def test_modify_frame_use_Pipeline(self):
traj = pt.iterload("data/tz2.ortho.nc", "data/tz2.ortho.parm7")
dslist = CpptrajDatasetList()
dslist.add_new('topology', name='mytop')
# add a new topology
dslist[0].data = pt.strip(traj.top, ':WAT')
commands = ['autoimage', 'strip :WAT', 'createcrd mycrd', ]
actlist = Pipeline(commands, top=traj.top, dslist=dslist)
for frame in traj:
actlist.compute(frame)
aa_eq(dslist['mycrd'].xyz,
pt.get_coordinates(traj,
mask='!:WAT',
autoimage=True))
def test_modify_frame_use_Pipeline(self):
traj = pt.iterload("data/tz2.ortho.nc", "data/tz2.ortho.parm7")
dslist = CpptrajDatasetList()
dslist.add_new('topology', name='mytop')
# add a new topology
dslist[0].data = pt.strip(traj.top, ':WAT')
commands = [
'autoimage',
'strip :WAT',
'createcrd mycrd',
]
actlist = Pipeline(commands, top=traj.top, dslist=dslist)
for frame in traj:
actlist.compute(frame)
aa_eq(dslist['mycrd'].xyz,
pt.get_coordinates(traj, mask='!:WAT', autoimage=True))
def test_reference(self):
traj = pt.iterload("data/tz2.ortho.nc", "data/tz2.ortho.parm7")
# store reference
dslist = CpptrajDatasetList()
ref = dslist.add_new('reference')
ref.top = traj.top
ref.append(traj[3])
fi = pt.pipe(traj, ['autoimage', 'rms refindex 0 @CA'], dslist=dslist)
xyz = np.array([frame.xyz.copy() for frame in fi])
t0 = (traj[:].autoimage().superpose(ref=traj[3], mask='@CA'))
print('ok')
aa_eq(xyz, t0.xyz)
t1 = traj[:].autoimage()
aa_eq(pt.rmsd(t1, ref=traj[3], mask='@CA'), dslist[-1].values)
def test_reference(self):
traj = pt.iterload("data/tz2.ortho.nc", "data/tz2.ortho.parm7")
# store reference
dslist = CpptrajDatasetList()
ref = dslist.add_new('reference')
ref.top = traj.top
ref.append(traj[3])
fi = pt.pipe(traj,
['autoimage', 'rms refindex 0 @CA'],
dslist=dslist)
xyz = np.array([frame.xyz.copy() for frame in fi])
t0 = (traj[:]
.autoimage()
.superpose(ref=traj[3], mask='@CA'))
print('ok')
aa_eq(xyz, t0.xyz)
t1 = traj[:].autoimage()
aa_eq(pt.rmsd(t1, ref=traj[3], mask='@CA'), dslist[-1].values)
