def test_reference(self):
traj = pt.iterload(fn("tz2.ortho.nc"), fn("tz2.ortho.parm7"))
# store reference
dslist = CpptrajDatasetList()
ref = dslist.add('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'))
aa_eq(xyz, t0.xyz)
t1 = traj[:].autoimage()
aa_eq(pt.rmsd(t1, ref=traj[3], mask='@CA'), dslist[-1].values)
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(fn("tz2.ortho.nc"), fn("tz2.ortho.parm7"))
dslist = CpptrajDatasetList()
dslist.add('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_rmsd(input_traj):
from pytraj.analysis.c_action.c_action import Action_Rmsd
from pytraj.datasets import DatasetList
dslist = DatasetList()
act = Action_Rmsd()
act.read_input('first @CA', top=input_traj.top, dslist=dslist)
act.setup(input_traj.top)
for frame in input_traj:
act.compute(frame)
return (dslist.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)
def test_constructor_from_command_list_TrajectoryIterator(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
commands = [
'rmsd @CA', 'distance :3 :7', 'distance :3 :7', 'vector :2 :3'
]
dslist = CpptrajDatasetList()
actlist = ActionList(commands, traj.top, dslist=dslist)
d0 = dslist.add('ref_frame', 'my_ref')
d0.add_frame(traj[3])
for frame in traj:
actlist.compute(frame)
aa_eq(pt.rmsd(traj, mask='@CA'), dslist[0])
aa_eq(pt.distance(traj, ':3 :7'), dslist[1])
aa_eq(pt.distance(traj, ':3 :7'), dslist[2])
aa_eq(pt.vector.vector_mask(traj(rmsfit=(0, '@CA')), ':2 :3'),
dslist[3].values)
def test_rmsd_actlist(input_traj):
from pytraj.analysis.c_action.c_action import Action_Rmsd
from pytraj import ActionList
from pytraj.datasets import DatasetList
alist = ActionList()
dslist = DatasetList()
act = Action_Rmsd()
alist.add(act, 'first @CA', top=input_traj.top, dslist=dslist)
for frame in input_traj:
alist.compute(frame)
return (dslist.values)
def test_constructor_from_command_list_TrajectoryIterator(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
commands = ['rmsd @CA', 'distance :3 :7', 'distance :3 :7',
'vector :2 :3']
dslist = CpptrajDatasetList()
actlist = ActionList(commands, traj.top, dslist=dslist)
d0 = dslist.add('ref_frame', 'my_ref')
d0.add_frame(traj[3])
for frame in traj:
actlist.compute(frame)
aa_eq(pt.rmsd(traj, mask='@CA'), dslist[0])
aa_eq(pt.distance(traj, ':3 :7'), dslist[1])
aa_eq(pt.distance(traj, ':3 :7'), dslist[2])
aa_eq(
pt.vector.vector_mask(
traj(rmsfit=(0, '@CA')),
':2 :3'),
dslist[3].values)
