def test_load():
filenames = [
"frame0.xtc", "frame0.trr", "frame0.dcd", "frame0.binpos", "traj.h5",
'legacy_msmbuilder_trj0.lh5', 'frame0.nc',
six.u('traj.h5')
]
num_block = 3
for filename in filenames:
t0 = md.load(get_fn(filename),
top=nat,
discard_overlapping_frames=True)
t1 = md.load(get_fn(filename),
top=nat,
discard_overlapping_frames=False)
t2 = md.load([get_fn(filename) for i in xrange(num_block)],
top=nat,
discard_overlapping_frames=False)
t3 = md.load([get_fn(filename) for i in xrange(num_block)],
top=nat,
discard_overlapping_frames=True)
# these don't actually overlap, so discard_overlapping_frames should have no effect
# the overlap is between the last frame of one and the first frame of the next.
yield lambda: eq(t0.n_frames, t1.n_frames)
yield lambda: eq(t0.n_frames * num_block, t2.n_frames)
yield lambda: eq(t3.n_frames, t2.n_frames)
def test_load():
filenames = [
"frame0.xtc",
"frame0.trr",
"frame0.dcd",
"frame0.binpos",
"traj.h5",
"legacy_msmbuilder_trj0.lh5",
"frame0.nc",
six.u("traj.h5"),
"frame0.lammpstrj",
"frame0.xyz",
]
num_block = 3
for filename in filenames:
t0 = md.load(get_fn(filename), top=nat, discard_overlapping_frames=True)
t1 = md.load(get_fn(filename), top=nat, discard_overlapping_frames=False)
t2 = md.load([get_fn(filename) for i in xrange(num_block)], top=nat, discard_overlapping_frames=False)
t3 = md.load([get_fn(filename) for i in xrange(num_block)], top=nat, discard_overlapping_frames=True)
# these don't actually overlap, so discard_overlapping_frames should have no effect
# the overlap is between the last frame of one and the first frame of the next.
yield lambda: eq(t0.n_frames, t1.n_frames)
yield lambda: eq(t0.n_frames * num_block, t2.n_frames)
yield lambda: eq(t3.n_frames, t2.n_frames)
def topology(self):
"""Get the topology out from the file
Returns
-------
topology : mdtraj.Topology
A topology object
"""
if np.all(self._handle.root.AtomID[:] == 0) and (np.all(self._handle.root.AtomNames[:] == b'')
or np.all(self._handle.root.eAtomNames[:] == u(''))):
return None
return _topology_from_arrays(
self._handle.root.AtomID[:], self._handle.root.AtomNames[:],
self._handle.root.ChainID[:], self._handle.root.ResidueID[:],
self._handle.root.ResidueNames[:])
def topology(self):
"""Get the topology out from the file
Returns
-------
topology : mdtraj.Topology
A topology object
"""
if np.all(self._handle.root.AtomID[:] == 0) and (np.all(self._handle.root.AtomNames[:] == b'')
or np.all(self._handle.root.eAtomNames[:] == u(''))):
return None
return _topology_from_arrays(
self._handle.root.AtomID[:], self._handle.root.AtomNames[:],
self._handle.root.ChainID[:], self._handle.root.ResidueID[:],
self._handle.root.ResidueNames[:])