def test_iterframe(self):
'''test iterframe for both Trajectory and TrajectoryIterator
'''
orig_traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
# iterframe (already in doctest), just throwing raise to increase coverage score
for traj in [orig_traj, orig_traj[:]]:
with pytest.raises(ValueError):
traj.iterframe(rmsfit='crazy')
# rmsfit is an int
t0 = orig_traj[:].rmsfit(ref=3)
aa_eq(pt.rmsd_nofit(traj(rmsfit=3), ref=orig_traj[-1]),
pt.rmsd_nofit(t0, ref=orig_traj[-1]))
# test TypeError if not has n_frames info
t0 = orig_traj[:]
def int_gen(k):
for i in range(k):
yield i
fi = pt.iterframe(t0, frame_indices=int_gen(3))
aa_eq(pt.radgyr(fi, top=traj.top), pt.radgyr(orig_traj[:3]))
def test_iterframe(self):
'''test iterframe for both Trajectory and TrajectoryIterator
'''
orig_traj = pt.iterload("./data/tz2.nc", "./data/tz2.parm7")
# iterframe (already in doctest), just throwing raise to increase coverage score
for traj in [orig_traj, orig_traj[:]]:
self.assertRaises(ValueError,
lambda: traj.iterframe(rmsfit='crazy'))
# rmsfit is an int
t0 = orig_traj[:].rmsfit(ref=3)
aa_eq(
pt.rmsd_nofit(
traj(rmsfit=3),
ref=orig_traj[-1]),
pt.rmsd_nofit(t0, ref=orig_traj[-1]))
# test TypeError if not has n_frames info
t0 = orig_traj[:]
def int_gen(k):
for i in range(k):
yield i
fi = pt.iterframe(t0, frame_indices=int_gen(3))
aa_eq(pt.radgyr(fi, top=traj.top), pt.radgyr(orig_traj[:3]))
def test_combine_cpptraj_iterating_with_pytraj(self):
traj = pt.iterload(fn("tz2.ortho.nc"), fn("tz2.ortho.parm7"))
commands = [
'autoimage',
'rms',
]
dslist = CpptrajDatasetList()
actlist = ActionList(commands, top=traj.top, dslist=dslist)
def get_fi(actlist, traj):
'''create a frame iterator with pre-processed by cpptraj
'''
for frame in traj:
actlist.compute(frame)
yield frame
ref = traj[3]
pt.autoimage(ref, top=traj.top)
fi = get_fi(actlist, traj)
rmsd_nofit_after_fitting = pt.rmsd_nofit(fi, ref=ref, top=traj.top)
t0 = traj[:].autoimage().superpose()
saved_rmsd_ = pt.rmsd_nofit(t0, ref=ref)
aa_eq(rmsd_nofit_after_fitting, saved_rmsd_)
def test_fit_and_then_nofit(self):
traj = pt.iterload(tc5b_trajin, tc5b_top)
t0 = traj[:]
pt.superpose(t0, ref=traj[3], mask='@CA')
rmsd_0 = pt.rmsd_nofit(traj, ref=traj[3], mask='@CB')
rmsd_1 = pt.rmsd(traj, ref=traj[3], mask='@CB', nofit=True)
aa_eq(rmsd_1, rmsd_0)
def calc_node_rmsd(self) -> float:
logger.info(f"calculating rmsd for node {self.node_id}")
crd_file = self.get_relative_file(SETTINGS["md"]["rst_file"])
top_file = self.get_relative_file(SETTINGS["md"]["top_file"])
ref_file = self.get_relative_file(SETTINGS["md"]["ref_file"])
if not all(
os.path.exists(file)
for file in [crd_file, top_file, ref_file]):
logger.warning(
f"Unable to calculate rmsd for node {self.node_id}. Some files are missing"
)
load_mask = SETTINGS["system"]["load_mask"]
traj = pytraj.load(crd_file, top=top_file, mask=load_mask)
# this one is causing some trouble in CI. need to inspect why, though.
# traj = pytraj.autoimage(traj)
ref_top_file = self.get_relative_file(
os.path.join(os.path.pardir,
SETTINGS["data_files"]["ref_top_file"]))
ref = pytraj.load(ref_file, top=ref_top_file, mask=load_mask)
align_mask = SETTINGS["system"]["protein_mask"]
pytraj.rmsd(traj, mask=align_mask, ref=ref)
ligand_mask = SETTINGS["system"]["ligand_mask"]
rmsd = pytraj.rmsd_nofit(traj, mask=ligand_mask, ref=ref)
self.rmsd = float(rmsd[0])
self.nrmsd = self.rmsd / traj[ligand_mask].top.n_atoms
self.write_node_info()
return self.rmsd
def test_fit_and_then_nofit(self):
traj = pt.iterload("data/Tc5b.x", "data/Tc5b.top")
t0 = traj[:]
pt.superpose(t0, ref=traj[3], mask='@CA')
rmsd_0 = pt.rmsd_nofit(traj, ref=traj[3], mask='@CB')
rmsd_1 = pt.rmsd(traj, ref=traj[3], mask='@CB', nofit=True)
aa_eq(rmsd_1, rmsd_0)
def test_trajectoryiterator_with_transformation(self):
traj_on_disk = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
traj_on_mem = pt.load(fn('tz2.nc'), fn('tz2.parm7'))
traj_on_disk.superpose(mask='@CA', ref=3)
traj_on_mem.superpose(mask='@CA', ref=3)
rmsd0_dict = pt.pmap(
pt.rmsd_nofit, traj_on_disk, mask='@CB', n_cores=2, ref=0)
rmsd1 = pt.rmsd_nofit(traj_on_mem, mask='@CB', ref=0)
aa_eq(pt.tools.dict_to_ndarray(rmsd0_dict), [rmsd1])
def test_combine_cpptraj_iterating_with_pytraj(self):
traj = pt.iterload("data/tz2.ortho.nc", "data/tz2.ortho.parm7")
commands = ['autoimage', 'rms', ]
dslist = CpptrajDatasetList()
actlist = ActionList(commands, top=traj.top, dslist=dslist)
def get_fi(actlist, traj):
'''create a frame iterator with pre-processed by cpptraj
'''
for frame in traj:
actlist.compute(frame)
yield frame
ref = traj[3]
pt.autoimage(ref, top=traj.top)
fi = get_fi(actlist, traj)
rmsd_nofit_after_fitting = pt.rmsd_nofit(fi, ref=ref, top=traj.top)
t0 = traj[:].autoimage().superpose()
saved_rmsd_ = pt.rmsd_nofit(t0, ref=ref)
aa_eq(rmsd_nofit_after_fitting, saved_rmsd_)