def test_volmap(self):
traj = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))[:1]
size = ''
center = ''
state = pt.load_cpptraj_state(
txt.format(fn('tz2.ortho.parm7'), fn('tz2.ortho.nc'), cm, size,
center))
state.run()
cpp_data = state.data[-2].values # last one is totalvolume
traj = traj.superpose(mask=':1-13').center(':1-13 mass origin')
ds = pt.volmap(traj,
mask=':WAT@O',
grid_spacing=(0.5, 0.5, 0.5),
buffer=2.0,
centermask='!:1-13',
radscale=1.36)
aa_eq(cpp_data, ds)
# assert
self.assertRaises(
AssertionError,
lambda: pt.volmap(traj, mask=':WAT@O', grid_spacing='0.5 0.5 0.5'))
self.assertRaises(
AssertionError,
lambda: pt.volmap(traj, mask=':WAT@O', grid_spacing=(0.5, 0.5)))
self.assertRaises(
ValueError, lambda: pt.volmap(traj,
mask=':WAT@O',
grid_spacing=(0.5, 0.5, 0.5),
size='20 20 20'))
def test_volmap(self):
traj = pt.iterload("./data/tz2.ortho.nc", "./data/tz2.ortho.parm7")[:1]
size = ''
center = ''
state = pt.load_cpptraj_state(txt.format(cm, size, center))
state.run()
cpp_data = state.data[-1].values
traj = traj.superpose(mask=':1-13').center(':1-13 mass origin')
ds = pt.volmap(traj,
mask=':WAT@O',
grid_spacing=(0.5, 0.5, 0.5),
buffer=2.0,
centermask='!:1-13',
radscale=1.36)
aa_eq(cpp_data, ds)
# assert
self.assertRaises(AssertionError, lambda: pt.volmap(traj, mask=':WAT@O', grid_spacing='0.5 0.5 0.5'))
self.assertRaises(AssertionError, lambda: pt.volmap(traj, mask=':WAT@O', grid_spacing=(0.5, 0.5)))
self.assertRaises(ValueError, lambda: pt.volmap(traj, mask=':WAT@O', grid_spacing=(0.5, 0.5, 0.5), size='20 20 20'))
# test size
cm_no_buffer = cm.replace('buffer 2.0', '')
state = pt.load_cpptraj_state(txt.format(cm_no_buffer, 'size 20,20,20', ''))
state.run()
cpp_data = state.data[-1].values
ds = volmap(traj,
mask=':WAT@O',
grid_spacing=(0.5, 0.5, 0.5),
size=(20, 20, 20),
buffer=2.0,
centermask='!:1-13',
radscale=1.36)
aa_eq(cpp_data, ds)
# test center
state = pt.load_cpptraj_state(txt.format(cm_no_buffer, 'size 20,20,20', 'center 0.5,0.5,0.5'))
state.run()
cpp_data = state.data[-1].values
ds = volmap(traj,
mask=':WAT@O',
grid_spacing=(0.5, 0.5, 0.5),
size=(20, 20, 20),
center=(0.5, 0.5, 0.5),
buffer=2.0,
centermask='!:1-13',
radscale=1.36)
aa_eq(cpp_data, ds)
# raise RuntimeError
dry_traj = pt.iterload('data/tz2.nc', 'data/tz2.parm7')
self.assertRaises(RuntimeError, lambda: pt.volmap(dry_traj, mask=':WAT@O',
grid_spacing=(0.5, 0.5, 0.5)))
def test_volmap(self):
traj = pt.iterload("data/tz2.ortho.nc", "data/tz2.ortho.parm7")
# raise if does not provide size
self.assertRaises(
AssertionError, lambda: pt.pmap(pt.volmap,
traj,
mask=':WAT@O',
grid_spacing=(0.5, 0.5, 0.5),
n_cores=2))
mask = ':WAT@O'
grid_spacing = (0.5, 0.5, 0.5)
for n_cores in [1, 2, 3]:
for size in [(20, 20, 20), (20, 40, 60)]:
serial_out = pt.volmap(traj,
mask=mask,
grid_spacing=grid_spacing,
size=size)
parallel_out = pt.pmap(pt.volmap,
