sel = Parser.parse('point 5.0 5.0 5.0 3.0', u.atoms)
if periodic:
sel.periodic = True
else:
sel.periodic = False
result = sel.apply(u.atoms)
box = u.dimensions if periodic else None
d = distance_array(np.array([[5.0, 5.0, 5.0]], dtype=np.float32),
u.atoms.positions,
box=box)
ref = set(np.where(d < 3.0)[1])
assert ref == set(result.indices)
def test_point(self, u, periodic):
sel = Parser.parse('point 5.0 5.0 5.0 3.0', u.atoms)
if periodic:
sel.periodic = True
else:
sel.periodic = False
result = sel.apply(u.atoms)
box = u.dimensions if periodic else None
d = distance_array(np.array([[5.0, 5.0, 5.0]], dtype=np.float32),
u.atoms.positions,
box=box)
ref = set(np.where(d < 3.0)[1])
assert ref == set(result.indices)
def test_spherical_layer(self, u, periodic):
sel = Parser.parse('sphlayer 2.4 6.0 resid 1', u.atoms)
if periodic:
sel.periodic = True
else:
sel.periodic = False
result = sel.apply(u.atoms)
r1 = u.select_atoms('resid 1')
box = u.dimensions if periodic else None
cog = r1.center_of_geometry().reshape(1, 3)
d = distance_array(u.atoms.positions, cog, box=box)
ref = set(np.where((d > 2.4) & (d < 6.0))[0])
assert ref == set(result.indices)
def _check_around(self, meth, periodic):
sel = Parser.parse('around 5.0 resid 1', self.u.atoms)
sel = self.choosemeth(sel, meth, periodic)
result = sel.apply(self.u.atoms)
r1 = self.u.select_atoms('resid 1')
cog = r1.center_of_geometry().reshape(1, 3)
box = self.u.dimensions if periodic else None
d = distance_array(self.u.atoms.positions, r1.positions,
box=box)
ref = set(np.where(d < 5.0)[0])
# Around doesn't include atoms from the reference group
ref.difference_update(set(r1.indices))
assert_(ref == set(result.indices))
def test_spherical_zone(self, u, periodic):
sel = Parser.parse('sphzone 5.0 resid 1', u.atoms)
if periodic:
sel.periodic = True
else:
sel.periodic = False
result = sel.apply(u.atoms)
r1 = u.select_atoms('resid 1')
box = u.dimensions if periodic else None
cog = r1.center_of_geometry().reshape(1, 3)
d = distance_array(u.atoms.positions, cog, box=box)
ref = set(np.where(d < 5.0)[0])
assert ref == set(result.indices)
def test_around(self, u, periodic):
sel = Parser.parse('around 5.0 resid 1', u.atoms)
if periodic:
sel.periodic = True
else:
sel.periodic = False
result = sel.apply(u.atoms)
r1 = u.select_atoms('resid 1')
cog = r1.center_of_geometry().reshape(1, 3)
box = u.dimensions if periodic else None
d = distance_array(u.atoms.positions, r1.positions, box=box)
ref = set(np.where(d < 5.0)[0])
# Around doesn't include atoms from the reference group
ref.difference_update(set(r1.indices))
assert ref == set(result.indices)
def test_around(self, u, periodic):
sel = Parser.parse('around 5.0 resid 1', u.atoms)
if periodic:
sel.periodic = True
else:
sel.periodic = False
result = sel.apply(u.atoms)
r1 = u.select_atoms('resid 1')
cog = r1.center_of_geometry().reshape(1, 3)
box = u.dimensions if periodic else None
d = distance_array(u.atoms.positions, r1.positions,
box=box)
ref = set(np.where(d < 5.0)[0])
# Around doesn't include atoms from the reference group
ref.difference_update(set(r1.indices))
assert ref == set(result.indices)
def _check_cyzone(self, meth, periodic):
sel = Parser.parse('cyzone 5 4 -4 resid 2', self.u.atoms)
sel.periodic = periodic
result = sel.apply(self.u.atoms)
other = self.u.select_atoms('resid 2')
pos = other.center_of_geometry()
vecs = self.u.atoms.positions - pos
if periodic:
box = self.u.dimensions[:3]
vecs -= box * np.rint(vecs / box)
mask = (vecs[:, 2] > -4) & (vecs[:, 2] < 4)
radii = vecs[:, 0]**2 + vecs[:, 1]**2
mask &= radii < 5**2
ref = set(self.u.atoms[mask].indices)
assert_(ref == set(result.indices))
def _check_cyzone(self, meth, periodic):
sel = Parser.parse('cyzone 5 4 -4 resid 2', self.u.atoms)
sel.periodic = periodic
result = sel.apply(self.u.atoms)
other = self.u.select_atoms('resid 2')
pos = other.center_of_geometry()
vecs = self.u.atoms.positions - pos
if periodic:
box = self.u.dimensions[:3]
vecs -= box * np.rint(vecs / box)
mask = (vecs[:,2] > -4) & (vecs[:,2] < 4)
radii = vecs[:,0] ** 2 + vecs[:, 1] ** 2
mask &= radii < 5**2
ref = set(self.u.atoms[mask].indices)
assert_(ref == set(result.indices))