def test_transform_trajectory_iterator(self):
traj0 = pt.load(fn, tn)
traj1 = pt.load(fn, tn)
traj2 = pt.load(fn, tn)
# Use ActionList for traj0
actlist = pt.ActionList(top=traj0.top)
actlist.add("translate", "x 1.2")
actlist.add("center", "origin")
actlist.add("rotate", "x 45.")
for frame in traj0:
actlist.compute(frame)
# use transformation
itertraj = pt.transform(
traj1, by=['translate x 1.2', 'center origin', 'rotate x 45.'])
for frame in itertraj:
pass
aa_eq(traj0.xyz, traj1.xyz)
# use API
traj2.translate('x 1.2')
traj2.center('origin')
traj2.rotate('x 45.')
aa_eq(traj0.xyz, traj2.xyz)
def test_unstrip(self):
from pytraj.datasets import CpptrajDatasetList
traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
dslist = CpptrajDatasetList()
actlist = pt.ActionList(['strip !@CA', 'unstrip', 'radgyr nomax'],
top=traj.top,
dslist=dslist)
actlist.compute(traj)
# make sure that after stripping and unstrip the Frame coords are restored
aa_eq(pt.radgyr(traj), dslist.values)
dslist2 = CpptrajDatasetList()
actlist2 = pt.ActionList(['strip !@CA', 'radgyr nomax'],
top=traj.top,
dslist=dslist2)
actlist2.compute(traj)
# make sure get correct radgyr after stripping all but CA atoms
aa_eq(dslist2.values, pt.radgyr(traj, '@CA'))
def test_reference_with_different_topology_basic(self):
traj1 = pt.iterload(filename=tc5b_trajin, top=tc5b_top)
traj2 = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
# re-establish ActionList
dslist = CpptrajDatasetList()
dslist.add('reference', name='myref')
dslist[0].top = traj2.top
dslist[0].add_frame(traj2[0])
actlist = pt.ActionList(['rmsd @1-11 @CB ref myref'],
top=traj1.top,
dslist=dslist)
for frame in traj1:
actlist.compute(frame)
# raise if ref_mask is given but not mask
self.assertRaises(ValueError,
lambda: pt.rmsd(traj1, ref=3, ref_mask='@CB'))
self.assertRaises(
ValueError, lambda: pt.rmsd(traj1, ref=traj2[:1], ref_mask='@CB'))
# assert to cpptraj
tc5b_traj = traj1[:]
tz2_traj = traj2[:1]
cm = '''
parm {} [tc5b]
trajin {}
parm {} [tz2]
reference {} parm [tz2] 1 [myref]
rms myrmsd ref [myref] @1-10 @11-20
'''.format(tc5b_top, tc5b_trajin, tz2_top, tz2_trajin)
print(cm)
state = pt.load_cpptraj_state(cm)
with tempfolder():
state.run()
expected_rmsd = state.data[-1].values
rmsd_data = pt.rmsd(tc5b_traj,
mask='@1-10',
ref=tz2_traj,
ref_mask='@11-20')
aa_eq(expected_rmsd, rmsd_data)
import pytraj as pt
from pytraj.testing import get_fn, aa_eq
fn, tn = get_fn('tz2_dry')
traj0 = pt.load(fn, tn)
traj1 = pt.load(fn, tn)
traj2 = pt.load(fn, tn)
print(traj0.xyz[0, 0], traj1.xyz[0, 0], traj2.xyz[0, 0])
# Use ActionList for traj0
actlist = pt.ActionList(top=traj0.top)
actlist.add("translate", "x 1.2")
actlist.add("center", "origin")
actlist.add("rotate", "x 45.")
for frame in traj0:
actlist.compute(frame)
# use transformation
itertraj = pt.transform(
traj1, by=['translate x 1.2', 'center origin', 'rotate x 45.'])
for frame in itertraj:
pass
aa_eq(traj0.xyz, traj1.xyz)
print(traj0.xyz[0, 0], traj1.xyz[0, 0], traj2.xyz[0, 0])
# use API
traj2.translate('x 1.2')
traj2.center('origin')