traj,
mask=mask,
grid_spacing=grid_spacing,
size=size,
n_cores=n_cores)
self.assertEqual(serial_out.shape, tuple(2 * x for x in size))
aa_eq(serial_out, parallel_out)
def test_volmap(self):
traj = pt.iterload("data/tz2.ortho.nc", "data/tz2.ortho.parm7")
# raise if does not provide size
self.assertRaises(AssertionError, lambda: pt.pmap(pt.volmap, traj, mask=':WAT@O',
grid_spacing=(0.5, 0.5, 0.5),
n_cores=2))
mask = ':WAT@O'
grid_spacing = (0.5, 0.5, 0.5)
for n_cores in [1, 2, 3]:
for size in [(20, 20, 20), (20, 40, 60)]:
serial_out = pt.volmap(traj, mask=mask, grid_spacing=grid_spacing, size=size)
parallel_out = pt.pmap(pt.volmap, traj, mask=mask, grid_spacing=grid_spacing,
size=size, n_cores=n_cores)
self.assertEqual(serial_out.shape, tuple(2 * x for x in size))
aa_eq(serial_out, parallel_out)
def test_volmap_RuntimeError(self):
# raise RuntimeError
dry_traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
self.assertRaises(
RuntimeError, lambda: pt.volmap(
dry_traj, mask=':WAT@O', grid_spacing=(0.5, 0.5, 0.5)))
def test_volmap_RuntimeError(self):
# raise RuntimeError
dry_traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
with pytest.raises(RuntimeError):
pt.volmap(dry_traj, mask=':WAT@O', grid_spacing=(0.5, 0.5, 0.5))
def test_volmap(self):
traj = pt.iterload("./data/tz2.ortho.nc", "./data/tz2.ortho.parm7")[:1]
size = ''
center = ''
state = pt.load_cpptraj_state(txt.format(cm, size, center))
state.run()
cpp_data = state.data[-1].values
traj = traj.superpose(mask=':1-13').center(':1-13 mass origin')
ds = pt.volmap(traj,
mask=':WAT@O',
grid_spacing=(0.5, 0.5, 0.5),
buffer=2.0,
centermask='!:1-13',
radscale=1.36)
aa_eq(cpp_data, ds)
# assert
self.assertRaises(
AssertionError,
lambda: pt.volmap(traj, mask=':WAT@O', grid_spacing='0.5 0.5 0.5'))
self.assertRaises(
AssertionError,
lambda: pt.volmap(traj, mask=':WAT@O', grid_spacing=(0.5, 0.5)))
self.assertRaises(
ValueError, lambda: pt.volmap(traj,
mask=':WAT@O',
grid_spacing=(0.5, 0.5, 0.5),
size='20 20 20'))
# test size
cm_no_buffer = cm.replace('buffer 2.0', '')
state = pt.load_cpptraj_state(
txt.format(cm_no_buffer, 'size 20,20,20', ''))
state.run()
cpp_data = state.data[-1].values
ds = volmap(traj,
mask=':WAT@O',
grid_spacing=(0.5, 0.5, 0.5),
size=(20, 20, 20),
buffer=2.0,
centermask='!:1-13',
radscale=1.36)
aa_eq(cpp_data, ds)
# test center
state = pt.load_cpptraj_state(
txt.format(cm_no_buffer, 'size 20,20,20', 'center 0.5,0.5,0.5'))
state.run()
cpp_data = state.data[-1].values
ds = volmap(traj,
mask=':WAT@O',
grid_spacing=(0.5, 0.5, 0.5),
size=(20, 20, 20),
center=(0.5, 0.5, 0.5),
buffer=2.0,
centermask='!:1-13',
radscale=1.36)
aa_eq(cpp_data, ds)
# raise RuntimeError
dry_traj = pt.iterload('data/tz2.nc', 'data/tz2.parm7')
self.assertRaises(
RuntimeError, lambda: pt.volmap(
dry_traj, mask=':WAT@O', grid_spacing=(0.5, 0.5, 0.5)))
